chado_integration.pod
Where we discuss how to integrate CMap with the chado database. This is specifically useful for connection of CMap with GBrowse.
This document assumes that you have a working installation of the chado database and you want to add CMap to it.
The goal is to walk you through adding the CMap tables to the chado database and creating links from features in Gbrowse to CMap.
Since the database is already created, all you have to do is create the tables in it.
$ psql chado_db < sql/cmap.create.postgresql
Then create the linking table. This connects the CMap features with the Chado features.
$ psql chado_db < chado_integration/linker_table.sql
Then all you need to is set up the correct privileges.
First you will populate the CMap tables with your data. For information on how to do this see docs/ADMINISTRATION.pod.
After you have data in both CMap and Chado portions of the database, you can populate the linker table, "feature_to_cmap". Since the data is going to be different from site to site, it is left to you to decide how exactly you want to populate the linker table.
The "feature_to_cmap" table has 2 important columns that you will need to insert. One is the "feature_id" of the Chado feature and the other is "cmap_feature_acc" which is the "accession_id" of a cmap feature.
Here is an example insert statement where the chado feature_id is '32' and the cmap accession id is 'EDEN1':
insert into feature_to_cmap (feature_id, cmap_feature_acc) values (32,'EDEN1')
To link a feature from GBrowse to a feature in CMap, you must first have that link in the "feature_to_cmap" table, as described above.
Then creating a link is as simple as editing the config file. Edit or add the link attribute to the track definition like the following:
link = sub {my $feature=shift; return $feature->cmap_link('DATASOURCE');}
You must change the DATASOURCE from above to the name of a CMap datasouce, which can be found as the <database> "name" in the cmap config file.
The cmap_link() method is located in
Bio::DB::Das::Chado::Segment::Feature.
That should allow you to link from GBrowse to CMap. If you have any troubles email the CMap developer's list:
gmod-cmap@lists.sourceforge.net
Ben Faga <faga@cshl.edu>.