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[bioontology-support] IDO Bioportal update

Alan Ruttenberg alanruttenberg at gmail.com
Wed Aug 10 22:03:28 PDT 2011


On Thu, Aug 11, 2011 at 12:30 AM, Trish Whetzel <whetzel at stanford.edu>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.
-Alan


>
> Trish
>
>
> On Thu, Aug 11, 2011 at 12:14 AM, Trish Whetzel <whetzel at stanford.edu>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:
>> http://purl.obolibrary.org/obo/ido.owl. 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 duke.edu". 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.
>
> Thanks,
> Alan
>
>
>
>>
>> Trish
>>
>> 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 stanford.edu>
>> 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: http://purl.org/obo/owl/IDO
>> >> modifieddate: 2009-07-23 04:56:43.0
>> >>
>> >> target:
>> http://infectious-disease-ontology.googlecode.com/svn/releases/2009-08-14/ido.owl
>> >> modifieddate: 2009-08-14 14:56:08.0
>> >>
>> >> target:
>> http://infectious-disease-ontology.googlecode.com/svn/releases/2010-05-26/ido.owl
>> >> modifieddate: 2010-05-26 14:36:32.0
>> >>
>> >> target:
>> http://infectious-disease-ontology.googlecode.com/svn/releases/2010-12-02/ido.owl
>> >> 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
>> >>
>>
>>
>
>
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