[Gmod-schema-cmts] schema/chado README.Apollo.pod,NONE,1.1

[Scott C. <sco...@us...>]

Update of /cvsroot/gmod/schema/chado
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv14088

Added Files:
	README.Apollo.pod 
Log Message:
updating and podifying the Apollo readme


--- NEW FILE: README.Apollo.pod ---
=head1 Reading and Writing to a Chado database with Apollo

This needs to be better documented, but here is a start:

In order to use Apollo read/write with chado, here are things that need to
be done:

=over

=item Grant privileges to users to several tables (list here)

In the absense of a complete list of tables, you can grant access to all
tables using sqlt and the perl Template::Toolkit template, bin/privileges.tmpl 

    sqlt -f PostgreSQL -t TTSchema --template bin/privileges.tmpl modules/nofuncs.sql | psql <databasename>

You can edit the template to grant privileges to just specific
users instead of PUBLIC, which of course would be a lot more secure.

=item Insert several ad hoc cv terms found in modules/sequence/apollo-bridge/cv_inserts.sql.

This file contains sql commands to insert several controlled vocabulary terms
that Apollo expects to be in the database.  This file can be recreated
with additional terms as needed by editing the file
modules/sequence/apollo-bridge/ad_hoc_cv and running the perl script
modules/sequence/apollo-bridge/insert_ad_doc_cv.pl.  The resulting 
sql file can be inserted into the database with this command:

    $ psql $DBNAME < modules/sequence/apollo-bridge/cv_inserts.sql 

=item Insert a few misc items like those found in modules/sequence/apollo-bridge/apollo.inserts

Essentially, Apollo and chado have to agree about what the names
of the programs in the analysis table are, and there needs to be a
few terms in the cv table.

About naming analysis results: there are no restrictions on what you
name them, however the GFF3 bulk loader will insert them typically 
one of two ways:

=over

=item 1

If you specify the -a (--analysis) flag with an argument, the 
loader will look for an entry in the analysis table where
analysis.name is equal to the argument supplied with -a.

=item 2

If you don't give an argument with -a, the loader will look
for analysis.name that is equal to the GFF source and type concatentated
with and underscore between them, ie 'source_type', eg, 'Rice_cDNA_match'.

=back

The inserts into the db table are there so that dbxref entries in GFF files
I typically process.  They can be ignored unless you are loading
GFF files with Dbxref entries.

Then there is the uniquename_id_generator sequence, for which
integers for building uniquenames are used. Then there are two
interts in to cvtermprop for the suffix and prefix for uniquename
generation.  Generated uniquenames with be of the form:

    $prefix . (int from uniquename_id sequence) . $suffix

For exmple, if you insert 'RICE' for the prefix and 'X' for the suffix, 
the resulting name of the first feature will be 'RICE000001X';

=item Add the functions and triggers to chado.

Use the perl script:

    % /usr/local/bin/gmod_apollo_triggers.pl create

Note that this script can also be used to drop and add the triggers
in case you want to do some bulk loading and want to disactivate
the triggers for that. 

=item Modify the Apollo configuration file, chado-adapter.xml. 

IS THERE DOCUMENTATION FOR DOING THAT IN APOLLO'S DOCS?  Yes, there is
a section for connecteding directly to flybase chado in the apollo
doc directory: doc/html/userguide.html but it is somewhat out of date.
I need to work with Mark to update it (it will probably need me to 
write it and have Mark proof it).

=back

I understand that these directions are somewhat vague.  Getting Apollo to
work with chado requires a little hands on tinkering.  If you find yourself
having difficulties, please contact me.

Scott Cain

L<ca...@cs...>

4/29/05