
   BioPerl DocBook ([1]BioPerl)

OBDA Access HOWTO

Aaron Mackey

   [2]University of Virginia

     <[3]amackey@virginia.edu>

Brian Osborne

   [4]Cognia Corporation

     <[5]brian-at-cognia.com>

Peter Schattner

   [6]UCSC

     <[7]schattner@alum.mit.edu>

Heikki Lehvaslaiho

   [8]EBI

     <[9]heikki@ebi.ac.uk>

Lincoln Stein

   [10]Cold Spring Harbor Laboratory

     <[11]lstein@cshl.org>

   This document is copyright Lincoln Stein, 2002. For reproduction other
   than personal use please contact lstein at cshl.org

   2002-07-14
   Revision History
   Revision 1.1 2003/02/20 lstein
   added some OBDA documentation plus flat file index load script
   Revision 1.2 2003/02/20 lstein
   check in reasonable howtos for database access and flat databases
   Revision 1.3 2003/02/20 lstein
   added new heading to biodatabase access doc for Heikki to fill in
   Revision 1.4 2003/02/20 heikki
   added explanation for biogetseq
   Revision 1.5 2003/03/01 peters
   documentation updates
   Revision 1.6 2003/03/12 amackey
   documentation updates
   Revision 1.7 2003/06/10 BIO
   convert to XML/SGML, corrections

   Abstract

   This is a HOWTO written in DocBook (XML) that explains how to set up
   and use the Open Biological Database Access system.
     _________________________________________________________________

   Table of Contents

   [12]1. Introduction
   [13]2. Using the OBDA Registry System
   [14]3. Installing the Registry File
   [15]4. Modifying the Search Path
   [16]5. Format of the Registry File
   [17]6. The Protocol Tag
   [18]7. The Location Tag
   [19]8. Other Tags
   [20]9. Installing Local Databases
   [21]10. Writing code to use the Registry
   [22]11. Using biogetseq to Access Registry Databases

1. Introduction

   Importing sequences with annotations is a central part of most
   bioinformatics tasks. Bioperl supports importing sequences from
   indexed flat-files, local relational databases and remote (internet)
   databases. Previously, separate programming syntax was required for
   each of these types of data access (see for example Section III.1 of
   the Bioperl tutorial). In addition, if one wanted to change one's mode
   of sequence-data acquisition (for example, by implementing a local
   relational database version of Genbank when previously the data had
   been stored in an indexed flat-file) one had to rewrite all of the
   data-access subroutines in one's application code.

   The Open Biological Database Access (OBDA) System was designed so that
   one could use the same application code to access data from all three
   of the database types by simply changing a few lines in a
   configuration file. This makes application code more portable and
   easier to maintain. This document shows how to set up the required
   OBDA-registry configuration file and how to access data from the
   databases referred to in the configuration file using a perl script as
   well as from the command line. The Web site for OBDA is
   [23]obda.open-bio.org.
   [Note]
   Note

   Accessing data via the OBDA system is optional in Bioperl. It is still
   possible to access sequence data via the old database-format-specific
   modules such as Bio::Index::Fasta or Bio::DB::Fasta.

2. Using the OBDA Registry System

   The OBDA BioDirectory Registry is a platform-independent system for
   specifying how BioPerl programs find sequence databases. It uses both
   local and site-wide configuration files, known as the registry, which
   define one or more databases and the access methods to use to access
   them.

   For instance, you might start out by accessing sequence data over the
   web, and later decide to install a locally mirrored copy of GenBank.
   By changing one line in the registry file, all
   Bio{Perl,Java,Python,Ruby} applications will start using the mirrored
   local copy automatically - no source code changes are necessary.

3. Installing the Registry File

   The registry file should be named seqdatabase.ini. By default, it
   should be installed in one or more of the following locations:
        $HOME/.bioinformatics/seqdatabase.ini
        /etc/bioinformatics/seqdatabase.ini


   The Bio{Perl,Java,Python,Ruby} registry-handling code will initialize
   itself from the registry file located in the home directory first, and
   then it will read the system-wide default in /etc. Windows Perl users
   should make sure to set the $HOME variable, otherwise the
   seqdatabase.ini file may not be found. Unix users need not do this
   since the code will use the getpwuid() method.

