Chris Mungall > go-perl-0.13 > GO::Parser

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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

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

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]
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