Provided by: libgo-perl_0.15-9_all 
NAME
go-perl - perl modules for GO and other OBO ontologies
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 -
DESCRIPTION
go-perl is part of the go-dev code distribution. It is also available as a separate
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:
parsers
Biological ontologies and associated data come in assorted formats. See:
GO::Parser
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
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:
GO::Model::Term -- a node/term within an ontology
GO::Model::Graph -- collection of terms and the relationships between them
GO::Model::Relationship -- a typed relationship between two terms
GO::Model::Xref -- a database xref, for a term or any other object
GO::Model::Association -- an association between a term and a gene product
GO::Model::GeneProduct -- a gene or product of a gene or similar annotated entity
GO::Model::Evidence -- supporting evidence for an association
GO::Model::Seq -- a biological sequence of residues for a gene product
SIMPLE PROGRAMMERS INTERFACE
GO::Basic
simple procedural access to GO files
SCRIPTS
These scripts come as part of the go-perl distribution
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 map2slim
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 go-dag-summary.pl
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 go-show-paths-to-root.pl
go-apply-xslt
Will apply a GO XSL transform (by name) on an OBO-XML file
For a full list of XSLs available, see <http://www.godatabase.org/xml/xsl>
go-export-graph.pl
Writes an obo file out as an ascii-tree, a graphviz PNG or other format
for full instructions, see go-export-graph.pl
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 go-show-assocs-by-node.pl
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 go-filter-subset.pl
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 go2fmt.pl
go2chadoxml
converts a file in any valid go/obo format to chadoxml. See also go2fmt.pl
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 DBIx::DBStag. See also go2fmt.pl
go2error_report
converts a file in any valid go/obo format to error_report. See also go2fmt.pl
go2obo_test (alias: go2obo)
converts a file in any valid go/obo format to obo. See also go2fmt.pl
go2obo_html
converts a file in any valid go/obo format to obo_html. See also go2fmt.pl
go2obo_xml (alias: go2xml)
converts a file in any valid go/obo format to obo_xml. See also go2fmt.pl
go2owl
converts a file in any valid go/obo format to owl. See also go2fmt.pl
go2pathlist
converts a file in any valid go/obo format to pathlist. See also go2fmt.pl
go2prolog
converts a file in any valid go/obo format to prolog. See also go2fmt.pl
go2rdfxml
converts a file in any valid go/obo format to rdfxml. See also go2fmt.pl
go2summary
converts a file in any valid go/obo format to summary. See also go2fmt.pl
go2sxpr
converts a file in any valid go/obo format to sxpr. See also go2fmt.pl
go2tbl
converts a file in any valid go/obo format to tbl. See also go2fmt.pl
go2text_html
converts a file in any valid go/obo format to text_html. See also go2fmt.pl
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:
go-perl
This package
http://www.godatabase.org/dev/go-perl/doc/go-perl-doc.html
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
GO::AppHandle
amigo
Ontology browser, written in perl
Requires installation of both go-perl and go-db-perl
java
The DAG-Edit curation tool
http://www.godatabase.org/dev
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
sql Schema and SQL code for the GO database
http://www.godatabase.org/dev/sql/doc/godb-sql-doc.html
AUTHORS
(C) Chris Mungall 2000-2006
This module is free software. You may distribute under the same terms as perl itself.