   If a local registry file cannot be found, the registry-handling code
   will attempt to copy the file located at this URL to a
   $HOME/.bioinformatics directory:
        http://www.open-bio.org/registry/seqdatabase.ini


4. Modifying the Search Path

   The registry file search path can be modified by setting the
   environment variable OBDA_SEARCH_PATH. This variable is a
   semicolon-delimited string of directories and URLs, for example:
 OBDA_SEARCH_PATH=/home/lstein/;http://foo.org/

   [Important]
   Important

   Note that the fact that the search path is for an entire file
   (seqdatabase.ini) rather than for single entry (e.g. 'genbank') means
   that you have to copy any default values you want to keep from the
   (old) default configuration file to your new configuration file.

   For example, say you have been using biofetch with the default
   configuration file http://www.open-bio.org/registry/seqdatabase.ini
   for all your sequence-data retrieval. If you now install a local copy
   of genbank, your local seqdatabase.ini must not only have a section
   indicating that the genbank copy is local but it must have sections
   configuring the web access for all the other databases you use, since
   http://www.open-bio.org/registry/seqdatabase.ini will no longer be
   found in a registry-file search.

5. Format of the Registry File

   The registry file is a simple text file, as shown in the following
   example:
 VERSION=1.00

 [embl]
 protocol=biofetch
 location=http://www.ebi.ac.uk/cgi-bin/dbfetch
 dbname=embl

 [swissprot]
 protocol=biofetch
 location=http://www.ebi.ac.uk/cgi-bin/dbfetch
 dbname=swall


   The first line is the registry format version number in the format
   VERSION=X.XX. The current version is 1.00.

   The rest of the file is composed of simple sections, formatted as:
  [database-name]
  tag=value
  tag=value

  [database-name]
  tag=value
  tag=value


   Each section starts with a symbolic database service name enclosed in
   square brackets. Service names are case-insensitive. The remainder of
   the section is followed by a series of tag=value pairs that configure
   access to the service.

   Database-name sections can be repeated, in which case the client
   should try each service in turn from top to bottom.

   The options under each section must have two non-optional tag=value
   lines being
  protocol="protocol-type"
  location="location-string"


6. The Protocol Tag

   The protocol tag species what access mode to use. Currently it can be
   one of:
  flat
  biofetch
  biosql


   "flat" is used to fetch sequences from local flat files that have been
   indexed using BerkeleyDB or binary search indexing.

   "biofetch" is used to fetch sequences from web-based databses. Due to
   restrictions on the use of these databases, this is recommended only
   for lightweight applications.

   "biosql" fetches sequences from BioSQL databases. To use this module
   you will need to have an instantiated relational database conforming
   to the BioSQL schema, and install the bioperl-db distribution.

   [Important]
   Important

   Support for the biosql protocol is disabled as of Bioperl version 1.4.
   We hope to remedy this in a subsequent release.

7. The Location Tag

   The location tag tells the bioperl sequence fetching code where the
   database is located. Its interpretation depends on the protocol
   chosen. For example, it might be a directory on the local file system,
   or a remote URL. See below for protocol-specific details.

8. Other Tags

   Any number of additional tag values are allowed. The number and nature
   of these tags depends on the access protocol selected. Some protocols
   require no additional tags, whereas others will require several.

   Protocol Tag Description
   flat location Directory in which the index is stored. The "config.dat"
   file generated during indexing must be found in this location
   flat dbname Name of database
   biofetch location Base URL for the web service. Currently the only
   compatible biofetch service is http://www.ebi.ac.uk/cgi-bin/dbfetch
   biofetch dbname Name of the database. Currently recognized values are
   "embl" (sequence and protein), "swall" (SwissProt + TREMBL), and
   "refseq" (NCBI RefSeq entries)
   biosql location host:port
   biosql dbname database name
   biosql driver
   mysql|postgres|oracle|sybase|sqlserver|access|csv|informix|odbc|rdb
   biosql user username
   biosql passwd password
   biosql biodbname biodatabase name

   Table 1. OBDA Protocols

9. Installing Local Databases

   If you are using the biofetch protocol, you're all set. You can start
   reading sequences immediately. For the flat protocol, you will need to
   create and initialize a local database. See the following
   documentation on how to do this:

   flat protocol:[24]Flat Databases HOWTO

   biosql protocol: BioSQL INSTALL (from the biosql-schema package,
   available at [25]obda.open-bio.org). Download the Biosql tar file to
   view all the documentation.

