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

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


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_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=Melanoma for '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


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