PUMAdb : Re-directing sequence identifiers to external databases

Contents

Overview
A "redirection" URL
Configuring Treeview for redirection
Troubleshooting problems

Overview

In the database, identifiers for the unique sequences corresponding to what was arrayed are stored. These are sometimes called "reporters" or "probes". Although these identifiers/sequences vary from platform to platform (Agilent, Affymetrix, homemade PCRed ORFs, etc.), all claim to report on similar canonical gene names. In an effort to provide a resource for "jumping" to a model organism database using a unspecified sequence identifier (from the microarray database), a redirection scheme is employed.

A "redirection" URL

Currently, we are able to redirect requests for some Saccharomyces cerevisiae (SC), Mus musculus (MM), and Homo Sapiens (HS) reporters, based on their sequence identifier name ("SEQNAME"). However, if researchers of other organisms require this functionality, please contact the curators. The template for the redirection URL is:

http://puma.princeton.edu/cgi-bin/tools/redirectNameLookup.pl?org=ORG&db=RESOURCE&id=HEADER

where :

HEADER is the sequence identifier name. (see below for configuring TreeView)
ORG is the 2-letter organism code, case insensitive
- SC = Saccharomyces cerevisiae
- MM = Mus musculus
- HS = Homo Sapiens
and RESOURCE is one of the following (case insensitive):
- SGD = http://db.yeastgenome.org
- YPD = http://www.proteome.com/databases/YPD/ (requires login)
- SOURCE = http://source-search.princeton.edu/
- MGI = http://www.informatics.jax.org/

Note: Not all combinations of organisms and resources make sense, of course. For example, combining SC with SOURCE, HS with MGI, or MM with SGD would not yield a usable link.

For an example of fully formatted links, using various reporters for the yeast gene SST2, the following URLs from various platform identifiers should all re-direct to SGD.

Affymetrix example : http://puma.princeton.edu/cgi-bin/tools/redirectNameLookup.pl?org=SC&db=sgd&id=9856_AT
Agilent example : http://puma.princeton.edu/cgi-bin/tools/redirectNameLookup.pl?org=SC&db=sgd&id=A_06_P5271
Oligo example : http://puma.princeton.edu/cgi-bin/tools/redirectNameLookup.pl?org=SC&db=sgd&id=YLR452C-O
or if you have access to YPD (note db parameter emphasis): http://puma.princeton.edu/cgi-bin/tools/redirectNameLookup.pl?org=SC&db=ypd&id=YLR452C-O

Or a human Agilent oligo, directed to SOURCE:: http://puma.princeton.edu/cgi-bin/tools/redirectNameLookup.pl?org=HS&db=SOURCE&id=A_24_P417546
or a mouse Affymetrix oligo, directed to MGI:: http://puma.princeton.edu/cgi-bin/tools/redirectNameLookup.pl?org=MM&db=MGI&id=1415682_AT

Configuring Java Treeview for redirection

The primary purpose for this redirection was to provide a means for external programs, like Java Treeview, to be able to find the preferred database, given a random microarray database sequence identifier. To configure your installation of Java Treeview to utilize the redirection URL, do the following.

Choose "Presets -> Gene Url Presets..." from the Java Treeview "Settings" menu, as depicted below.
Edit one (or more) of the slots with the name and template URL, as depicted below (second slot), and save it. You should be able to copy and paste the template above, and replace the ORG and RESOURCE codes, as you prefer.
You can now select (or change from) the redirection preset by choosing Url Settings... from the "Settings" menu...
... then choose the appropriate header (usually YORF or CLID, depending on organism) and click the appropriate preset button. In the example below, it would be the second button labeled "PUMAdb SC redirection" (or whatever you named the preset in step 2, above. Verify that the example URL is appropriately formatted (see example URLs above or image below).

Troubleshooting problems

Windows-specific issue of Java TreeView : special case URL formatting
Because of the way TreeView uses the Windows OS shell to launch URLs, multi-parameter CGIs (like redirectNameLookup.pl), need to be specially quoted in order to pass all parameter values.

NOTE: the double quotation marks enclosing all CGI parametershttp://puma.princeton.edu/cgi-bin/tools/redirectNameLookup.pl?"org=SC&db=sgd&id=A_06_P5271"

General debugging
Example problems:
A reporter id, when redirected, does not result in a gene page at the destination resource.
You suspect that either TreeView, or your template URL is not sending an interpretable URL.

In order to determine what the issue might be for the concerns above, add a debug parameter to the template URL, for example:
http://puma.princeton.edu/cgi-bin/tools/redirectNameLookup.pl?org=SC&db=sgd&id=A_06_P5271&debug=1

This will cause redirectNameLookup.pl to launch the destination resource in a lower frame/panel, and use the top of the frameset to display relevant information like the interpreted resource and sequence identifier parameters, and the resulting resource URL it was attempting to redirect to. Not all sequence identifier have systematic/gene names, but if your suspect missing annotation (or a misannotation), pelase inform the database curators.