SYNOPSIS

#create new GFF database connection
my $db = Bio::DB::GFF->new( -adaptor => 'dbi::pg_fts',
-dsn => 'dbi:Pg:dbname=worm');
#add full text indexing 'stuff'
#assumes that TSearch2 is available to PostgreSQL
#this will take a VERY long time for a reasonably large database
$db->install_TSearch2();
...some time later...
#we don't like full text searching...
$db->remove_TSearch2();

DESCRIPTION

This adaptor is based on Bio::DB::GFF::Adaptor::dbi::pg but it implements the TSearch2 PostgreSQL contrib module for fast full text searching. To use this module with your PostgreSQL GFF database, you need to make TSearch2 available in the database.

To use this adaptor, follow these steps:

Install TSearch2 contrib module for Pg

Can be as easy as `sudo yum install postgresql-contrib`, or you may need to recompile PostgreSQL to include it. See <http://www.sai.msu.su/~megera/postgres/gist/tsearch/V2/docs/tsearch-V2-intro.html> for more details

Load the TSearch2 functions to you database

  % cat tsearch2.sql | psql <your database>

Load your data using the pg adaptor:

 % bp_pg_bulk_load_gff.pl -c -d yeast saccharomyces_cerevisiae.gff

or

 % bp_load_gff.pl -c -d yeast -a dbi::pg saccharomyces_cerevisiae.gff

Add GFF/TSearch2 specific modifications

Execute a perl script like this one:

  #!/usr/bin/perl -w
  use strict;
  use Bio::DB::GFF;
  my $db = Bio::DB::GFF->new(
      -adaptor   => 'dbi::pg_fts',
      -dsn       => 'dbi:Pg:dbname=yeast',
      -user      => 'scott',
    );
  print "Installing TSearch2 columns...\n";
  $db->install_TSearch2();
  print "Done\n";

Note that this last step will take a long time. For a S. cerevisiae database with 15K rows, it took over an hour on my laptop, and with a C. elegans database (~10 million rows) it took well over a day.

If at some point you add more data you your database, you need to run a similar script to the one above, only executing the update_TSearch2() method. Finally, if you want to remove the TSearch2 columns from your database and go back to using the pg adaptor, you can execute a script like the one above, only executing the remove_TSearch2() method.

NOTES ABOUT TSearch2 SEARCHING

You should know a few things about how searching with TSearch2 works in the GBrowse environment:

1.

TSearch2 does not do wild cards, so you should encourage your users not to use them. If wild cards are used, the adaptor will fall back on an ILIKE search, which will be much slower.

2.

However, TSearch2 does do 'word stemming'. That is, if you search for 'copy', it will find 'copy', 'copies', and 'copied'.

3.

TSearch2 does not do phrase searching; all of the terms in the search string are ANDed together.

ACKNOWLEDGEMENTS

Special thanks to Russell Smithies and Paul Smale at AgResearch in New Zealand for giving me their recipe for doing full text indexing in a GFF database.

AUTHOR

Scott Cain, [email protected]

APPENDIX

search_notes

 Title   : search_notes
 Usage   : @search_results = $db->search_notes("full text string",$limit)
 Function: Search the notes for a text string, using PostgreSQL TSearch2
 Returns : array of results
 Args    : full text search string, and an optional row limit
 Status  : public

This is based on the mysql-specific method that makes use of the TSearch2 functionality in PosgreSQL's contrib directory. Given a search string, it performs a full-text search of the notes table and returns an array of results. Each row of the returned array is a arrayref containing the following fields:

  column 1   A Bio::DB::GFF::Featname object, for passing to segment()
  column 2   The text of the note
  column 3   A relevance score.

make_features_by_name_where_part

 Title   : make_features_by_name_where_part
 Function: constructs a TSearch2-compliant WHERE clause for a name search
 Status  : protected

install_TSearch2

 Title   : install_TSearch2
 Function: installs schema modifications for use with TSearch2
 Usage   : $db->install_TSearch2
 Status  : public

update_TSearch2

 Title   : update_TSearch2
 Function: Updates TSearch2 columns
 Usage   : $db->update_TSearch2
 Status  : public

remove_TSearch2

 Title   : remove_TSearch2
 Function: Removes TSearch2 columns
 Usage   : $db->remove_TSearch2
 Status  : public