Bio::OntologyIO dagflat
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Summary
Bio::OntologyIO::dagflat - a base class parser for GO flat-file type formats
Package variables
No package variables defined.
Included modules
Bio::Annotation::DBLink
Bio::Ontology::OBOEngine
Bio::Ontology::Ontology
Bio::Ontology::OntologyStore
Bio::Ontology::TermFactory
Bio::Root::IO
Inherit
Bio::OntologyIO
Synopsis
  use Bio::OntologyIO;
# do not use directly -- use via Bio::OntologyIO # e.g., the GO parser is a simple extension of this class my $parser = Bio::OntologyIO->new ( -format => "go", -defs_file => "/home/czmasek/GO/GO.defs", -files => ["/home/czmasek/GO/component.ontology", "/home/czmasek/GO/function.ontology", "/home/czmasek/GO/process.ontology"] ); my $go_ontology = $parser->next_ontology(); my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" ); my $RELATED_TO = Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" );
Description
Needs Graph.pm from CPAN.
Methods
_initialize
No description
Code
ontology_nameDescriptionCode
parseDescriptionCode
next_ontologyDescriptionCode
defs_fileDescriptionCode
defs_url
No description
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url
No description
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closeDescriptionCode
_flat_filesDescriptionCode
_defs_ioDescriptionCode
_add_ontology
No description
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_add_term
No description
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_part_of_relationship
No description
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_is_a_relationship
No description
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_related_to_relationship
No description
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_add_relationship
No description
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_has_term
No description
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_parse_flat_file
No description
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_get_first_termid
No description
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_get_name
No description
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_get_synonyms
No description
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_get_db_cross_refs
No description
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_get_secondary_termids
No description
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_count_spaces
No description
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_next_term
No description
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_ont_engine
No description
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_create_ont_entry
No description
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_not_first_record
No description
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_done
No description
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_term
No description
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_to_annotation
No description
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Methods description
ontology_namecode    nextTop
 Title   : ontology_name
Usage : $obj->ontology_name($newval)
Function: Get/set the name of the ontology parsed by this module.
Example :
Returns : value of ontology_name (a scalar)
Args : on set, new value (a scalar or undef, optional)
parsecodeprevnextTop
 Title   : parse()
Usage : $parser->parse();
Function: Parses the files set with "new" or with methods
defs_file and _flat_files.
Normally you should not need to call this method as it will be called automatically upon the first call to next_ontology(). Returns : [Bio::Ontology::OntologyEngineI] Args :
next_ontologycodeprevnextTop
 Title   : next_ontology
Usage :
Function: Get the next available ontology from the parser. This is the
method prescribed by Bio::OntologyIO.
Example :
Returns : An object implementing Bio::Ontology::OntologyI, and undef if
there is no more ontology in the input.
Args :
defs_filecodeprevnextTop
 Title   : defs_file
Usage : $parser->defs_file( "GO.defs" );
Function: Set/get for the term definitions filename.
Returns : The term definitions file name [string].
Args : On set, the term definitions file name [string] (optional).
closecodeprevnextTop
 Title   : close
Usage :
Function: Closes this ontology stream and associated file handles.
Clients should call this method especially when they write ontologies. We need to override this here in order to close the file handle for the term definitions file. Example : Returns : none Args : none
_flat_filescodeprevnextTop
 Title   : _flat_files
Usage : $files_to_parse = $parser->_flat_files();
Function: Get the array of ontology flat files that need to be parsed.
Note that this array will decrease in elements over the parsing process. Therefore, it\'s value outside of this module will be limited. Also, be careful not to alter the array unless you know what you are doing. Returns : a reference to an array of zero or more strings Args : none
_defs_iocodeprevnextTop
 Title   : _defs_io
Usage : $obj->_defs_io($newval)
Function: Get/set the Bio::Root::IO instance representing the
definition file, if provided (see defs_file()).
Example :
Returns : value of _defs_io (a Bio::Root::IO object)
Args : on set, new value (a Bio::Root::IO object or undef, optional)
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my ($self, %arg) = @_;

