[Bioperl-l] GOengine, GOparser PODs
Chris Zmasek
czmasek@gnf.org
Mon, 14 Oct 2002 10:14:03 -0700
Hi,
Here are the PODs for OntologyEngineI, simpleGOengine, simpleGOparser.
CZ
OntologyEngineI
------------------------
NAME
OntologyEngineI - DESCRIPTION of Interface
SYNOPSIS
Give standard usage here
DESCRIPTION
Describe the interface here
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of
the bugs and their resolution. Bug reports can be submitted via email or
the web:
bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/
AUTHOR - Peter Dimitrov
Email dimitrov@gnf.org
Describe contact details here
CONTRIBUTORS
Additional contributors names and emails here
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
add_term
Title : add_term
Usage : add_term(TermI term): TermI
Function:
Example :
Returns :
Args :
add_relationship
Title : add_relationship
Usage : add_relationship(RelationshipI relationship)
add_relatioship(TermI parent, TermI child, TermI relationship_type)
Function:
Example :
Returns :
Args :
get_relationships
Title : get_relationships
Usage : get_relationships([TermI term]): RelationshipI[]
Function:
Example :
Returns :
Args :
get_relationship_types
Title : get_relationship_types
Usage : get_relationship_types(): TermI[]
Function:
Example :
Returns :
Args :
get_child_terms
Title : get_child_terms
Usage : get_child_terms(TermI term, TermI[] rel_types): TermI[]
Function:
Example :
Returns :
Args :
get_descendant_terms
Title : get_descendant_terms
Usage : get_descendant_terms(TermI term, TermI[] rel_types): TermI[]
Function:
Example :
Returns :
Args :
get_parent_terms
Title : get_parent_terms
Usage : get_parent_terms(TermI term, TermI[] rel_types): TermI[]
Function:
Example :
Returns :
Args :
get_ancestor_terms
Title : get_ancestor_terms
Usage : get_ancestor_terms(TermI term, TermI[] rel_types): TermI[]
Function:
Example :
Returns :
Args :
get_leaf_terms
Title : get_leaf_terms
Usage :
Function:
Example :
Returns :
Args :
get_root_terms()
Title : get_root_terms()
Usage : get_root_terms()
Function:
Example :
Returns :
Args :
simpleGOengine
------------------------
NAME
simpleGOengine - a Ontology Engine for GO implementing OntologyEngineI
SYNOPSIS
use Bio::Ontology::simpleGOparser;
my $parser = Bio::Ontology::simpleGOparser->new( -go_defs_file_name =>
"/home/czmasek/GO/GO.defs", -components_file_name =>
"/home/czmasek/GO/component.ontology", -functions_file_name =>
"/home/czmasek/GO/function.ontology", -processes_file_name =>
"/home/czmasek/GO/process.ontology" );
my $engine = $parser->parse();
my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); my
$PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
DESCRIPTION
Needs Graph.pm from CPAN.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
Reporting Bugs
report bugs to the Bioperl bug tracking system to help us keep track the
bugs and their resolution. Bug reports can be submitted via email or the
web:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/
AUTHOR
Christian M. Zmasek
Email: czmasek@gnf.org or zmasek@yahoo.com
WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : $engine = Bio::Ontology::simpleGOengine->new()
Function: Creates a new simpleGOengine
Returns : A new simpleGOengine object
Args :
init
Title : init()
Usage : $engine->init();
Function: Initializes this Engine.
Returns :
Args :
is_a_relationship
Title : is_a_relationship()
Usage : $IS_A = $engine->is_a_relationship();
Function: Returns a Bio::Ontology::RelationshipType object for "is-a"
relationships
Returns : Bio::Ontology::RelationshipType set to "IS_A"
Args :
part_of_relationship
Title : part_of_relationship()
Usage : $PART_OF = $engine->part_of_relationship();
Function: Returns a Bio::Ontology::RelationshipType object for "part-of"
relationships
Returns : Bio::Ontology::RelationshipType set to "PART_OF"
Args :
add_term
Title : add_term
Usage : $engine->add_term( $GOterm_obj );
Function: Adds a Bio::Ontology::GOterm to this engine
Returns : true
Args : Bio::Ontology::GOterm
has_term
Title : has_term
Usage : $engine->has_term( $term );
Function: Checks whether this engine contains a particular GO term
Returns : true or false
Args : Bio::Ontology::GOterm
or
GO term identifier (e.g. "GO:0012345")
add_relationship
Title : add_relationship
Usage : $engine->add_relationship( $relationship );
$engine->add_relatioship( $parent_obj, $child_obj, $relationship_type );
$engine->add_relatioship( $parent_id, $child_id, $relationship_type);
Function: Adds a relationship to this engine
Returns : true if successfully added, false otherwise
Args : GO id, GO id, Bio::Ontology::RelationshipType
or
Bio::Ontology::GOterm, Bio::Ontology::GOterm, Bio::Ontology::RelationshipType
or
Bio::Ontology::RelationshipI
get_relationships
Title : get_relationships
Usage : $engine->get_relationships( $term );
Function: Returns all relationships of a term
Returns : Relationship[]
Args : GO id
or
Bio::Ontology::GOterm
get_relationship_types
Title : get_relationship_types
Usage : $engine->get_relationship_types();
Function: Returns the types of relationships this engine contains
Returns : Bio::Ontology::RelationshipType[]
Args :
get_child_terms
Title : get_child_terms
Usage : $engine->get_child_terms( $term_obj, @rel_types );
$engine->get_child_terms( $term_id, @rel_types );
Function: Returns the children of this term
Returns : Bio::Ontology::GOterm[]
