Ubuntu Manpage: go-perl - perl modules for GO and other OBO ontologies

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.