  my ( $defs_file_name,$files,$defs_url,$url,$name,$eng ) =
        $self->_rearrange([qw( DEFS_FILE
                           FILES
                           DEFS_URL
                           URL
                           ONTOLOGY_NAME
                           ENGINE)
                      ],
                      %arg );

  delete($arg{-url}); #b/c GO has 3 files...
$self->SUPER::_initialize( %arg ); $self->_done( FALSE ); $self->_not_first_record( FALSE ); $self->_term( "" ); delete $self->{'_ontologies'}; # ontology engine (and possibly name if it's an OntologyI)
$eng = Bio::Ontology::OBOEngine->new() unless $eng; if($eng->isa("Bio::Ontology::OntologyI")) { $self->ontology_name($eng->name()); $eng = $eng->engine() if $eng->can('engine'); } $self->_ont_engine($eng); # flat files to parse
if(defined($defs_file_name) && defined($defs_url)){ $self->throw('cannot provide both -defs_file and -defs_url'); } else { defined($defs_file_name) && $self->defs_file( $defs_file_name ); defined($defs_url) && $self->defs_url( $defs_url ); } if(defined($files) && defined($url)){ } elsif(defined($files)){ $self->{_flat_files} = $files ? ref($files) ? $files : [$files] : []; } elsif(defined($url)){ $self->url($url); } # ontology name (overrides implicit one through OntologyI engine)
$self->ontology_name($name) if $name; } # _initialize
}
ontology_namedescriptionprevnextTop
sub ontology_name {
    my $self = shift;

    return $self->{'ontology_name'} = shift if @_;
    return $self->{'ontology_name'};
}
parsedescriptionprevnextTop
sub parse {
    my $self = shift;

    #warn "PARSING";
# setup the default term factory if not done by anyone yet
$self->term_factory(Bio::Ontology::TermFactory->new( -type => "Bio::Ontology::Term")) unless $self->term_factory(); # create the ontology object itself
my $ont = Bio::Ontology::Ontology->new(-name => $self->ontology_name(), -engine => $self->_ont_engine()); # parse definitions
while( my $term = $self->_next_term() ) { $self->_add_term( $term, $ont ); } # set up the ontology of the relationship types
foreach ($self->_part_of_relationship(), $self->_is_a_relationship(), $self->_related_to_relationship()) { $_->ontology($ont); } # pre-seed the IO system with the first flat file if -file wasn't provided
if(! $self->_fh) { if($self->url){ if(ref($self->url) eq 'ARRAY'){ #warn "BA";
foreach my $url (@{ $self->url }){ #warn $url;
#warn $ont;
#warn scalar($ont->get_all_terms());
$self->_initialize_io(-url => $url); $self->_parse_flat_file($ont); } $self->close(); } else { $self->_initialize_io(-url => $self->url); } } elsif($self->_flat_files){ $self->_initialize_io(-file => shift(@{$self->_flat_files()})); } } while($self->_fh) { $self->_parse_flat_file($ont); # advance to next flat file if more are available
if(@{$self->_flat_files()}) { $self->close(); $self->_initialize_io(-file => shift(@{$self->_flat_files()})); } else { last; # nothing else to parse so terminate the loop
} } $self->_add_ontology($ont); # not needed anywhere, only because of backward compatibility
return $self->_ont_engine(); } # parse
}
next_ontologydescriptionprevnextTop
sub next_ontology {
  my $self = shift;

  # parse if not done already
$self->parse() unless exists($self->{'_ontologies'}); # return next available ontology
if(exists($self->{'_ontologies'})){ my $ont = shift (@{$self->{'_ontologies'}}); if($ont){ my $store = Bio::Ontology::OntologyStore->new(); $store->register_ontology($ont); return $ont; } } return;
}
defs_filedescriptionprevnextTop
sub defs_file {
  my $self = shift;

  if ( @_ ) {
        my $f = shift;
    $self->{ "_defs_file_name" } = $f;
        $self->_defs_io->close() if $self->_defs_io();
        if(defined($f)) {
      $self->_defs_io( Bio::Root::IO->new( -input => $f ) );
    }
  }
  return $self->{ "_defs_file_name" };
} # defs_file
}
defs_urldescriptionprevnextTop
sub defs_url {
  my $self = shift;
  my $val = shift;
  if(defined($val)){
    $self->{'_defs_url'} = $val;

