Download "Creating Databases for Biological Information: An Introduction". In

Table 9.10.1 A Brief Description of Perl Modules
Module
Description
DBI
A common database interface for Perl. Defines a set of methods, variables, and
conventions that provide a consistent database interface, independent of the actual
database being used. The Reactome Perl API uses DBI to interact with Reactome
database.
DBD::mysql
The MySQL driver for DBI, which mediates communication between DBI and the
MySQL API
BioPerl
Perl modules for biology. Please note, though, that only the Bio::Root modules of
the BioPerl core package are required. These are used for throwing exceptions and
handling file input/output.
GD
Modules for programmatic drawing and manipulation of images. Used for drawing
reaction diagrams and “reaction map.” The module is an interface to gd graphics
library in C (libgd), which is thus also required. libgd is available from
http://www.libgd.org and requires the libpng library for creation and manipulation
of images in Portable Network Graphics (PNG) format. libpng further requires
zlib compression. linpng and zlib are available from http://www.libpng.org
and http://www.zlib.net, respectively.
XML::Simple
An Easy API to maintain XML. Used to read an XML configuration file which
determines the types of lists downloadable from dynamically created content pages
and also contains the instructions for creating those lists. The module requires
XML::Parser Perl module which itself requires expat XML parser library in C.
expat is available from http://sourceforge.net/projects/expat.
PDF::API2
Module for creation and modification of Portable Document Format (PDF) files.
Used for exporting description of Reactome pathways and reactions in PDF.
Requires Compress::Zlib, Compress::Raw::Zlib,
IO::Compress::Base, and IO::Compress::Zlib Perl modules.
GraphViz
Perl interface to the identically named toolkit for layout and image generation of
directed and undirected graphs. Used for automatic layout of entity-level pathway
diagrams. GraphViz toolkit is available from http://www.graphviz.org.
Archive::Tar Module for manipulations of tar archives. Used for exporting Reactome data as
Protégé projects. Requires IO::Zlib Perl module.
WWW::Search
Requires Date::Manip, IO::Capture, User, and Test::File.
Search::
Tools::
HiLiterm
Requires Data::Dump, File::Slurp, and Search::QueryParser
COMMENTARY
Background Information
Installing
Reactome Locally
The concept of a pathway database is not a
novel one and there are numerous sources offering information under various access terms
ranging from free-for-all to paying-subscriberonly. However, the feature that distinguishes
the Reactome project from many of its peers is
that, in addition to freely accessible data, it also
offers the possibility to download and replicate
the whole database and Web site. While the
Reactome project attempts to provide easy access to various bits of information in various
formats, having a local copy of the database
and API code gives the ultimate freedom and
flexibility to extract whatever is necessary.
While the Reactome project’s own curation efforts concentrate mainly on human biology, the setup can be used to annotate
biochemical processes of any cellular organism. Indeed, the Reactome project also
produces orthology-based computational predictions of pathways in numerous other organisms. These can be used as a starting
point for manual curation of pathways in
other species. The Reactome Curator Tool,
available from the Reactome download page
9.10.8
Supplement 21
Current Protocols in Bioinformatics