=head1 NAME Bioperl databases 1.4 - how to use databases with Bioperl =head1 SYNOPSIS Not really appropiate for a synopsis. Read on... =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. Other layers above flat file indexing are provided, allowing users to retrieve sequences from remote databases via the Web or build and query in-house relational databases (RDBs). Different scripts are provided to get you started with the Bioperl backend, for example: =over 2 =item scripts/bp_fetch.PLS Fetches sequences from a Database =item scripts/bp_index.PLS Builds indexes for flat files databases which are easily accessible by bp_fetch.PLS. These scripts are discussed in more detail below. =back The core of the backend system is found in following modules =over 2 =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. 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, L, and L 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 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 for more information. =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 below. =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, L, L, L, L, L, and L, and L 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 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 : 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 and B 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, L, L, L, L, and L for more. Flat file indexing of Fasta files is also provided by Bio::DB::Fasta, please see L 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, L, L, and L 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, L, L, and L.