        $self->_defs_io->close() if $self->_defs_io();
    $self->_defs_io( Bio::Root::IO->new( -url => $val ) );
  }
  return $self->{'_defs_url'};
}
urldescriptionprevnextTop
sub url {
  my $self = shift;
  my $val = shift;
  if(defined($val)){
    $self->{'_url'} = $val;
  }
  return $self->{'_url'};
}
closedescriptionprevnextTop
sub close {
    my $self = shift;

    # first call the inherited implementation
$self->SUPER::close(); # then close the defs file io (if there is one)
$self->_defs_io->close() if $self->_defs_io();
}
_flat_filesdescriptionprevnextTop
sub _flat_files {
    my $self = shift;

    $self->{_flat_files} = [] unless exists($self->{_flat_files});
    return $self->{_flat_files};
}


# INTERNAL METHODS
# ----------------
}
_defs_iodescriptionprevnextTop
sub _defs_io {
    my $self = shift;

    return $self->{'_defs_io'} = shift if @_;
    return $self->{'_defs_io'};
}
_add_ontologydescriptionprevnextTop
sub _add_ontology {
    my $self = shift;
    $self->{'_ontologies'} = [] unless exists($self->{'_ontologies'});
    foreach my $ont (@_) {
        $self->throw(ref($ont)." does not implement Bio::Ontology::OntologyI")
            unless ref($ont) && $ont->isa("Bio::Ontology::OntologyI");
        # the ontology name may have been auto-discovered while parsing
# the file
$ont->name($self->ontology_name) unless $ont->name(); push(@{$self->{'_ontologies'}}, $ont); } } # This simply delegates. See SimpleGOEngine.
}
_add_termdescriptionprevnextTop
sub _add_term {
    my ( $self, $term, $ont ) = @_;
    $term->ontology($ont) if $ont && (! $term->ontology);
    $self->_ont_engine()->add_term( $term );
} # _add_term
# This simply delegates. See SimpleGOEngine
}
_part_of_relationshipdescriptionprevnextTop
sub _part_of_relationship {
    my $self = shift;

    return $self->_ont_engine()->part_of_relationship(@_);
} # _part_of_relationship
# This simply delegates. See SimpleGOEngine
}
_is_a_relationshipdescriptionprevnextTop
sub _is_a_relationship {
    my $self = shift;

    return $self->_ont_engine()->is_a_relationship(@_);
} # _is_a_relationship
# This simply delegates. See SimpleGOEngine
}
_related_to_relationshipdescriptionprevnextTop
sub _related_to_relationship {
    my $self = shift;

    return $self->_ont_engine()->related_to_relationship(@_);
} # _is_a_relationship
# This simply delegates. See SimpleGOEngine
}
_add_relationshipdescriptionprevnextTop
sub _add_relationship {
    my ( $self, $parent, $child, $type, $ont ) = @_;

    # note the triple terminology (subject,predicate,object) corresponds to
# (child,type,parent)
$self->_ont_engine()->add_relationship( $child, $type, $parent, $ont ); } # _add_relationship
# This simply delegates. See SimpleGOEngine
}
_has_termdescriptionprevnextTop
sub _has_term {
    my $self = shift;

    return $self->_ont_engine()->has_term( @_ );
} # _add_term
# This parses the relationships files
}
_parse_flat_filedescriptionprevnextTop
sub _parse_flat_file {
  my $self = shift;
  my $ont  = shift;

  my @stack       = ();
  my $prev_spaces = -1;
  my $prev_term   = "";

