# $Id: go-perl.pod,v 1.21 2009/08/17 00:46:42 cmungall Exp $
#
# see also - http://www.geneontology.org
#          - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself

=head1 NAME

go-perl           - perl modules for GO and other OBO ontologies

=head1 SYNOPSIS

  # ** FETCHING GRAPH OBJECTS FROM AN ONTOLOGY FILE **
  use GO::Parser;
  my $parser = new GO::Parser({handler=>'obj'}); # create parser object
  $parser->parse("gene_ontology.obo"); # parse file -> objects
  my $graph = $parser->handler->graph;  # get L<GO::Model::Graph> object
  my $term = $graph->get_term("GO:0001303");   # fetch a term by ID
  printf "Got term: %s %s\n", $term->acc, $term->name;
  my $ancestor_terms =
    $graph->get_recursive_parent_terms($term->acc);
  foreach my $anc_term (@$ancestor_terms) {
    printf "  Ancestor term: %s %s\n", $anc_term->acc, $anc_term->name;
  }

  # ** FROM THE COMMAND LINE ** (requires go-dev/xml)
  go2xml gene_ontology.obo | xsltproc $GO_ROOT/xml/xsl/my-transform.xsl -

=head1 DESCRIPTION

go-perl is part of the go-dev code distribution. It is also available
as a seperate library in its own right.

go-perl is a collection of perl modules for working with ontologies
and data, in particular the Gene Ontology and other Open
Bio-Ontologies. For background on these projects, see

http://www.geneontology.org

http://obo.sourceforge.net

go-perl provides the following functionality:

=over

=item parsers

Biological ontologies and associated data come in assorted formats. See:

L<GO::Parser>

=item handlers/writers

All parsers are XML event based - they emit Obo-XML, which can be caught
by different handlers. Some of these handlers effectively transform
the parsed file into a different format or summary.

If you are not interested in generating XML, you can use an object
handler, which will give you objects for traversing an ontology; see
below

=item a graph-based object model

Biological ontologies typically have graph-based structures
(DAGs). go-perl provides a perl object model representing ontologies
and associations to ontologies. Classes include:

L<GO::Model::Term> -- a node/term within an ontology

L<GO::Model::Graph> -- collection of terms and the relationships between them

L<GO::Model::Relationship> -- a typed relationship between two terms

L<GO::Model::Xref> -- a database xref, for a term or any other object

L<GO::Model::Association> -- an association between a term and a gene product

L<GO::Model::GeneProduct> -- a gene or product of a gene or similar annotated entity

L<GO::Model::Evidence> -- supporting evidence for an association

L<GO::Model::Seq> -- a biological sequence of residues for a gene product

=begin html

<img src="http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/go-perl/doc/gomodel.png"/>

=end html

=back

=head2 SIMPLE PROGRAMMERS INTERFACE

L<GO::Basic>

simple procedural access to GO files

=head1 SCRIPTS

These scripts come as part of the go-perl distribution

=over

=item map2slim

Given a GO slim file, and a current ontology (in one or more files),
this script will map a gene association file (containing annotations
to the full GO) to the terms in the GO slim.  The script can be used
to either create a new gene association file, containing the most
pertinent GO slim accessions, or in count-mode, in which case it will
give distinct gene product counts for each slim term.

for full instructions, see L<map2slim>

=item go-dag-summary.pl

Generates a summary of the DAG structure of an ontology file

A row will be generated for every ontology in the file, with the
following data columns:

  input filename
  total no of terms
  total no of relationships
  total no of paths
  avg no of paths per term (p/t)
  maximum no of paths for any term
  ID of term with maximum no of paths

for full instructions, see L<go-dag-summary.pl>

=item go-show-paths-to-root.pl

Will show all possible paths from a term to the root/top in the
ontology

for full instructions, see L<go-show-paths-to-root.pl>

=item go-apply-xslt

Will apply a GO XSL transform (by name) on an OBO-XML file

For a full list of XSLs available, see
L<http://www.godatabase.org/xml/xsl>

=item go-export-graph.pl

Writes an obo file out as an ascii-tree, a graphviz PNG or other format

for full instructions, see L<go-export-graph.pl>

=item go-show-assocs-by-node.pl

given a GO ontology file and an association file and a term ID, will
list all products associated to that ID

for full instructions, see L<go-show-assocs-by-node.pl>

=item go-filter-subset.pl

Exports a subset of an ontology from a file. The subset can be based
on a specified set of IDs, a preset "subset" filter in the ontology
file (eg a GO "slim" or subset), or a user-defined filter.

The subset can be exported in any format, including a graphical image

for full instructions, see L<go-filter-subset.pl>

=item go2fmt.pl

generic file converter. This will convert any go/obo formatted file
such as ontology files and association files and write output in some
other format or report. See the full list of convenience scripts below.

for full instructions, see L<go2fmt.pl>

=item go2chadoxml

converts a file in any valid go/obo format to chadoxml. See also L<go2fmt.pl>

=item go2godb_prestore

converts a file in any valid go/obo format to an xml format that is
isomorphic to the GO MySQL Db schema, and can be loaded with
L<DBIx::DBStag>. See also L<go2fmt.pl>

=item go2error_report

converts a file in any valid go/obo format to error_report. See also L<go2fmt.pl>

=item go2obo_test (alias: go2obo)

converts a file in any valid go/obo format to obo. See also L<go2fmt.pl>

=item go2obo_html

converts a file in any valid go/obo format to obo_html. See also L<go2fmt.pl>

=item go2obo_xml  (alias: go2xml)

converts a file in any valid go/obo format to obo_xml. See also L<go2fmt.pl>

=item go2owl

converts a file in any valid go/obo format to owl. See also L<go2fmt.pl>

=item go2pathlist

converts a file in any valid go/obo format to pathlist. See also L<go2fmt.pl>

=item go2prolog

converts a file in any valid go/obo format to prolog. See also L<go2fmt.pl>

=item go2rdfxml

converts a file in any valid go/obo format to rdfxml. See also L<go2fmt.pl>

=item go2summary

converts a file in any valid go/obo format to summary. See also L<go2fmt.pl>

=item go2sxpr

converts a file in any valid go/obo format to sxpr. See also L<go2fmt.pl>

=item go2tbl

converts a file in any valid go/obo format to tbl. See also L<go2fmt.pl>

=item go2text_html

converts a file in any valid go/obo format to text_html. See also L<go2fmt.pl>

=back

=head1 RELATED PACKAGES

Download the full go-dev distribution for access to more
functionality. go-perl is a subset of go-dev

go-dev includes the following:

=over

=item go-perl

This package

http://www.godatabase.org/dev/go-perl/doc/go-perl-doc.html

=item go-db-perl

Database API for use in conjunction with go-perl

Allows for loading of GO databases and fetching graph objects from the
database

http://www.godatabase.org/dev/go-db-perl/doc/go-db-perl-doc.html

L<GO::AppHandle>

=item amigo

Ontology browser, written in perl

Requires installation of both go-perl and go-db-perl

=item java

The DAG-Edit curation tool

http://www.godatabase.org/dev

=item xml

DTDs for the Obo-XML format, and XSL stylesheets for converting to and
from Obo-XML format

http://www.godatabase.org/dev/xml/doc/xml-doc.html

=item sql

Schema and SQL code for the GO database

http://www.godatabase.org/dev/sql/doc/godb-sql-doc.html

=back

=head1 AUTHORS

(C) Chris Mungall 2000-2006

This module is free software. You may distribute under the same terms
as perl itself.

=cut

package go-perl;
$VERSION='0.14';
1;