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[bioontology-support] update OBI on BioPortal

Trish Whetzel plwhetzel at gmail.com
Tue Dec 23 01:03:51 PST 2008


Comments in-line.

On Mon, Dec 22, 2008 at 10:06 PM, Alan Ruttenberg
<alanruttenberg at gmail.com>wrote:

> On Mon, Dec 22, 2008 at 8:10 PM, Trish Whetzel <plwhetzel at gmail.com>
> wrote:
> > To recap, sorry about loading the wrong file-clicked the wrong selection
> to
> > save the page. I've since gone back to save the correct .owl file and
> > upload. As for the other OBI, all I can gather is that this was uploaded
> by
> > the pull from the OBO Foundry site and somehow the flag to indicate not
> to
> > do this was altered due to the file upload process that failed.
> >
> > As for removing the duplicate, that can be done by the developers however
> > Stanford is shut down until Jan 5. I'll see if I can get in touch with
> > anyone to update in the meantime...
> >
> > Also, do the IDs look proper? Perhaps this is only an internal BioPortal
> > issue, but I did not anticipate the obo: prefix.
>
> That works. OBI URLs now look like:
> http://purl.obofoundry.org/obo/OBI_XXXXXXX
>
> obo: means, in this case, http://purl.obofoundry.org/obo/
>
> However, someone reading the bioportal page doesn't know that.
> Particularly for the ID field, the full URL should be given. If any
> namespaces/prefixes *are* used on the page, there should be a legend
> somewhere  on the page that says what they stand for.


Your request to display the full URL was submitted to the tracker when
originally requested. The additional bit for the legend has been added to
this feature request. This is bug #838 located at:
https://bmir-gforge.stanford.edu/gf/project/bioportal_core/tracker/?action=TrackerItemEdit&tracker_item_id=838


>
> Note that I now see 5 versions of the recent ontology, the last 3 of
> which, when clicking the explore button, show "There is no data to
> support this query at this time. If you have questions, please contact
> us at admin at bioontology.org."
>
> Will it be possible to remove all but one of them?


Yes, when this is tasked by Benjamin. This is entered as bug #923 at:
https://bmir-gforge.stanford.edu/gf/project/bioportal_core/tracker/?action=TrackerItemEdit&tracker_item_id=923



>
> BTW, FYA, what's wrong with the attached picture (dialog shown when I
> clicked "show notes" button visible on the right.
>

Hmm, what do mean other than that mapping may not be valid. The notes link
is for any additional comments on the mapping, however there are none.