  while ( my $line = $self->_readline() ) {

        if ( $line =~ /^!/ ) {
          next;
        }

        # split into term specifications
my @termspecs = split(/ (?=[%<])/, $line); # the first element is whitespace only
shift(@termspecs) if $termspecs[0] =~ /^\s*$/; # parse out the focus term
my $current_term = $self->_get_first_termid( $termspecs[0] ); my @syns = $self->_get_synonyms( $termspecs[0] ); my @sec_go_ids = $self->_get_secondary_termids( $termspecs[0] ); my @cross = $self->_get_db_cross_refs( $termspecs[0] ); my @cross_refs; foreach my $cross_ref (@cross) { $cross_ref eq $current_term && next; push(@cross_refs, $cross_ref); } # parse out the parents of the focus term
shift(@termspecs); my @isa_parents = (); my @partof_parents = (); foreach my $parent (@termspecs) { if (index($parent, "%") == 0) { push(@isa_parents, $self->_get_first_termid($parent)); } elsif (index($parent, "<") == 0) { push(@partof_parents, $self->_get_first_termid($parent)); } else { $self->warn("unhandled relationship type in '".$parent."'"); } } if ( ! $self->_has_term( $current_term ) ) { my $term =$self->_create_ont_entry($self->_get_name($line, $current_term), $current_term ); $self->_add_term( $term, $ont ); } my $current_term_object = $self->_ont_engine()->get_terms( $current_term ); my $anno = $self->_to_annotation(\@cross_refs); $current_term_object->add_dbxref(-dbxrefs => $anno); $current_term_object->add_secondary_id( @sec_go_ids ); $current_term_object->add_synonym( @syns ); unless ( $line =~ /^\$/ ) { $current_term_object->ontology( $ont ); } foreach my $parent ( @isa_parents ) { if ( ! $self->_has_term( $parent ) ) { my $term = $self->_create_ont_entry($self->_get_name($line, $parent), $parent ); $self->_add_term( $term, $ont ); } $self->_add_relationship( $parent, $current_term, $self->_is_a_relationship(), $ont); } foreach my $parent ( @partof_parents ) { if ( ! $self->_has_term( $parent ) ) { my $term = $self->_create_ont_entry($self->_get_name($line, $parent), $parent ); $self->_add_term( $term, $ont ); } $self->_add_relationship( $parent, $current_term, $self->_part_of_relationship(), $ont); } my $current_spaces = $self->_count_spaces( $line ); if ( $current_spaces != $prev_spaces ) { if ( $current_spaces == $prev_spaces + 1 ) { push( @stack, $prev_term ); } elsif ( $current_spaces < $prev_spaces ) { my $n = $prev_spaces - $current_spaces; for ( my $i = 0; $i < $n; ++$i ) { pop( @stack ); } } else { $self->throw( "format error (file ".$self->file.")" ); } } my $parent = $stack[ @stack - 1 ]; # add a relationship if the line isn\'t the one with the root term
# of the ontology (which is also the name of the ontology)
if ( index($line,'$') != 0 ) { #adding @reltype@ syntax
if ( $line !~ /^\s*([<%~]|\@\w+?\@)/ ) { $self->throw( "format error (file ".$self->file.") offending line:\n$line" ); } my($relstring) = $line =~ /^\s*([<%~]|\@[^\@]+?\@)/; my $reltype; if ($relstring eq '<') { $reltype = $self->_part_of_relationship; } elsif ($relstring eq '%') { $reltype = $self->_is_a_relationship; } elsif ($relstring eq '~') { $reltype = $self->_related_to_relationship; } else { $relstring =~ s/\@//g; if ($self->_ont_engine->get_relationship_type($relstring)) { $reltype = $self->_ont_engine->get_relationship_type($relstring); } else { $self->_ont_engine->add_relationship_type($relstring, $ont); $reltype = $self->_ont_engine->get_relationship_type($relstring); } } #my $reltype = ($line =~ /^\s*</) ?
#$self->_part_of_relationship() :
#$self->_is_a_relationship();
$self->_add_relationship( $parent, $current_term, $reltype, $ont); } $prev_spaces = $current_spaces; $prev_term = $current_term; } return $ont; } # _parse_relationships_file
# Parses the 1st term id number out of line.
}
_get_first_termiddescriptionprevnextTop
sub _get_first_termid {
    my ( $self, $line ) = @_;
    if ( $line =~ /;\s*([A-Z_]{1,8}:\d{1,})/ ) {
#    if ( $line =~ /;\s*(\w+:\w+)/ ) {
return $1; } else { $self->throw( "format error: no term id in line\" $line\"" ); } } # _get_first_termid
# Parses the name out of line.
}
_get_namedescriptionprevnextTop
sub _get_name {
    my ( $self, $line, $termid ) = @_;

