=head1 NAME

Bioperl databases 1.4

=head1 SYNOPSIS

How to use databases with Bioperl

=head1 DESCRIPTION

This document is designed to let you use Bioperl with databases.
Bioperl can work with a number of sequence formats and allows users
to interconvert easily amongst these formats. Bioperl can also index
flat files in some of these standard formats, allowing very fast retrieval.
You can also use Bioperl to retrieve sequences from remote databases
via the Web or to build and query in-house relational databases (RDBs).

Different scripts are provided to get you started with some of these
approaches, for example:

=over 3

=item scripts/bp_fetch.PLS

Fetches sequences from a flat-file database

=item scripts/bp_index.PLS

Builds indexes for flat files databases which are accessed
by bp_fetch.PLS. These scripts are discussed in more detail below.

=item scripts/DB/bioflat_index.PLS

Build indexes for flat file databases that can be used by the
OBDA sequence retrieval system.

=back

The core of the backend system is found in following modules

=over 3

=item Bio::DB::*

Generic access to databases, whether flat file, web or RDB. At the
moment, this provides random access retrieval, on the basis of ids or
accession numbers, but does not provide the ability to loop over the
entire database, nor does it provide any complex querying ability. For
these advanced features see L<USING BIOPERL WITH A RELATIONAL DATABASE (bioperl-db)>.

Bio::DB::BioSeqI is the abstract interface for the databases (hence
the I). Bio::DB::GenBank and Bio::DB::GenPept are concrete
implementations for network access to the GenBank and GenPept
databases at NCBI, and others, using HTTP as a protocol. See
L<Bio::DB::GenBank>, L<Bio::DB::GenPept>, and 
L<REMOTE SEQUENCE RETRIEVAL (Bio::DB::*)> for more information.

=item Bio::Index::* and Bio::DB::Fasta

Flat file indexing system, for read-only, flat file distributions. These
provide for format-specific, generic type access, but the underlying
machinery can be customised for any number of different flat file systems.
The indices allow extremely fast retrieval based on unique keys.

The Index modules EMBL and Fasta, as they are designed as sequence databases,
conform to the Bio::DB::BioSeqI interface, meaning they can be used whereever
the Bio::DB::BioSeqI is expected.

Flat file indexing of Fasta files is also provided by Bio::DB::Fasta,
please see L<Bio::DB::Fasta> for more information - this module has some
useful features not contained in Bio::Index::Fasta.

=item Bio::SeqIO::*

Conversion systems for Bio::Seq objects, either to or from sequence
streams. The movement of things into SeqIO prevents the Bio::Seq object
bloating up with format code, and the SeqIO system has the benefit
of being very easy to extend to new formats. Please see L<Bio::SeqIO>
for more information, or the SeqIO HOWTO (http://bioperl.org/HOWTOs).

=back

=over 2

=item bioperl-db

The bioperl-db package is installed separately from Bioperl but is
tightly integrated with Bioperl's objects. The bioperl-db package
works with the BioSQL schema and maps to Bioperl's Seq and SeqFeature
objects, and sequences in familiar formats can be loaded into
the schema in relational form, and retrieved as Seq objects as well.
Currently Mysql, Oracle, and Postgres are supported. See
L<USING BIOPERL WITH A RELATIONAL DATABASE (bioperl-db)> below.

=item The OBDA system

Open Biological Database Access is a system for sequence retrieval
that wraps all the different data sources mentioned above together
with a single interface.

=back

=head1 REMOTE SEQUENCE RETRIEVAL (Bio::DB::*)

Bioperl offers a number of modules for retrieving sequences over the
network. The available remote databases include GenBank, GenPept, GDB,
EMBL, SwissProt, XEMBL, and remote Ace servers. A typical method is

   get_Seq_by_id($id)

which returns a Seq object, or

   get_Stream_by_id($ref_to_array_of_ids)

which returns a SeqIO object. See L<Bio::DB::GenBank>, L<Bio::DB::GenPept>,
L<Bio::DB::GDB>, L<Bio::DB::EMBL>, L<Bio::DB::SwissProt>, L<Bio::DB::XEMBL>,
and L<Bio::DB::Ace>, and L<Bio::SeqIO> for more information.


