GO::Parser(3pm) User Contributed Perl Documentation GO::Parser(3pm)
NAME
GO::Parser - parses all GO files formats and types
SYNOPSIS
fetch GO::Model::Graph objects using a parser:
# Scenario 1: Getting objects from a file
use GO::Parser;
my $parser = new GO::Parser({handler=>'obj',use_cache=>1});
$parser->parse("function.ontology"); # ontology
$parser->parse("GO.defs"); # definitions
$parser->parse("ec2go"); # external refs
$parser->parse("gene-associations.sgd"); # gene assocs
# get GO::Model::Graph object
my $graph = $parser->handler->graph;
# Scenario 2: Getting OBO XML from a file
use GO::Parser;
my $parser = new GO::Parser({handler=>'xml'});
$parser->handler->file("output.xml");
$parser->parse("gene_ontology.obo");
# Scenario 3: Using an XSL stylesheet to convert the OBO XML
use GO::Parser;
my $parser = new GO::Parser({handler=>'xml'});
# xslt files are kept in in $ENV{GO_ROOT}/xml/xsl
# (if $GO_ROOT is not set, defaults to install directory)
$parser->xslt("oboxml_to_owl");
$parser->handler->file("output.owl-xml");
$parser->parse("gene_ontology.obo");
# Scenario 4: via scripts
my $cmd = "go2xml gene_ontology.obo | xsltproc my-transform.xsl -";
my $fh = FileHandle->new("$cmd |") || die("problem initiating $cmd");
while(<$fh>) { print $_ }
$fh->close || die("problem running $cmd");
DESCRIPTION
Module for parsing GO flat files; for examples of GO/OBO flatfile formats see:
<ftp://ftp.geneontology.org/pub/go/ontology>
ftp://ftp.geneontology.org/pub/go/gene-associations <ftp://ftp.geneontology.org/pub/go/gene-associations>
For a description of the various file formats, see:
<http://www.geneontology.org/GO.format.html>
<http://www.geneontology.org/GO.annotation.html#file>
This module will generate XML events from a correctly formatted GO/OBO file
SEE ALSO
This module is a part of go-dev, see:
<http://www.godatabase.org/dev>
for more details
PUBLIC METHODS
new
Title : new
Usage : my $p = GO::Parser->new({format=>'obo_xml',handler=>'obj'});
$p->parse("go.obo-xml");
my $g = $p->handler->graph;
Synonyms:
Function: creates a parser object
Example :
Returns : GO::Parser
Args : a hashref of arguments:
format: a format for which a parser exists
handler: a format for which a perl handler exists
use_cache: (boolean) see caching below
parse
Title : parse
Usage : $p->parse($file);
Synonyms:
Function: parses a file
Example :
Returns :
Args : str filename
handler
Title : handler
Usage : my $handler = $p->handler;
Synonyms:
Function: gets/sets a GO::Handler object
Example :
Returns : L<GO::Handlers::base>
Args : L<GO::Handlers::base>
FORMATS
This module is a front end wrapper for a number of different GO/OBO formats - see the relevant module documentation below for details.
The full list of parsers can be found in the go-perl/GO/Parsers/ directory
obo_text
Files with suffix ".obo"
This is a new file format replacement for the existing GO flat file formats. It handles ontologies, definitions and xrefs (but not
associations)
go_ont
Files with suffix ".ontology"
These store the ontology DAGs
go_def
Files with suffix ".defs"
go_xref
External database references for GO terms
Files with suffix "2go" (eg ec2go, metacyc2go)
go_assoc
Annotations of genes or gene products using GO
Files with prefix "gene-association."
obo_xml
Files with suffix ".obo.xml" or ".obo-xml"
This is the XML version of the OBO flat file format above
See http://www.godatabase.org/dev/xml/doc/xml-doc.html <http://www.godatabase.org/dev/xml/doc/xml-doc.html>
obj_yaml
A YAML dump of the perl GO::Model::Graph object. You need YAML from CPAN for this to work
obj_storable
A dump of the perl GO::Model::Graph object. You need Storable from CPAN for this to work. This is intended to cache objects on the
filesystem, for fast access. The obj_storable representation may not be portable
PARSING ARCHITECTURE
Each parser fires XML events. The XML events are known as Obo-XML.