Trish


>> On Dec 22, 2008, at 4:03 PM, "Alan Ruttenberg" <alanruttenberg at gmail.com>>
> wrote:>>> I just had a look. There are two entries for OBI (as if there were
> two>> ontologies) Image attached.
> >> The second one seems to have the current OBI.
> >> Can we have the first removed?
> >>
> >> Thanks,
> >> Alan
> >>
> >>
> >> On Mon, Dec 22, 2008 at 2:57 PM, Melanie Courtot <mcourtot at gmail.com>
> >> wrote:
> >>>
> >>> Hi Trish,
> >>> I was having a look at the OBI upload on Bioportal, and there seem to
> >>> have
> >>> been a problem with the link used.
> >>> There was still no explore button, so I wanted to check on the
> downlaoded
> >>> file. I attach it here, basically it is the sourceforge svn html page.
> >>> Would you mind giving it an other try?
> >>> The URL http://purl.obofoundry.org/obo/obi.owl should be working all
> the
> >>> time as we redirect towards the latest release each time we produce a
> new
> >>> one.
> >>> Thanks,
> >>> Melanie
> >>>
> >>>
> >>> On 21-Dec-08, at 2:12 PM, Trish Whetzel wrote:
> >>>
> >>> PS - did you hear from Benjamin on the status of the reported bugs?
> >>>
> >>> Trish
> >>>
> >>> On Sun, Dec 21, 2008 at 2:11 PM, Trish Whetzel <plwhetzel at gmail.com>
> >>> wrote:
> >>>>
> >>>> No problem, it has been uploaded and will check back later to see how
> >>>> the
> >>>> parsing, display, etc looks.
> >>>>
> >>>> Trish
> >>>>
> >>>>
> >>>> On Sat, Dec 20, 2008 at 5:35 PM, Melanie Courtot <mcourtot at gmail.com>
> >>>> wrote:
> >>>>>
> >>>>> Hi Trish,
> >>>>> If you don't mind yes that would be great - it would allow us to have
> >>>>> "inside monitoring" in case there is any further problem.
> >>>>> As said, current version is revision 1213, date 2008-11-28,
> >>>>> available at http://purl.obofoundry.org/obo/obi.owl
> >>>>> Thanks,
> >>>>> Melanie
> >>>>>
> >>>>> On 20-Dec-08, at 11:40 AM, Trish Whetzel wrote:
> >>>>>
> >>>>> Hi Alan and Melanie,
> >>>>>
> >>>>> I went back to read the entire thread and in the message where Alan
> >>>>> mentions loading the file twice, I thought that was referring to an
> >>>>> earlier
> >>>>> attempt to load OBI (the September version) not the November version
> so
> >>>>> I
> >>>>> did not realize that the November version was ever loaded. I can load
> >>>>> the
> >>>>> latest version if you want since the ownership of OBI was re-pointed
> to
> >>>>> the
> >>>>> OBI group login.
> >>>>>
> >>>>> I will re-visit my request to extend the automatic loading process to
> >>>>> include any URL +metadata file that is provided and keep you posted.
> >>>>>
> >>>>> Trish
> >>>>>
> >>>>>
> >>>>> On Sat, Dec 20, 2008 at 12:53 AM, Alan Ruttenberg
> >>>>> <alanruttenberg at gmail.com> wrote:
> >>>>>>
> >>>>>> No. Even if I had I uploaded it twice in order to properly say the
> >>>>>> date, something that the bioportal entry no longer reflects.
> >>>>>> Oh well, needs to be updated again....
> >>>>>> Trish, is there some api for doing an update programatically? It
> would
> >>>>>> be nice to be able to script this.
> >>>>>> -Alan
> >>>>>>
> >>>>>> On Fri, Dec 19, 2008 at 9:46 PM, Melanie Courtot <
> mcourtot at gmail.com>
> >>>>>> wrote:
> >>>>>>>
> >>>>>>> That's indeed strange, as per email below Alan updated it beginning
> >>>>>>> of
> >>>>>>> december.
> >>>>>>> revision 1213, date 2008-11-28, available
> >>>>>>> at http://purl.obofoundry.org/obo/obi.owl
> >>>>>>> cc'ing Alan, if he has an idea - Alan, is it possible you uploaded
> >>>>>>> the
> >>>>>>> old
> >>>>>>> version by mistake?
> >>>>>>> Thanks,
> >>>>>>> Melanie
> >>>>>>>
> >>>>>>>