   [Important]
   Important

   Support for the biosql protocol in OBDA is disabled as of Bioperl
   version 1.4. We hope to remedy this in a subsequent release.

   Once the flat database is created you can configure your
   seqdatabase.ini file. Let's say that you have used the
   bioflat_index.pl script to create the flat database and a new
   directory called "ppp" has been created in your /home/sally/bioinf/
   directory (and the ppp/ directory contains the config.dat file). Your
   sequence.ini entry should contain these lines:
        protocol=flat
        location=/home/sally/bioinf
        dbname=ppp


   The "database-name" can be any useful name, it does not have to refer
   to existing files or directories, but the "dbname" should be the name
   of the newly created directory.

10. Writing code to use the Registry

   Once you've set up the OBDA registry file, accessing sequence data
   from within a perl script is simple. The following example shows how;
   note that nowhere in the script do you explicitly specify whether the
   data is stored in a flat file, a local relational database or a
   database on the internet.

   To use the registry from a Perl script, use the following idiom:
    1 use Bio::DB::Registry;
    2 $registry = Bio::DB::Registry->new;
    3 $db = $registry->get_database('embl');
    4 $seq = $db->get_Seq_by_acc("J02231");
    5 print $seq->seq,"\n";


   In lines 1 and 2, we bring in the Bio::DB::Registry module and create
   a new Bio::DB::Registry object. We then ask the registry to return a
   database accessor for the symbolic data source "embl", which must be
   defined in an [embl] section in the seqdatabase.ini registry file.

   The returned accessor is a Bio::DB::RandomAccessI object (see the
   appropriate manual page), which has just three methods:
   $db->get_Seq_by_id($id);
   $db->get_Seq_by_acc($acc);
   $db->get_Seq_by_version($versioned_acc);


   These methods return Bio::Seq objects by searching for their primary
   IDs, accession numbers and accession.version numbers respectively. The
   returned objects have all the methods defined by Bio::Seq (see the
   appropriate manual page, online at [26]doc.bioperl.org). In line 5, we
   call the sequence object's seq() method to fetch and print out the DNA
   or protein string.

11. Using biogetseq to Access Registry Databases

   As a convenience, the Bioperl distribution includes the script
   biogetseq.PLS that enables one to have OBDA access to sequence data
   from the command line. It's located in the scripts/DB directory of the
   bioperl distribution (it may also have been installed in your system
   if you you asked for a script installation after 'make install'. Move
   or add it into your path to run it. You can get this help text by
   running it with no arguments:
Usage: biogetseq --dbname embl --format embl --namespace acc id [ id ... ]*
       dbname defaults to embl
       format defaults to embl
       namespace defaults to 'acc' ['id', 'acc', 'version']
       rest of the arguments is a list of ids in the given namespace


   If you have a set of ids you want to fetch from EMBL database, you
   just give them as space-separated parameters:
  % biogetseq J02231 A21530 A10516


   The output is directed to STDOUT, so it can be redirected to a file.
   The options can be given in the long "double hyphen" format or
   abbreviated to one-letter format ("--fasta" or "-f"):
        % biogetseq -f fasta -n acc J02231 A21530 A10516 > filed.seq


   BioPerl DocBook ([27]BioPerl)

References

   1. http://bioperl.org/
   2. http://www.virginia.edu/
   3. mailto:amackey@virginia.edu
   4. http://www.cognia.com/
   5. mailto:brian-at-cognia.com
   6. http://www.ucsc.edu/
   7. mailto:schattner@alum.mit.edu
   8. http://ebi.ac.uk/
   9. mailto:heikki@ebi.ac.uk
  10. http://www.cshl.org/
  11. mailto:lstein@cshl.org
  12. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#introduction
  13. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#registry
  14. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#installation
  15. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#modifying
  16. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#format
  17. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#protocol
  18. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#location
  19. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#others
  20. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#local
  21. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#code
  22. file://localhost/Users/bosborne/bioperl-live/doc/howto/xml/OBDA_Access.html#biogetseq
  23. http://obda.open-bio.org/
  24. http://bioperl.org/HOWTOs/html/Flat_Databases.html
  25. http://obda.open-bio.org/
  26. http://doc.bioperl.org/
  27. http://bioperl.org/