These XML events can be caught by a handler written in perl, or they can be caught by an XML parser written in some other language, or by
using XSL stylesheets.
go-dev comes with a number of stylesheets in the
go-dev/xml/xsl directory
Anything that catches these XML events is known as a handler
go-perl comes with some standard perl XML handlers, in addition to some standard XSL stylesheets. These can be found in the
go-dev/go-perl/GO/Handlers directory
If you are interested in getting perl objects from files then you will want the obj handler, which gives back GO::Model::Graph objects
The parsing architecture gives you the option of using the go-perl object model, or just parsing the XML events directly
If you are using the go-db-perl library, the load-go-into-db.pl script will perform the following processes when loading files into the
database
Obo-XML events fired using GO::Parser::* classes
Obo-XML transformed into godb xml using oboxml_to_godb_prestore.xsl
godb_prestore.xml stored in database using generic loader
Obo-XML
The Obo-XML format DTD is stored in the go-dev/xml/dtd directory
HOW IT WORKS
Currently the various parsers and perl event handlers use the stag module for this - see Data::Stag for more details, or
http://stag.sourceforge.net
NESTED EVENTS
nested events can be thought of as xml, without attributes; nested events can easily be turned into xml
events have a start, a body and an end
event handlers can *catch* these events and do something with them.
an object handler can turn the events into objects, centred around the GO::Model::Graph object; see GO::Handlers::obj
other handlers can catch the events and convert them into other formats, eg OWL or OBO
Or you can bypass the handler and get output as an XML stream - to do this, just run the go2xml script
a database loading event handler can catch the events and turn them into SQL statements, loading a MySQL or postgres database (see the go-
db-perl library)
the advantage of an event based parsing architecture is that it is easy to build lightweight parsers, and heavy weight object models can be
bypassed if prefered.
EXAMPLES
To see examples of the events generated by the GO::Parser class, run the script go2xml; for example
go2xml function.ontology
on any GO-formatted flatfile
This also works on OBO-formatted files:
go2xml gene_ontology.obo
You can also use the script "stag-parse.pl" which comes with the Data::Stag distribution. for example
stag-parse.pl -p GO::Parsers::go_assoc_parser gene-association.fb
XSLT HANDLERS
The full list can be found in the go-dev/xml/xsl directory
PERL HANDLERS
see GO::Handlers::* for all the different handlers possible; more can be added dynamically.
you can either create the handler object yourself, and pass it as an argument, e.g.
my $apph = new GO::AppHandle(-db=>"go");
my $handler = new GO::Handlers::godb({apph=>$apph});
my $parser = new GO::Parser({handler=>$handler});
$parser->parse(@files);
or you can use one of the registered handlers:
my $parser = new GO::Parser({handler=>'db',
handler_args=>{apph=>$apph}});
or you can just do things from the command line
go2fmt.pl -w oboxml function.ontology
the registered perl handlers are as follows:
obo_xml
writes out OBO-XML (which is basically a straightforward conversion of the event stream into XML)
obo_text
go_ont
legacy GO-ontology file format
go_xref
GO xref file, for linking GO terms to terms and dbxrefs in other ontologies
go_defs
legacy GO-definitions file format
go_assoc
GO association file format
rdf GO XML-RDF file format
owl OWL format (default: OWL-DL)
OWL is a W3C standard format for ontologies
You will need the XSL files from the full go-dev distribution to run this; see the XML section in <http://www.godatabase.org/dev>
prolog
