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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Using go-perl</title>
<link rel="stylesheet" type="text/css" href="../../doc/stylesheet.css">
</head>
<body>
<h1>Using go-perl</h1>
<h2>Introduction</h2>
<p>
The go-perl library provides modules to help parse and navigate
GO/OBO style ontologies together with associated gene product
annotations.
</p>
<p>
The go-perl library does not deal with interfacing or querying
the GO database; for this you need <a
href="../../go-db-perl/doc/go-db-perl-doc.html">go-db-perl</a>,
part of this distribution. You need go-perl in order for
go-db-perl to work
</p>
<h2>
Background
</h2>
<p>
You should already be familiar with the Gene Ontology project:
<ul>
<li>
<a href="http://www.geneontology.org">http://www.geneontology.org</a>
</li>
<li>
<a href="http://obo.sourceforge.net">http://obo.sourcefore.net</a>
</li>
<li>
<a
href="http://www.geneontology.org/GO.contents.doc.html">GO
documentation</a>
</li>
</ul>
</p>
<p>
You should also be familiar with the file formats GO uses:
<ul>
<li>
<a href="http://www.geneontology.org/GO.format.shtml">goflat and
OBO file formats</a>
</li>
<li>
<a href="http://www.geneontology.org/GO.annotation.shtml">annotation
format</a>
</li>
</ul>
</p>
<p>
Documentation on the rest of the go-dev distribution:
<ul>
<li>
<a href="../../doc/go-dev-doc.html">go-dev documentation</a>
</li>
</ul>
</p>
<p>
GO Database and Developers page:
<ul>
<li>
<a
href="http://www.godatabase.org/dev">http://www.godatabase.org/dev</a>
</li>
</ul>
</p>
<p>
And you should be familiar with perl, particularly
object-oriented perl (unless you just want to run the scripts
that are part of go-perl)
</p>
<h2>Download</h2>
<p>
You can get the official release from CPAN - <a
href="http://search.cpan.org/~cmungall/go-perl/go-perl.pod">http://search.cpan.org/~cmungall/go-perl</a>. You
can get the latest bleeding edge version from <a
href="http://sourceforge.net/cvs/?group_id=36855">Sourceforge
CVS</a>. In addition, the GO Database <a
href="http://archive.godatabase.org/termdb/">daily</a>,
<a href="http://archive.godatabase.org/lite/">weekly</a>,
and <a href="http://archive.godatabase.org/full/">monthly</a>
releases come with the version of the code used to build that
release.
</p>
<h2>Installation</h2>
<p>
go-perl requires installation of several third-party perl
modules. The instructions below should help guide you through
this process. If you have never installed perl modules before,
and you do not have full write privileges on your machine, you
may need the help of a system administrator here.
</p>
<p>
Full installation instructions are in the file <a
href="../INSTALL.html">INSTALL.html</a> or <a
href="INSTALL">INSTALL</a>
</p>
<h2>Scripts</h2>
<p>
The go-perl distribution comes with a number of scripts. These
should all be executable if you follow the installation
instructions.
</p>
<p>
See <a href="/dev/pod/go-perl.html">go-perl</a> for a full list
of scripts.
</p>
<h2>About</h2>
<p>
To use the <b>NOTE:</b> if you do not intend to use the go-perl
library as a programmer then you don't need to read any further
here. Simply follow the installation instructions above, and you
will be able to use any of the tools in the scripts directory.
</p>
<p>
go-perl is a set of perl modules for parsing, manipulating and
exporting GO or OBO style ontology files. It includes parsers
for the various GO/OBO formats, extendable handlers for dealing
with the results of a parse, and an object model.
</p>
<p>
Unlike packages such as BioPerl, the object model is not
strictly necessary for performing a lot of useful tasks. You can
actually get by quite well with just using the Parser/Handler
framework
</p>
<h2>Documentation</h2>
<p>
Most of the relevant documentation is kept in POD format. You
can read the HTML version here:
<ul>
<li><a href="/dev/pod/go-perl.html">go-perl</a> introduction</li>
<li><a href="/dev/pod/GO/Parser.html">GO::Parser</a> parsing
using go-perl</li>
<li><a
href="/dev/pod/GO/Model/Graph.html">GO::Model::Graph</a>
the core of the go-perl object model</li>
</ul>
</p>
<h3>Event Handling Architecture</h3>
<p>
You can also read about the internal details of the event
handling mechanism and how to write your own perl event handlers
here: <a href="go-perl-event-handling.html">go-perl event handling</a>
</p>
<h2>Database API</h2>
<p>
The go-perl module does not have a database API - you need the
<a
href="../../go-db-perl/doc/go-db-perl-doc.html">go-db-perl</a>
modules, also part of the go-dev distribution. You also need the
go-database - see the GO Database SQL Docs <a
href="../../sql/doc/godb-sql-doc.html">go-dev/sql</a>, or
download the latest build from <a href="http://www.godatabase.org/dev/database">http://www.godatabase.org/dev/database</a>
</p>
<h2>Mail Lists</h2>
<p>
<ul>
<li>
<a
href="http://mail.fruitfly.org/mailman/listinfo/go-database">http://mail.fruitfly.org/mailman/listinfo/go-database</a>
-- Announcements and user help with the GO Database
downloads and schema
</li>
<li>
<a href="http://lists.sourceforge.net/lists/listinfo/gmod-ontol-sw-dev">http://lists.sourceforge.net/lists/listinfo/gmod-ontol-sw-dev</a> -- go-dev software discussion
</li>
</p>
<hr>
<address><a href="mailto:cjm@fruitfly.org">Chris Mungall</a></address>
<!-- Created: Fri Jan 23 14:30:13 PST 2004 -->
<!-- hhmts start -->
Last modified: Sat Feb 12 18:00:02 PST 2005
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</body>
</html>
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