[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).