nelsonlab / Bugs / #149 set up NCBI LinkOut to Celsius

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from louis fridkis <loufridkis@gmail.com> hide details 1:59 pm (0 minutes ago)
to "Edgar, Ron (NIH/NLM/NCBI) [E]" <edgar@ncbi.nlm.nih.gov>
cc "Kwan, Kathy (NIH/NLM/NCBI) [E]" <kwan@ncbi.nlm.nih.gov>
date Jul 20, 2007 1:59 PM
subject Re: FW: Both GEO and GDS are setup for LinkOut
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Ron,

Thanks for your reply. Here is an example I worked through:

If I go to:
http://www.ncbi.nlm.nih.gov/

and select from the Search pull down menu:

GEO Datasets

then I get to:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=gds&cmd=search&term=

If I then enter

GSM199358

in the "for" field I get to:

http://www.ncbi.nlm.nih.gov/sites/entrez

This page now contains an entry for

GSE8052 record:

if I click on this entry I go to:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8052

which contains a similar entry for:

Series GSE8052

Now, this item (GSM199358/GSE8052) corresponds to our SN id:

1087475

and if I go to:

http://celsius.genomics.ctrl.ucla.edu/report/cel?id=SN:1087475

I will see the web page for this item giving more information.

Therefore, I proposed providing a list mapping GSE and SN numbers as the source
for linking between

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=<GSE###>

and

http://celsius.genomics.ctrl.ucla.edu/report/cel?id=<SN:###>
- Hide quoted text -

On 7/19/07, Edgar, Ron (NIH/NLM/NCBI) [E] <edgar@ncbi.nlm.nih.gov> wrote:

Hi Louis,

You can only use the linkout mechanism to link from a record on our side to a record on your side, what you have effectively asked for here is to link our Entrez database to a search page on your database (which also claims to be experimental BTW).

If you have a set of records, with urls for each you want to link to a set of our records this should be possible.
You might want to link from GEO Platforms for certain Affymetrix arrays for example but you must provide a single link (that works and stable) to each query or accession record on our side.

Hope this helps

thanks

Ron

From: louis fridkis [mailto:loufridkis@gmail.com]
Sent: Wednesday, July 18, 2007 6:22 PM
To: NLM/NCBI List linkout
Subject: [LinkOut] Re: link out request

Dear Friends:

I sent the email (below) and never received a responce. We are still interested in this and would appreciate hearing from you.

Also, based on comments from Ron Edgar, if might be better to use:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gds

On 3/26/07, louis fridkis <loufridkis@gmail.com> wrote:

Lou Fridkis, loufridkis@gmail.com, 310-825-7920.

Here is the URL that we would like to link out to from GEO:

http://celsius.genomics.ctrl.ucla.edu/

We provide a set of consistently processed Affymetrix data that is appropriate for large-scale meta-analysis.

The GEO URL from which we would like to link out is:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=geo

The idea is that the link will show more information about a given GSM id.
--
Lou Fridkis

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Unfortunately, the url you have pointed to (acc.cgi) is not an Entrez database and thus has no linkout capacity. The only approximation is to link to the GSE record on the previous page by providing a search term GSExxx[ACCN] or fully: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gds&Cmd=Search&Term=GSE8052\[accn]

If this is agreeable to you, all you need is to provide the linkout folks with the proper files

Please see the documentation at:

http://www.ncbi.nlm.nih.gov/entrez/linkout/doc/nonbiblinkout.html

epecially the part on "File Preparation".

When you are ready, please send linkout@ncbi.nlm.nih.gov a small sample file of the links.

Please let us know if you have any questions on making the files.

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#149 set up NCBI LinkOut to Celsius

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