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.\" ========================================================================
.\"
.IX Title "go-perl 3pm"
.TH go-perl 3pm "2021-01-09" "perl v5.32.0" "User Contributed Perl Documentation"
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.SH "NAME"
go\-perl           \- perl modules for GO and other OBO ontologies
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 12
\&  # ** FETCHING GRAPH OBJECTS FROM AN ONTOLOGY FILE **
\&  use GO::Parser;
\&  my $parser = new GO::Parser({handler=>\*(Aqobj\*(Aq}); # 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\en", $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\en", $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 \-
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
go-perl is part of the go-dev code distribution. It is also available
as a separate library in its own right.
.PP
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
.PP
http://www.geneontology.org
.PP
http://obo.sourceforge.net
.PP
go-perl provides the following functionality:
.IP "parsers" 4
.IX Item "parsers"
Biological ontologies and associated data come in assorted formats. See:
.Sp
GO::Parser
.IP "handlers/writers" 4
.IX Item "handlers/writers"
All parsers are \s-1XML\s0 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.
.Sp
If you are not interested in generating \s-1XML,\s0 you can use an object
handler, which will give you objects for traversing an ontology; see
below
.IP "a graph-based object model" 4
.IX 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:
.Sp
GO::Model::Term \*(-- a node/term within an ontology
.Sp
GO::Model::Graph \*(-- collection of terms and the relationships between them
.Sp
GO::Model::Relationship \*(-- a typed relationship between two terms
.Sp
GO::Model::Xref \*(-- a database xref, for a term or any other object
.Sp
GO::Model::Association \*(-- an association between a term and a gene product
.Sp
GO::Model::GeneProduct \*(-- a gene or product of a gene or similar annotated entity
.Sp
GO::Model::Evidence \*(-- supporting evidence for an association
.Sp
GO::Model::Seq \*(-- a biological sequence of residues for a gene product
.SS "\s-1SIMPLE PROGRAMMERS INTERFACE\s0"
.IX Subsection "SIMPLE PROGRAMMERS INTERFACE"
GO::Basic
.PP
simple procedural access to \s-1GO\s0 files
.SH "SCRIPTS"
.IX Header "SCRIPTS"
These scripts come as part of the go-perl distribution
.IP "map2slim" 4
.IX Item "map2slim"
Given a \s-1GO\s0 slim file, and a current ontology (in one or more files),
this script will map a gene association file (containing annotations
to the full \s-1GO\s0) to the terms in the \s-1GO\s0 slim.  The script can be used
to either create a new gene association file, containing the most
pertinent \s-1GO\s0 slim accessions, or in count-mode, in which case it will
give distinct gene product counts for each slim term.
.Sp
for full instructions, see map2slim
.IP "go\-dag\-summary.pl" 4
.IX Item "go-dag-summary.pl"
Generates a summary of the \s-1DAG\s0 structure of an ontology file
.Sp
A row will be generated for every ontology in the file, with the
following data columns:
.Sp
.Vb 7
\&  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
.Ve
.Sp
for full instructions, see go\-dag\-summary.pl
.IP "go\-show\-paths\-to\-root.pl" 4
.IX Item "go-show-paths-to-root.pl"
Will show all possible paths from a term to the root/top in the
ontology
.Sp
for full instructions, see go\-show\-paths\-to\-root.pl
.IP "go-apply-xslt" 4
.IX Item "go-apply-xslt"
Will apply a \s-1GO XSL\s0 transform (by name) on an OBO-XML file
.Sp
For a full list of XSLs available, see
<http://www.godatabase.org/xml/xsl>
.IP "go\-export\-graph.pl" 4
.IX Item "go-export-graph.pl"
Writes an obo file out as an ascii-tree, a graphviz \s-1PNG\s0 or other format
.Sp
for full instructions, see go\-export\-graph.pl
.IP "go\-show\-assocs\-by\-node.pl" 4
.IX Item "go-show-assocs-by-node.pl"
given a \s-1GO\s0 ontology file and an association file and a term \s-1ID,\s0 will
list all products associated to that \s-1ID\s0
.Sp
for full instructions, see go\-show\-assocs\-by\-node.pl
.IP "go\-filter\-subset.pl" 4
.IX 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 \*(L"subset\*(R" filter in the ontology
file (eg a \s-1GO\s0 \*(L"slim\*(R" or subset), or a user-defined filter.