> >>>>>>> On 19-Dec-08, at 6:39 PM, Trish Whetzel wrote:
> >>>>>>>
> >>>>>>> No worries, I may have missed that email and thought that there was
> a
> >>>>>>> more
> >>>>>>> recent version than the one from 09/26/2008 so just wanted to
> >>>>>>> check-in
> >>>>>>> that
> >>>>>>> everything was working smoothly. Have a great holiday!
> >>>>>>>
> >>>>>>> Trish
> >>>>>>>
> >>>>>>> On Fri, Dec 19, 2008 at 6:23 PM, Melanie Courtot <
> mcourtot at gmail.com>
> >>>>>>> wrote:
> >>>>>>>>
> >>>>>>>> Hi Trish,
> >>>>>>>>
> >>>>>>>> Sorry I thought I sent you an email?
> >>>>>>>> Alan did the last updated with his account, and I did check the
> >>>>>>>> change
> >>>>>>>> went through.
> >>>>>>>> So things should be ok from now on.
> >>>>>>>> Enjoy the holidays, and I'll see you soon in Vancouver!
> >>>>>>>>
> >>>>>>>> Thanks for taking care of us :)
> >>>>>>>> Melanie
> >>>>>>>>
> >>>>>>>> On 19-Dec-08, at 6:19 PM, Trish Whetzel wrote:
> >>>>>>>>
> >>>>>>>>> Hi Melanie,
> >>>>>>>>>
> >>>>>>>>> Just wanted to check-in on loading the new version of OBI, do you
> >>>>>>>>> want me
> >>>>>>>>> to do that?
> >>>>>>>>>
> >>>>>>>>> Trish
> >>>>>>>
> >>>>>>> Begin forwarded message:
> >>>>>>>
> >>>>>>> From: "Alan Ruttenberg" <alanruttenberg at gmail.com>
> >>>>>>> Date: December 3, 2008 10:00:23 PM PST (CA)
> >>>>>>> To: "Trish Whetzel" <plwhetzel at gmail.com>
> >>>>>>> Cc: "Melanie Courtot" <mcourtot at gmail.com>,  "Benjamin Dai"
> >>>>>>> <benjamin.dai at stanford.edu>
> >>>>>>> Subject: Re: update OBI on BioPortal
> >>>>>>> On Wed, Dec 3, 2008 at 10:08 PM, Trish Whetzel <
> plwhetzel at gmail.com>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>> Hi Alan,
> >>>>>>>
> >>>>>>> Absolutely, there should be some message to let the user know that
> >>>>>>> the
> >>>>>>> file
> >>>>>>>
> >>>>>>> has been uploaded successfully and a request for this feature has
> >>>>>>> been
> >>>>>>>
> >>>>>>> submitted.  There is an "Edit Ontology" button, that can be used to
> >>>>>>> change
> >>>>>>>
> >>>>>>> metadata without uploading a new version. Was this not possible?
> >>>>>>>
> >>>>>>> I noticed that later, though I couldn't use it on the ontology
> >>>>>>> because
> >>>>>>> there was no indication of the newly uploaded ontology.
> >>>>>>> -Alan
> >>>>>>>
> >>>>>>>
> >>>>>>> Trish
> >>>>>>>
> >>>>>>>
> >>>>>>> On Wed, Dec 3, 2008 at 4:11 PM, Alan Ruttenberg
> >>>>>>> <alanruttenberg at gmail.com>
> >>>>>>>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>> I uploaded a new version (twice).
> >>>>>>>
> >>>>>>> The second time I set the release date correctly.
> >>>>>>>
> >>>>>>> It would be good to be able to fix some metadata about an upload
> >>>>>>>
> >>>>>>> without uploading it a second time.
> >>>>>>>
> >>>>>>> There is no confirmation whatsoever that it succeeded in the
> upload.
> >>>>>>>
> >>>>>>> (an email or a page say "good job" or somesuch would be nice).
> >>>>>>>
> >>>>>>> -Alan
> >>>>>>>
> >>>>>>> On Wed, Dec 3, 2008 at 6:49 PM, Trish Whetzel <plwhetzel at gmail.com
> >
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>> Quick update - the developer that is able to handle this is in what
> >>>>>>>
> >>>>>>> appears
> >>>>>>>
> >>>>>>> to be a meeting until the end of the day :-(
> >>>>>>>
> >>>>>>> Trish
> >>>>>>>
> >>>>>>>
> >>>>>>> On Wed, Dec 3, 2008 at 1:20 PM, Melanie Courtot <
> mcourtot at gmail.com>
> >>>>>>>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>> Hi Trish,
> >>>>>>>
> >>>>>>> This is what we did by creating the ontology.bio.investigations
> >>>>>>> account
> >>>>>>>
> >>>>>>> as
