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

Nigam Shah nigam at stanford.edu
Fri Apr 23 20:18:41 PDT 2010


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_index
for
'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
- 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>
> *Date: *April 23, 2010 12:06:38 PM PDT
> *To: *"info at bioontology.org" <info at bioontology.org>
> *Cc: *"Bhagwat, Medha \(NIH/OD/ORS\) \[E\]" <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
> http://nihlibrary.nih.gov
> _____________________________
> Amazing Research. Amazing Help.
>
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>
>
>
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