Args : Bio::Ontology::GOterm, Bio::Ontology::RelationshipType[]
or
GO id, Bio::Ontology::RelationshipType[]
if NO Bio::Ontology::RelationshipType[] is indicated: children
of ALL types are returned
get_descendant_terms
Title : get_descendant_terms
Usage : $engine->get_descendant_terms( $term_obj, @rel_types );
$engine->get_descendant_terms( $term_id, @rel_types );
Function: Returns the descendants of this term
Returns : Bio::Ontology::GOterm[]
Args : Bio::Ontology::GOterm, Bio::Ontology::RelationshipType[]
or
GO id, Bio::Ontology::RelationshipType[]
if NO Bio::Ontology::RelationshipType[] is indicated: descendants
of ALL types are returned
get_parent_terms
Title : get_parent_terms
Usage : $engine->get_parent_terms( $term_obj, @rel_types );
$engine->get_parent_terms( $term_id, @rel_types );
Function: Returns the parents of this term
Returns : Bio::Ontology::GOterm[]
Args : Bio::Ontology::GOterm, Bio::Ontology::RelationshipType[]
or
GO id, Bio::Ontology::RelationshipType[]
if NO Bio::Ontology::RelationshipType[] is indicated: parents
of ALL types are returned
get_ancestor_terms
Title : get_ancestor_terms
Usage : $engine->get_ancestor_terms( $term_obj, @rel_types );
$engine->get_ancestor_terms( $term_id, @rel_types );
Function: Returns the ancestors of this term
Returns : Bio::Ontology::GOterm[]
Args : Bio::Ontology::GOterm, Bio::Ontology::RelationshipType[]
or
GO id, Bio::Ontology::RelationshipType[]
if NO Bio::Ontology::RelationshipType[] is indicated: ancestors
of ALL types are returned
get_leaf_terms
Title : get_leaf_terms
Usage : $engine->get_leaf_terms();
Function: Returns the leaf terms
Returns : Bio::Ontology::GOterm[]
Args :
get_root_terms()
Title : get_root_terms
Usage : $engine->get_root_terms();
Function: Returns the root terms
Returns : Bio::Ontology::GOterm[]
Args :
get_term
Title : get_term
Usage : $engine->get_term( "GO:1234567" );
Function: Returns a GO term with a given identifier
Returns : Bio::Ontology::GOterm is present, false otherwise
Args : GO id
get_terms
Title : get_terms
Usage : $engine->get_term( "GO:1234567", "GO:2234567" );
Function: Returns a GO terms with given identifiers
Returns : Bio::Ontology::GOterm[]
Args : GO id[]
each_term
Title : each_term
Usage : $engine->each_term();
Function: Returns all terms in this engine
Returns : Bio::Ontology::GOterm[]
Args :
graph
Title : graph()
Usage : $engine->graph();
Function: Returns the Graph this engine is based on
Returns : Graph
Args :
simpleGOparser
------------------------
NAME
simpleGOparser - a simple GO parser returning a simpleGOengine
SYNOPSIS
use Bio::Ontology::simpleGOparser;
my $parser = Bio::Ontology::simpleGOparser->new( -go_defs_file_name =>
"/home/czmasek/GO/GO.defs", -components_file_name =>
"/home/czmasek/GO/component.ontology", -functions_file_name =>
"/home/czmasek/GO/function.ontology", -processes_file_name =>
"/home/czmasek/GO/process.ontology" );
my $engine = $parser->parse();
my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); my
$PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
DESCRIPTION
Needs Graph.pm from CPAN.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
Reporting Bugs
report bugs to the Bioperl bug tracking system to help us keep track the
bugs and their resolution. Bug reports can be submitted via email or the
web:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/
AUTHOR
Christian M. Zmasek
Email: czmasek@gnf.org or zmasek@yahoo.com
WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : $parser = Bio::Ontology::simpleGOparser->new( -go_defs_file_name => "/path/to/GO.defs",
-components_file_name => "/path/to/component.ontology"
-functions_file_name => "/path/to/function.ontology"
-processes_file_name => "/path/to/process.ontology" );
Function: Creates a new simpleGOparser.
Returns : A new simpleGOparser object.
Args : -go_defs_file_name => the GO defs-file name
-components_file_name => the component.ontology-file name
-functions_file_name => the function.ontology-file name
-processes_file_name => the process.ontology-file name
init
Title : init()
Usage : $parser->init();
Function: Initializes this object.
Returns :
Args :
parse
Title : parse()
Usage : $parser->parse();
Function: Parses the files set wirh "new" or with methods
go_defs_file_name, components_file_name, functions_file_name,
processes_file_name.
Returns : [Bio::Ontology::simpleGOengine]
Args :
go_defs_file_name
Title : go_defs_file_name
Usage : $parser->go_defs_file_name( "GO.defs" );
Function: Set/get for the GO defs-file_name.
Returns : The GO defs-file_name [string].
Args : The GO defs-file_name [string] (optional).
components_file_name
Title : components_file_name
Usage : $parser-> components_file_name( "function.ontology" );
Function: Set/get for the function ontology file name.
Returns : The function ontology file name [string].
Args : The function ontology file name [string] (optional).
functions_file_name
Title : functions_file_name
Usage : $parser->functions_file_name( "function.ontology" );
Function: Set/get for functions file name.
Returns : The functions file name [string].
Args : The functions file name [string] (optional).
processes_file_name
Title : processes_file_name
Usage : $parser->processes_file_name( "GO.defs" );
Function: Set/get for the processes file name.
Returns : The processes file name [string].
Args : The processes file name [string] (optional).