=head1 SETTING UP BIOPERL INDICES (Bio::Index::*)

If you want to use Bioperl indicies of Fasta, EMBL/SwissProt .dat files,
SwissPfam, GenBank, or Blast files then the bp_fetch.PLS and
bp_index.PLS scripts are great ways to start off (and also reading the
scripts shows you how to use the Bioperl indexing stuff). bp_fetch.PLS 
and bp_index.PLS coordinate using two environment variables

  BIOPERL_INDEX - directory where the indices are kept

  BIOPERL_INDEX_TYPE - type of DBM file to use for the index

The basic way of indexing a database, once BIOPERL_INDEX has been
set up, is to go

  bp_index.pl <index-name> <filenames as full path>

e.g., for Fasta files

  bp_index.pl est /nfs/somewhere/fastafiles/est*.fa

Or, for EMBL/Swissprot files

  bp_index.pl -fmt=EMBL swiss /nfs/somewhere/swiss/swissprot.dat

To retrieve sequences from the index go

  bp_fetch.pl <index-name>:<id>

eg,

  bp_fetch.pl est:AA01234

or

  bp_fetch.pl swiss:VAV_HUMAN


bp_fetch.pl also has other options to connect to Genbank across the network.


=head1 CHECKLIST

   mkdir /nfs/datadisk/bioperlindex/

or any other directory

   setenv BIOPERL_INDEX /nfs/datadisk/bioperlindex/
   setenv BIOPERL_INDEX_TYPE DB_File

in .cshrc or .tcshrc (or B<set> and B<export> in bash and its .bashrc).
Another BIOPERL_INDEX_TYPE is SDBM_File, this one should come with a
standard Perl package.

go 

   bp_index.pl swissprot /nfs/datadisk/swiss/swissprot.dat

etc. You are now ready to use bp_fetch.pl. See L<Bio::Index::Fasta>, 
L<Bio::Index::GenBank>, L<Bio::Index::Blast>, L<Bio::Index::EMBL>,
L<Bio::Index::SwissPfam>, and L<Bio::Index::Swissprot> for more.

Flat file indexing of Fasta files is also provided by Bio::DB::Fasta,
please see L<Bio::DB::Fasta> for more information - this module provides
some functionality absent from Bio::Index::Fasta.


=head1 USING BIOPERL WITH A RELATIONAL DATABASE (bioperl-db)

The bioperl-db package works in conjunction with the BioSQL relational 
schema (http://obda.open-bio.org/). The most recent version of the
bioperl-db package can be obtained at 
http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=bioperl 

The bioperl-db and BioSQL packages integrate neatly with Bioperl's 
objects and contain tables for sequences, entries, sequence features, 
taxonomic information, references, keywords, a wide variety of genetic 
markers, and more. With a Seq object and a built-in database "adaptor" 
one can load the object's data in one step, as in 

  $adaptor->store($newid,$seqobj)

Similarly, one can query the database with id's or using query objects
and retrieve arrays of Seq objects. For example

  @seqobjs = $adaptor->fetch_by_query( -constraints =>
            ["or", 
                  ["and", # find all human topoisomerases
                         "species=Human",
                         "keywords like *topoisomerase*"],
                  ["and", # and Escherichia gyrases
                         "species like Escherichia*",
                         "keywords like *gyrase*"],
            ]);

See L<Bio::DB::BioSQL::SeqAdaptor>, L<Bio::DB::Query::QueryConstraint>, 
L<Bio::DB::BioSQL::CommentAdaptor>, and L<Bio::DB::Query::BioQuery> for
more examples.

With bioperl-db and BioSQL installed you will also be able to load 
sequence data, GO Ontology data, and NCBI taxonomic data into your own
RDB.


=head1 BIOPERL AND BIOSQL

BioSQL is joint project of the OpenBio efforts: bioperl, biopython,
biojava, and bioruby. BioSQL creates a single relational 
schema that's accessible using any of these packages. To use BioSQL
with Perl you'll need Bioperl, version 1.2 or later, bioperl-db from 
www.bioperl.org, and BioSQL. The BioSQL package can be obtained at 
www.open-bio.org. BioSQL currently supports the Mysql, Postgres, and 
Oracle database servers. Consult the BioSQL package for more details 
on installing and using BioSQL.


=head1 BIO::DB::GFF: INDEXING AND RETRIEVAL OF SEQUENCE FEATURE DATA

An alternative view of sequence feature data is provided by the
Bio::DB::GFF module, part of the core package.  This module takes a
set of sequence features stored in GFF (gene-finding format) format
and loads them into a relational database optimized for positional
queries.  This allows a variety of data mining operations, such as
finding sequence features that are within a certain distance of each
other or which overlap. The module can also store large contiguous
sequences and extract subsequences rapidly.

See L<Bio::DB::GFF>, L<Bio::DB::GFF::RelSegment>,
L<Bio::DB::GFF::Feature>, and L<Bio::DB::GFF::Adaptor::dbi>.


=head1 OBDA

The Open Biological Database Access (OBDA) system provides a single,
configurable retrieval interface to sequence databases regardless of their
format: relational (as in BioSQL), local indexed flat file, or remote and
Internet-accessible. The user creates a single configuration file, a
"registry", that describes the data source and OBDA handles the rest.
See the OBDA_Access HOWTO for more information
(http://bioperl.org/HOWTOs) or L<Bio::DB::Registry>.