    if ( $line =~ /([^;<%~]+);\s*$termid/ ) {
        my $name = $1;
        # remove trailing and leading whitespace
$name =~ s/\s+$//; $name =~ s/^\s+//; $name =~ s/\@.+?\@//; # remove leading dollar character; also we default the name of the
# ontology to this name unless it is preset to something else
if(index($name,'$') == 0) { $name = substr($name,1); # replace underscores by spaces for setting the ontology name
$self->ontology_name(join(" ",split(/_/,$name))) unless $self->ontology_name(); } return $name; } else { return; } } # _get_name
# Parses the synonyms out of line.
}
_get_synonymsdescriptionprevnextTop
sub _get_synonyms {
    my ( $self, $line ) = @_;

    my @synonyms = ();

    while ( $line =~ /synonym\s*:\s*([^;<%~]+)/g ) {
        my $syn = $1;
        $syn =~ s/\s+$//;
        $syn =~ s/^\s+//;
        push( @synonyms, $syn );
    }
    return @synonyms;

} # _get_synonyms
# Parses the db cross refs out of line.
}
_get_db_cross_refsdescriptionprevnextTop
sub _get_db_cross_refs {
    my ( $self, $line ) = @_;

    my @refs = ();

    while ( $line =~ /;([^;<%~:]+:[^;<%~:]+)/g ) {
        my $ref = $1;
        if ( $ref =~ /synonym/ || $ref =~ /[A-Z]{1,8}:\d{3,}/ ) {
            next;
        }
        $ref =~ s/\s+$//;
        $ref =~ s/^\s+//;

        $ref = $self->unescape( $ref );

        push( @refs, $ref ) if defined $ref;
    }
    return @refs;

}


# Parses the secondary go ids out of a line
}
_get_secondary_termidsdescriptionprevnextTop
sub _get_secondary_termids {
    my ( $self, $line ) = @_;
    my @secs = ();

#    while ( $line =~ /,\s*([A-Z]{1,8}:\d{3,})/g ) {
while ( $line =~ /,\s*(\w+:\w+)/g ) { my $sec = $1; push( @secs, $sec ); } return @secs; } # _get_secondary_termids
# Counts the spaces at the beginning of a line in the relationships files
}
_count_spacesdescriptionprevnextTop
sub _count_spaces {
    my ( $self, $line ) = @_;

    if ( $line =~ /^(\s+)/ ) {
         return length( $1 );
    }
    else {
         return 0;
    }
} # _count_spaces
# "next" method for parsing the defintions file
}
_next_termdescriptionprevnextTop
sub _next_term {
  my ( $self ) = @_;

  if ( ($self->_done() == TRUE) || (! $self->_defs_io())) {
    return;
  }

  my $line      = "";
  my $termid    = "";
  my $next_term = $self->_term();
  my $def       = "";
  my $comment   = "";
  my @def_refs  = ();
  my $isobsolete;