> >>>>>>>
> >>>>>>> per previous email.
> >>>>>>>
> >>>>>>> Could you ensure the database gets updated then?
> >>>>>>>
> >>>>>>> Thanks a lot for checking so quickly,
> >>>>>>>
> >>>>>>> Melanie
> >>>>>>>
> >>>>>>> On 3-Dec-08, at 1:11 PM, Trish Whetzel wrote:
> >>>>>>>
> >>>>>>> OBI is linked to Alan as the owner. Currently, only 1 entity can be
> >>>>>>>
> >>>>>>> linked
> >>>>>>>
> >>>>>>> to an ontology as the owner, ie to update new versions or edit. My
> >>>>>>>
> >>>>>>> suggestion would be to create an account that can be shared amongst
> >>>>>>>
> >>>>>>> people
> >>>>>>>
> >>>>>>> that may submit OBI (you can include me in that group if you like)
> >>>>>>> and
> >>>>>>>
> >>>>>>> then
> >>>>>>>
> >>>>>>> let us know what that account is and we can link OBI to that
> account.
> >>>>>>>
> >>>>>>> Albeit
> >>>>>>>
> >>>>>>> perhaps not the best solution, it will take care of the immediate
> >>>>>>> need.
> >>>>>>>
> >>>>>>> There is a feature request to make modifications to allow multiple
> >>>>>>>
> >>>>>>> people
> >>>>>>>
> >>>>>>> to be the owner of an ontology. Benjamin, can you give an update on
> >>>>>>> the
> >>>>>>>
> >>>>>>> status of Feature request #723?
> >>>>>>>
> >>>>>>> Apologies for the trouble with this item,
> >>>>>>>
> >>>>>>> Trish
> >>>>>>>
> >>>>>>>
> >>>>>>> On Wed, Dec 3, 2008 at 12:25 PM, Trish Whetzel <
> plwhetzel at gmail.com>
> >>>>>>>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>> Hmm, I'll look in the database to see who is listed as the owner.
> Be
> >>>>>>>
> >>>>>>> back
> >>>>>>>
> >>>>>>> in a few....
> >>>>>>>
> >>>>>>> As for "My Projects" - that relates to a different feature, ie to
> add
> >>>>>>>
> >>>>>>> a
> >>>>>>>
> >>>>>>> description of a project that uses ontologies in BioPortal.
> >>>>>>>
> >>>>>>> Trish
> >>>>>>>
> >>>>>>> PS - I've requested that there be a mechanism to add documentation
> to
> >>>>>>>
> >>>>>>> the
> >>>>>>>
> >>>>>>> site so that these items are not so cryptic and will check-in to
> see
> >>>>>>>
> >>>>>>> where
> >>>>>>>
> >>>>>>> that request is in the queue.
> >>>>>>>
> >>>>>>>
> >>>>>>> On Wed, Dec 3, 2008 at 12:10 PM, Melanie Courtot <
> mcourtot at gmail.com>
> >>>>>>>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>> Hi Trish,
> >>>>>>>
> >>>>>>> Thanks for the quick reply.
> >>>>>>>
> >>>>>>> That is the procedure I used to follow before the BioPortal update,
> >>>>>>>
> >>>>>>> but
> >>>>>>>
> >>>>>>> since then, I am not owner of OBI anymore.
> >>>>>>>
> >>>>>>> So "my projects" is empty, and when clicking on OBI I don't get the
> >>>>>>>
> >>>>>>> extra buttons.
> >>>>>>>
> >>>>>>> My login is mcourtot.
> >>>>>>>
> >>>>>>> Thanks,
> >>>>>>>
> >>>>>>> Melanie
> >>>>>>>
> >>>>>>> On 3-Dec-08, at 12:05 PM, Trish Whetzel wrote:
> >>>>>>>
> >>>>>>> Hi Melanie
> >>>>>>>
> >>>>>>> Did someone manually load the previous versions? The general
> >>>>>>>
> >>>>>>> procedure
> >>>>>>>
> >>>>>>> is:
> >>>>>>>
> >>>>>>> 1) Register for BioPortal
> >>>>>>>
> >>>>>>> 2) Login
> >>>>>>>
> >>>>>>> 3) Select ontology from Browse tab
> >>>>>>>
> >>>>>>> 4) Since logged in and owner of the ontology, 2 additional buttons
> >>>>>>>
> >>>>>>> will
> >>>>>>>
> >>>>>>> appear, "Submit New Version" and "Edit Version"
> >>>>>>>
> >>>>>>> 5) Select the appropriate option
> >>>>>>>
> >>>>>>> Note that the changes to the Browse tab are not immediately
> reflected
> >>>>>>>
> >>>>>>> due to a delay in the refresh for this page.
> >>>>>>>
> >>>>>>> Trish
> >>>>>>>
> >>>>>>>
> >>>>>>> On Wed, Dec 3, 2008 at 11:45 AM, Melanie Courtot <
