go-perl3pm

Usage

  # ** 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 -

Overview

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

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