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[bioontology-support] IDO Bioportal update

Alan Ruttenberg alanruttenberg at gmail.com
Wed Aug 10 21:22:35 PDT 2011


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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