  while( $line = ( $self->_defs_io->_readline() ) ) {
    if ( $line !~ /\S/
         ||   $line =~ /^\s*!/ ) {
      next;
    }
    elsif ( $line =~ /^\s*term:\s*(.+)/ ) {
      $self->_term( $1 );
      last if $self->_not_first_record();
      $next_term = $1;
      $self->_not_first_record( TRUE );
    }
    elsif ( $line =~ /^\s*[a-z]{0,8}id:\s*(.+)/ ) {
      $termid = $1;
    }
    elsif ( $line =~ /^\s*definition:\s*(.+)/ ) {
      $def = $self->unescape($1);
      $isobsolete = 1 if index($def,"OBSOLETE") == 0;
    }
    elsif ( $line =~ /^\s*definition_reference:\s*(.+)/ ) {
      push( @def_refs, $self->unescape($1) );
    }
    elsif ( $line =~ /^\s*comment:\s*(.+)/ ) {
      $comment = $self->unescape($1);
    }
  }
  $self->_done( TRUE ) unless $line; # we'll come back until done
return $self->_create_ont_entry( $next_term, $termid, $def, $comment,\@ def_refs, $isobsolete); } # _next_term
# Holds the GO engine to be parsed into
}
_ont_enginedescriptionprevnextTop
sub _ont_engine {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_ont_engine" } = $value;
    }

    return $self->{ "_ont_engine" };
} # _ont_engine
# Used to create ontology terms.
# Arguments: name, id
}
_create_ont_entrydescriptionprevnextTop
sub _create_ont_entry {
    my ( $self, $name, $termid, $def, $cmt, $dbxrefs, $obsolete ) = @_;

    if((!defined($obsolete)) && (index(lc($name),"obsolete") == 0)) {
      $obsolete = 1;
    }
    my $anno = $self->_to_annotation($dbxrefs);
    my $term = $self->term_factory->create_object(-name => $name,
                                                  -identifier => $termid,
                                                  -definition => $def,
                                                  -comment => $cmt,
                                                  -dbxrefs => $anno,
                                                  -is_obsolete => $obsolete);

    return $term;
} # _create_ont_entry
# Holds whether first record or not
}
_not_first_recorddescriptionprevnextTop
sub _not_first_record {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_not_first_record" } = $value;
    }

    return $self->{ "_not_first_record" };
} # _not_first_record
# Holds whether done or not
}
_donedescriptionprevnextTop
sub _done {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_done" } = $value;
    }

    return $self->{ "_done" };
} # _done
# Holds a term.
}
_termdescriptionprevnextTop
sub _term {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{ "_term" } = $value;
    }

    return $self->{ "_term" };
} # _term
# convert simple strings to Bio::Annotation::DBLinks
}
_to_annotationdescriptionprevnextTop
sub _to_annotation {
    my ($self , $links) = @_;
    return unless $links;
    my @dbxrefs;
    for my $string (@{$links}) {
        my ($db, $id) = split(':',$string);
        push @dbxrefs, Bio::Annotation::DBLink->new(-database => $db, -primary_id => $id);
    }
    return\@ dbxrefs;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
  Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
CONTRIBUTORTop
 Hilmar Lapp, hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
newTop
 Title   : new
Usage : $parser = Bio::OntologyIO->new(
-format => "go",
-defs_file => "/path/to/GO.defs",
-files => ["/path/to/component.ontology",
"/path/to/function.ontology",
"/path/to/process.ontology"] );
Function: Creates a new dagflat parser.
Returns : A new dagflat parser object, implementing Bio::OntologyIO.
Args : -defs_file => the name of the file holding the term
definitions
-files => a single ontology flat file holding the
term relationships, or an array ref holding
the file names (for GO, there will usually be
3 files: component.ontology, function.ontology,
process.ontology)
-file => if there is only a single flat file, it may
also be specified via the -file parameter
-ontology_name => the name of the ontology; if not specified the
parser will auto-discover it by using the term
that starts with a $, and converting underscores
to spaces
-engine => the Bio::Ontology::OntologyEngineI object
to be reused (will be created otherwise); note
that every Bio::Ontology::OntologyI will
qualify as well since that one inherits from the
former.
See Bio::OntologyIO.