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[bioontology-support] [ncbo-execs] Fwd: [bioontology-info] bioportal

Nigam Shah nigam at stanford.edu
Sat Apr 24 10:15:10 PDT 2010


That is indeed wierd .. coz for me the link,
http://bioportal.bioontology.org/visualize/40397/?conceptid=T321#resource_index
shows
a page (see screenshot attached).

This one: http://bioportal.bioontology.org/visualize/40392/?conceptid=68 is
malformed link. "68" is the wrong thing to link with I believe .. so a bug
at our end.

The one where you see results only for NextBio is where we have not used
that ontology at our end for indexing yet, we link out to nextbio (who do
their own indexing) and they might have results.

Right now, there is no easy way of knowing which link has annotation before
clicking .. precisely the reason for building a custom search API (the one
in alpha).  I agree that right now, *accessing* the annotations we have in
an easy manner (i.e. in a UI) is a problem. The API access works and we are
building UIs on top of it.

Best regards,
Nigam

On Sat, Apr 24, 2010 at 10:09 AM, Bhagwat, Medha (NIH/OD/ORS) [E] <
bhagwat at mail.nih.gov> wrote:

> Hi Nigam,
>
> Thanks.  I just tried your steps and clicked on first few melanoma terms in
> the results page
>
> I got
>
>
> http://bioportal.bioontology.org/visualize/40397/?conceptid=T321#resource_index
>
> The resources tab is currently undergoing maintenance.
>
>
> http://bioportal.bioontology.org/visualize/40392/?conceptid=68
>
> The page you are looking for wasn't found. Please try again.
>
>
>
> http://bioportal.bioontology.org/visualize/4525/?conceptid=Melanoma#resource_index
>
> I got results.
>
>
>
> http://bioportal.bioontology.org/visualize/40402/?conceptid=C4116#resource_index
>
> has annotations only in NextBio
>
>
>
> How do I know which links has annotations before clicking on each link?
>
>
> thanks,
>
> Medha
>
> _____________________________
>
> Medha Bhagwat, PhD
> Informationist
> NIH Library
> National Institutes of Health
> Building 10, Room 1L13F
> 10 Center Drive
> Bethesda, Maryland 20892-1150
> T. 301-496-2185
> F. 301-402-0254
> E. bhagwat at mail.nih.gov
> http://nihlibrary.nih.gov
> _____________________________
> Amazing Research. Amazing Help.
>
>
> ________________________________________
> From: drnigam at gmail.com [drnigam at gmail.com] On Behalf Of Nigam Shah [
> nigam at stanford.edu]
> Sent: Friday, April 23, 2010 11:18 PM
> To: Bhagwat, Medha (NIH/OD/ORS) [E]
> Cc: info at bioontology.org; support at bioontology.org; Mark Musen
> Subject: Re: [ncbo-execs] Fwd: [bioontology-info] bioportal
>
> Dear Medha,
>
> The error you are seeing is the result of an unfortunate situation of
> having 3 ways of accessing annotated resources (such as expression datasets)
>  at Bioportal. Below I explain the three mechanisms and which work and which
> don't. They are:
>
> (1) via the 'All Resources' UI at
> http://bioportal.bioontology.org/resources (which is in "alpha" status)
>
> (2) via the Resources tab (e.g. at
> http://bioportal.bioontology.org/visualize/42693/?conceptid=Melanoma#resource_indexfor 'Melanoma')
>
> (3) via the Resource index REST API (e.g. at
> http://rest.bioontology.org/resource_index/byconcept/virtual/1032/false/true/0/10?conceptID=Melanomafor 'Melanoma).
>
> So, the content is there .. and (2) is just a nice way of seeing the same
> information as in (3). In order to see the desired search result in the
> resources tab (option 2, above), right now the steps are as follows:
>
> - search for your desired term at: http://bioportal.bioontology.org/search
> - click on the term (column 1)  in the ontology of your choice .. e.g.
> Melanoma in NCIT is the 12th one down.
> - that will get you to:
> bioportal.bioontology.org/visualize/42693/?conceptid=Melanoma<
> http://bioportal.bioontology.org/visualize/42693/?conceptid=Melanoma>
> - then click on the resource index (4 tabs to the left of the 'details').
> - that shows you public datasets annotated with 'Melanoma'.
>
> The UI at http://bioportal.bioontology.org/resource<
> http://bioportal.bioontology.org/resources> -- the one that didn't work --
> is being prototyped to avoid this circuitous route of searching for
> annotated resources such as GEO datasets. Unfortunately, when you tried it
> the alpha version (true to its status) didn't work.
>
> We will announce on the bioportal list when that UI is in production.
> Meanwhile, the steps above will allow you to search bioportal for annotated
> resources.
>
> Best regards,
> Nigam.
>
> From: "Bhagwat, Medha (NIH/OD/ORS) [E]" <bhagwat at mail.nih.gov<mailto:
> bhagwat at mail.nih.gov>>
> Date: April 23, 2010 12:06:38 PM PDT
> To: "info at bioontology.org<mailto:info at bioontology.org>" <
> info at bioontology.org<mailto:info at bioontology.org>>
> Cc: "Bhagwat, Medha \(NIH/OD/ORS\) \[E\]" <bhagwat at mail.nih.gov<mailto:
> bhagwat at mail.nih.gov>>
> Subject: [bioontology-info] bioportal
>
>
> Hi,
>
> I recently heard Mark Musen's talk and learnt that Bioportal can be used to
> search various resources such as expression datasets.  I tried using
>
> http://bioportal.bioontology.org/resources
>
> Today, I get request timed out message in the beginning even before typing
> any query.
> earlier, I had searched with term melanoma.  I don't get any results and
> but get the timed out message.
>
> Can you help?
>
> Medha
>
> _____________________________
>
> Medha Bhagwat, PhD
> Informationist
> NIH Library
> National Institutes of Health
> Building 10, Room 1L13F
> 10 Center Drive
> Bethesda, Maryland 20892-1150
> T. 301-496-2185
> F. 301-402-0254
> E. bhagwat at mail.nih.gov<mailto:bhagwat at mail.nih.gov>
> http://nihlibrary.nih.gov
> _____________________________
> Amazing Research. Amazing Help.
>
> _______________________________________________
> bioontology-info mailing list
> bioontology-info at lists.stanford.edu<mailto:
> bioontology-info at lists.stanford.edu>
> https://mailman.stanford.edu/mailman/listinfo/bioontology-info
>
>
> _______________________________________________
> ncbo-execs mailing list
> ncbo-execs at lists.stanford.edu<mailto:ncbo-execs at lists.stanford.edu>
> https://mailman.stanford.edu/mailman/listinfo/ncbo-execs
>
>
>
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