prolog facts - you will need a prolog compiler/interpreter to use these. You can reason over these facts using Obol or the forthcoming
Bio-LP project
sxpr
lisp style S-Expressions, conforming to the OBO-XML schema; you will need lisp to make full use of these. you can also do some nice
stuff just within emacs (use lisp-mode and load an sxpr file into your buffer)
godb
this is actually part of the go-db-perl library, not the go-perl library
catches events and loads them into a database conforming to the GO database schema; see the directory go-dev/sql, as part of the whole
go-dev distribution; or www.godatabase.org/dev/database
obj_yaml
A YAML dump of the perl GO::Model::Graph object. You need YAML from CPAN for this to work
obj_storable
A dump of the perl GO::Model::Graph object. You need Storable from CPAN for this to work. This is intended to cache objects on the
filesystem, for fast access. The obj_storable representation may not be portable
EXAMPLES OF DATATYPE TEXT FORMATS
go_ont format
eg format: go_ont for storing graphs and metadata; for example:
!version: $Revision: 1.15 $
!date: $Date: 2006/04/20 22:48:23 $
!editors: Michael Ashburner (FlyBase), Midori Harris (SGD), Judy Blake (MGD)
$Gene_Ontology ; GO:0003673
$cellular_component ; GO:0005575
%extracellular ; GO:0005576
<fibrinogen ; GO:0005577
<fibrinogen alpha chain ; GO:0005972
<fibrinogen beta chain ; GO:0005973
See GO::Parsers::go_ont_parser for more details
this is the following file parsed with events turned directly into OBO-XML:
<?xml version="1.0" encoding="UTF-8"?>
<obo>
<source>
<source_type>file</source_type>
<source_path>z.ontology</source_path>
<source_mtime>1075164285</source_mtime>
</source>
<term>
<id>GO:0003673</id>
<name>Gene_Ontology</name>
<ontology>root</ontology>
</term>
<term>
<id>GO:0005575</id>
<name>cellular_component</name>
<ontology>root</ontology>
<is_a>GO:0003673</is_a>
</term>
<term>
<id>GO:0005576</id>
<name>extracellular</name>
<ontology>root</ontology>
<is_a>GO:0005575</is_a>
</term>
<term>
<id>GO:0005577</id>
<name>fibrinogen</name>
<ontology>root</ontology>
<relationship>
<type>part_of</type>
<to>GO:0005576</to>
</relationship>
</term>
<term>
<id>GO:0005972</id>
<name>fibrinogen alpha chain</name>
<ontology>root</ontology>
<relationship>
<type>part_of</type>
<to>GO:0005577</to>
</relationship>
</term>
<term>
<id>GO:0005973</id>
<name>fibrinogen beta chain</name>
<ontology>root</ontology>
<relationship>
<type>part_of</type>
<to>GO:0005577</to>
</relationship>
</term>
</obo>
go_def format
eg format: go_defs for storing definitions:
!Gene Ontology definitions
!
term: 'de novo' protein folding
goid: GO:0006458
definition: Processes that assist the folding of a nascent peptide chain into its correct tertiary structure.
definition_reference: Sanger:mb
See GO::Parsers::go_def_parser for more details
go_xref format
eg format: go_xrefs for storing links between GO IDs and IDs for terms in other DBs:
EC:1.-.-.- > GO:oxidoreductase ; GO:0016491
EC:1.1.-.- > GO:1-phenylethanol dehydrogenase ; GO:0018449
See GO::Parsers::go_xref_parser for more details
go_assoc format
eg format: go-assocs for storing gene-associations:
SGD S0004660 AAC1 GO:0005743 SGD:12031|PMID:2167309 TAS C ADP/ATP translocator YMR056C gene taxon:4932 20010118
SGD S0004660 AAC1 GO:0006854 SGD:12031|PMID:2167309 IDA P ADP/ATP translocator YMR056C gene taxon:4932 20010118
See GO::Parsers::go_assoc_parser for more details
obo_text format
<http://www.geneontology.org/GO.format.html>
new
Usage - my $parser = GO::Parser->new()
Returns - GO::Parser
creates a new parser
create_handler
Usage - my $handler = GO::Parser->create_handler('obj');
Returns - L<GO::Handlers::base>
Args - handler type [str]
perl v5.14.2 2013-02-07 GO::Parser(3pm)