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[bioontology-support] IDO Bioportal update

Alan Ruttenberg alanruttenberg at gmail.com
Wed Aug 10 22:13:46 PDT 2011


Looks like it is working now.
-Alan

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

>
>
> 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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