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[bioontology-support] IDO Bioportal update

Lindsay Cowell Lindsay.Cowell at
Thu Aug 11 10:49:10 PDT 2011

Great.  Thanks.
On Aug 11, 2011, at 12:13 AM, Alan Ruttenberg wrote:

Looks like it is working now.

On Thu, Aug 11, 2011 at 1:03 AM, Alan Ruttenberg <alanruttenberg at<mailto:alanruttenberg at>> wrote:

On Thu, Aug 11, 2011 at 12:30 AM, Trish Whetzel <whetzel at<mailto:whetzel at>> wrote:
Please login again.

I now get the administer button, but when I select edit ontology information I am redirected to the bioportal front page.


On Thu, Aug 11, 2011 at 12:14 AM, Trish Whetzel <whetzel at<mailto:whetzel at>> wrote:
Hi Lindsay,

There are two options to upload a new ontology version, one is to upload the ontology from a local file. Using this option, the administrator of the ontology logs into BioPortal and manually uploads the new ontology file. The second option is to automatically load the ontology from a specified URL with new ontology versions detected using a MD5 checksum. IDO is currently set-up to be loaded when new versions are detected at this URL: Is that the preferred mechanism and URL?

No. We will use the second option.

Regarding updating the IDO metadata, Lindsay was set as the administrator of IDO with the username "ido at<mailto:ido at>". This is now changed to have the account "ido-devel" as the administrator of IDO.  I've submitted a request to have the previous versions removed and the 2010 and 2009 versions uploaded.

I just checked and ido-devel still doesn't seem to be the administrator.
Please do remove the previous versions, but please *do not* add the 2010 and 2009 versions - I will handle that.



PS - Alan is included in the reply as well as the support mailing list for tracking purposes.

On Aug 10, 2011, at 12:44 PM, Lindsay Cowell wrote:

> Hi Trish,
> I wanted to follow up on a couple of the points Alan raises below.  First, you mentioned that you would upload the IDO versions listed on the IDO site and delete the versions listed on the BioPortal site.  That's great and will correct the historical record, but what about ensuring that future versions are correctly imported into BioPortal?  Is there some system whereby BioPortal "knows" there is a new release and imports it via the default PURL.  Or do we need to upload the new version each time (which we are happy to do)?  In case of the former, how do we ensure that the metadata associated with these newer versions is correct?
> Currently, neither I nor Alan can edit the metadata.  This means that we cannot correct version information but also cannot change things such as the list of projects that use IDO.  We created an account (ido-devel) for this purpose, but it appears not to have admin rights for the IDO page.  If you can give admin rights to IDO-devel and delete the incorrect versions, then we will be happy to upload the coorect versions and correct all the metadata.  Then we can also stay on top of it going forward so we don't have to bother you about it each time.
> Please be sure to copy Alan on email correspondence regarding IDO as he is in charge of the technical side of things for this project.
> Thanks,
> Lindsay
> On Aug 9, 2011, at 12:24 PM, Alan Ruttenberg wrote:
>> On Tue, Aug 9, 2011 at 1:02 PM, Trish Whetzel <whetzel at<mailto:whetzel at>> wrote:
>>> Are new versions not being loaded? Can you point out the differences?
>> The current issue is that there isn't confidence that Bioportal will
>> do the right thing in this setup. So I am not looking for new
>> versions. The versions we have published are:
>> id: /obo/ido.owl
>> target:
>> modifieddate: 2009-07-23 04:56:43.0
>> target:
>> modifieddate: 2009-08-14 14:56:08.0
>> target:
>> modifieddate: 2010-05-26 14:36:32.0
>> target:
>> modifieddate: 2011-07-06 17:33:09.0
>> The versions you have are:
>> 2010-12-02  07/06/2011
>> unknown       11/18/2010
>> r243 archived         08/05/2010
>> 1.3   06/26/2009
>> As you can see, the only correspondence in dates are for the current version.
>> I can't administer again - not sure what's up, but logging in with any
>> of the accounts I control doesn't give me the ability to edit the
>> metadata. I have "alanruttenberg", "ido-devel", "obi".
>> Is possible for an administrator to fix the metadata for individual
>> versions, or to remove them?
>> Unless this feature works flawlessly, and we have the ability to fix
>> versions (e.g. if we publish a mistake and bioportal sucks it before
>> we have a chance to fix it), it is better for us to manage this
>> manually. The feature I asked for - to upload one version given a URL,
>> would make the moderately easier.
>> -Alan

Lindsay G. Cowell, PhD
Division of Biomedical Informatics
Department of Clinical Sciences
University of Texas Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX  75390-9066

F4.212b, MC9066

phone: 214-648-2289
fax: 214-648-2064
Lindsay.Cowell at<mailto:Lindsay.Cowell at>


UT Southwestern Medical Center
The future of medicine, today.
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