> mcourtot at gmail.com>
> >>>>>>>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>> Hi Benjamin,
> >>>>>>>
> >>>>>>> I am facing the same issue. We released a new OBI, version
> 1.0.1213,
> >>>>>>>
> >>>>>>> on
> >>>>>>>
> >>>>>>> Friday, but I don't know how I could get it into BioPortal.
> >>>>>>>
> >>>>>>> It is available at http://purl.obofoundry.org/obo/obi.owl
> >>>>>>>
> >>>>>>> Could you tell me how to proceed?
> >>>>>>>
> >>>>>>> Thanks,
> >>>>>>>
> >>>>>>> Melanie
> >>>>>>>
> >>>>>>> On 26-Sep-08, at 11:21 AM, Alan Ruttenberg wrote:
> >>>>>>>
> >>>>>>> Hi Benjamin,
> >>>>>>>
> >>>>>>> We've just released a new version of OBI and don't really know how
> >>>>>>>
> >>>>>>> we
> >>>>>>>
> >>>>>>> are supposed to update BioPortal to include it.
> >>>>>>>
> >>>>>>> I also notice that there are two versions of OBI listed in the
> >>>>>>>
> >>>>>>> browse
> >>>>>>>
> >>>>>>> tab, and neither have an "explore" link. If I look at the detail
> >>>>>>>
> >>>>>>> for
> >>>>>>>
> >>>>>>> the OWL-DL version (the current one) I notice that there are two
> >>>>>>>
> >>>>>>> copies of the same version, one with an explore link and one with
> >>>>>>>
> >>>>>>> not.
> >>>>>>>
> >>>>>>> Please advise on how we should proceed to clean this up and to put
> >>>>>>>
> >>>>>>> up
> >>>>>>>
> >>>>>>> the current version.
> >>>>>>>
> >>>>>>> Thanks,
> >>>>>>>
> >>>>>>> Alan
> >>>>>>>
> >>>>>>> On Wed, Sep 24, 2008 at 7:25 PM, Benjamin Dai
> >>>>>>>
> >>>>>>> <benjamin.dai at stanford.edu> wrote:
> >>>>>>>
> >>>>>>> Hi Alan,
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Nick Griffith, our NCBO UI guru, is working on the meta-data bug
> >>>>>>>
> >>>>>>> and
> >>>>>>>
> >>>>>>> will
> >>>>>>>
> >>>>>>> assist you.  Based on his analysis, displaying the email contact
> >>>>>>>
> >>>>>>> info
> >>>>>>>
> >>>>>>> for
> >>>>>>>
> >>>>>>> OBI should be very easy.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Regards,
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> BD
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> From: Alan Ruttenberg [mailto:alanruttenberg at gmail.com]
> >>>>>>>
> >>>>>>> Sent: Tuesday, September 23, 2008 11:11 PM
> >>>>>>>
> >>>>>>> To: Benjamin Dai
> >>>>>>>
> >>>>>>> Cc: Melanie Courtot; mmontegut at stanford.edu; Michael Dorf; Nick
> >>>>>>>
> >>>>>>> Griffith;
> >>>>>>>
> >>>>>>> Natasha Noy
> >>>>>>>
> >>>>>>> Subject: Re: Could you associate my login with OBI?
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> BTW, I notice that the metadata
> >>>>>>>
> >>>>>>> page http://bioportal.bioontology.org/ontologies/38617 doesn't
> >>>>>>>
> >>>>>>> list
> >>>>>>>
> >>>>>>> the
> >>>>>>>
> >>>>>>> email contact for OBI. Could it please?
> >>>>>>>
> >>>>>>> Since the metadata changes aren't sticking, could you please set
> >>>>>>>
> >>>>>>> the
> >>>>>>>
> >>>>>>> date of
> >>>>>>>
> >>>>>>> release to 7/25/2008 and the location url to
> >>>>>>>
> >>>>>>> http://purl.obofoundry.org/obo/obi.owl ?
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Thanks,
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> -Alan
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>
> >>>>>
> >>>>> ---
> >>>>> Mélanie Courtot
> >>>>> TFL- BCCRC
> >>>>> 675 West 10th Avenue
> >>>>> Vancouver, BC
> >>>>> V5Z 1L3, Canada
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>
> >>>
> >>> ---
> >>> Mélanie Courtot
> >>> TFL- BCCRC
> >>> 675 West 10th Avenue
> >>> Vancouver, BC
> >>> V5Z 1L3, Canada
> >>>
> >>>
> >>>
> >>>
> >>>
> >> <Picture 11.png>
> >
>
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