.Sp
The subset can be exported in any format, including a graphical image
.Sp
for full instructions, see go\-filter\-subset.pl
.IP "go2fmt.pl" 4
.IX 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.
.Sp
for full instructions, see go2fmt.pl
.IP "go2chadoxml" 4
.IX Item "go2chadoxml"
converts a file in any valid go/obo format to chadoxml. See also go2fmt.pl
.IP "go2godb_prestore" 4
.IX Item "go2godb_prestore"
converts a file in any valid go/obo format to an xml format that is
isomorphic to the \s-1GO\s0 MySQL Db schema, and can be loaded with
DBIx::DBStag. See also go2fmt.pl
.IP "go2error_report" 4
.IX Item "go2error_report"
converts a file in any valid go/obo format to error_report. See also go2fmt.pl
.IP "go2obo_test (alias: go2obo)" 4
.IX Item "go2obo_test (alias: go2obo)"
converts a file in any valid go/obo format to obo. See also go2fmt.pl
.IP "go2obo_html" 4
.IX Item "go2obo_html"
converts a file in any valid go/obo format to obo_html. See also go2fmt.pl
.IP "go2obo_xml  (alias: go2xml)" 4
.IX Item "go2obo_xml (alias: go2xml)"
converts a file in any valid go/obo format to obo_xml. See also go2fmt.pl
.IP "go2owl" 4
.IX Item "go2owl"
converts a file in any valid go/obo format to owl. See also go2fmt.pl
.IP "go2pathlist" 4
.IX Item "go2pathlist"
converts a file in any valid go/obo format to pathlist. See also go2fmt.pl
.IP "go2prolog" 4
.IX Item "go2prolog"
converts a file in any valid go/obo format to prolog. See also go2fmt.pl
.IP "go2rdfxml" 4
.IX Item "go2rdfxml"
converts a file in any valid go/obo format to rdfxml. See also go2fmt.pl
.IP "go2summary" 4
.IX Item "go2summary"
converts a file in any valid go/obo format to summary. See also go2fmt.pl
.IP "go2sxpr" 4
.IX Item "go2sxpr"
converts a file in any valid go/obo format to sxpr. See also go2fmt.pl
.IP "go2tbl" 4
.IX Item "go2tbl"
converts a file in any valid go/obo format to tbl. See also go2fmt.pl
.IP "go2text_html" 4
.IX Item "go2text_html"
converts a file in any valid go/obo format to text_html. See also go2fmt.pl
.SH "RELATED PACKAGES"
.IX Header "RELATED PACKAGES"
Download the full go-dev distribution for access to more
functionality. go-perl is a subset of go-dev
.PP
go-dev includes the following:
.IP "go-perl" 4
.IX Item "go-perl"
This package
.Sp
http://www.godatabase.org/dev/go\-perl/doc/go\-perl\-doc.html
.IP "go-db-perl" 4
.IX Item "go-db-perl"
Database \s-1API\s0 for use in conjunction with go-perl
.Sp
Allows for loading of \s-1GO\s0 databases and fetching graph objects from the
database
.Sp
http://www.godatabase.org/dev/go\-db\-perl/doc/go\-db\-perl\-doc.html
.Sp
GO::AppHandle
.IP "amigo" 4
.IX Item "amigo"
Ontology browser, written in perl
.Sp
Requires installation of both go-perl and go-db-perl
.IP "java" 4
.IX Item "java"
The DAG-Edit curation tool
.Sp
http://www.godatabase.org/dev
.IP "xml" 4
.IX Item "xml"
DTDs for the Obo-XML format, and \s-1XSL\s0 stylesheets for converting to and
from Obo-XML format
.Sp
http://www.godatabase.org/dev/xml/doc/xml\-doc.html
.IP "sql" 4
.IX Item "sql"
Schema and \s-1SQL\s0 code for the \s-1GO\s0 database
.Sp
http://www.godatabase.org/dev/sql/doc/godb\-sql\-doc.html
.SH "AUTHORS"
.IX Header "AUTHORS"
(C) Chris Mungall 2000\-2006
.PP
This module is free software. You may distribute under the same terms
as perl itself.