Bio::OntologyIO obo
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Summary
Bio::OntologyIO::obo - a parser for OBO flat-file format from Gene Ontology Consortium
Package variables
No package variables defined.
Included modules
Bio::Annotation::Collection
Bio::Ontology::OBOEngine
Bio::Ontology::Ontology
Bio::Ontology::OntologyStore
Bio::Ontology::TermFactory
Bio::Root::IO
Text::Balanced qw ( extract_quotelike extract_bracketed )
Inherit
Bio::OntologyIO
Synopsis
  use Bio::OntologyIO;

  # do not use directly -- use via Bio::OntologyIO
  my $parser = Bio::OntologyIO->new
        ( -format       => "obo",
          -file        =>  "gene_ontology.obo");

  while(my $ont = $parser->next_ontology()) {
  print "read ontology ",$ont->name()," with ",
               scalar($ont->get_root_terms)," root terms, and ",
               scalar($ont->get_all_terms)," total terms, and ",
               scalar($ont->get_leaf_terms)," leaf terms\n";
  }
Description
Needs Graph.pm from CPAN.
Methods
_initialize
No description
Code
ontology_nameDescriptionCode
parseDescriptionCode
next_ontologyDescriptionCode
closeDescriptionCode
_add_ontology
No description
Code
_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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_regulates_relationship
No description
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_positively_regulates_relationship
No description
Code
_negatively_regulates_relationship
No description
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_add_relationship
No description
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_has_term
No description
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_ont_engine
No description
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_filter_line
No description
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_header
No description
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_next_term
No description
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_create_term_object
No description
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_extract_quals
No description
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_extract_qstr
No description
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_split_on_comma
No description
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_check_colon
No description
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_handle_relationship_tag
No description
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_to_annotation
No description
Code
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 nothing if
           there is no more ontology in the input.
 Args    :
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
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ( $self, %arg ) = @_;

    my ( $file, $name, $eng ) = $self->_rearrange(
        [
            qw( FILE
              ONTOLOGY_NAME
              ENGINE)
        ],
        %arg
    );

    $self->SUPER::_initialize(%arg);
    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);

    $self->ontology_name($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;

    # setup the default term factory if not done by anyone yet
    $self->term_factory(
        Bio::Ontology::TermFactory->new( -type => "Bio::Ontology::OBOterm" ) )
      unless $self->term_factory();

    ## Parse the file header
    my $annotations_collection = $self->_header();

    # create the default ontology object itself
    my $ont = Bio::Ontology::Ontology->new(
        -name   => $self->ontology_name(),
        -engine => $self->_ont_engine()
    );

    ## Assign the file headers
    $ont->annotation($annotations_collection);

    # set up the ontology of the relationship types
    foreach (
        $self->_part_of_relationship(),
        $self->_is_a_relationship(),
        $self->_related_to_relationship(),
        $self->_regulates_relationship(),
        $self->_positively_regulates_relationship(),
        $self->_negatively_regulates_relationship(),
      )
    {
        $_->ontology($ont);
    }

##################################
    $self->_add_ontology($ont);
##################################

    ### Adding new terms
    while ( my $term = $self->_next_term() ) {

        ### CHeck if the terms has a valid ID and NAME otherwise ignore the term
        if ( !$term->identifier() || !$term->name() ) {
            $self->throw( "OBO File Format Error on line "
                  . $self->{'_current_line_no'}
                  . "\n The term does not have a id/name tag. This term will be ignored.\n"
            );
            next;
        }

				#print $term->identifier(),"\t",$term->name(),"\n";

        my $new_ontology_flag    = 1;
        my $ontologies_array_ref = $self->{'_ontologies'};
        foreach my $ontology (@$ontologies_array_ref) {
            my ($oname, $t_ns) = ($ontology->name(), $term->namespace() );
            next unless (defined($oname) && defined($t_ns));
            if ( $oname eq $t_ns ) {
                ### No need to create new ontology
                $new_ontology_flag = 0;
                $ont               = $ontology;
            }
        }

        if ( $new_ontology_flag && $term->namespace() ) {
            my $new_ont = Bio::Ontology::Ontology->new(
                -name   => $term->namespace(),
                -engine => $self->_ont_engine()
            );
            $new_ont->annotation($annotations_collection);
            $self->_add_ontology($new_ont);
            $ont = $new_ont;
        }


        $self->_add_term( $term, $ont );

        #### Addding the IS_A relationship
        my $isa_parents_array_ref = $self->{'_isa_parents'};
        foreach my $parent_term (@$isa_parents_array_ref) {
            ### Check if parent exist, if not then add the term to the graph.
            if ( !( $self->_has_term($parent_term) ) ) {
                $self->_add_term( $parent_term, $ont );
            }

            $self->_add_relationship( $parent_term, $term,
                $self->_is_a_relationship(), $ont );
        }

        #### Addding the other relationships like part_of, realted_to, develpos_from
        my $relationship_hash_ref = $self->{'_relationships'};
        foreach my $relationship ( keys %$relationship_hash_ref ) {
            my $reltype;
            #### Check if relationship exist, if not add it.
            if ( $self->_ont_engine->get_relationship_type($relationship) ) {
                $reltype =
                  $self->_ont_engine->get_relationship_type($relationship);
            }
            else {
                $self->_ont_engine->add_relationship_type( $relationship,
                    $ont );
                $reltype =
                  $self->_ont_engine->get_relationship_type($relationship);
            }

            #### Check if the id already exist in the graph
            my $id_array_ref = $$relationship_hash_ref{$relationship};
            foreach my $id (@$id_array_ref) {
                my $parent_term = $self->_create_term_object();
                $parent_term->identifier($id);
                $parent_term->ontology($ont);

                if ( !( $self->_has_term($parent_term) ) ) {
                    $self->_add_term( $parent_term, $ont );
                }

                $self->_add_relationship( $parent_term, $term, $reltype, $ont );
            }

        }

    }
    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;
}
closedescriptionprevnextTop
sub close {
    my $self = shift;

    # first call the inherited implementation
    $self->SUPER::close();
}

# INTERNAL METHODS
# ----------------
}
_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 OBOEngine.
}
_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 OBOEngine
}
_part_of_relationshipdescriptionprevnextTop
sub _part_of_relationship {
    my $self = shift;

    return $self->_ont_engine()->part_of_relationship(@_);
}    # _part_of_relationship

# This simply delegates. See OBOEngine
}
_is_a_relationshipdescriptionprevnextTop
sub _is_a_relationship {
    my $self = shift;

    return $self->_ont_engine()->is_a_relationship(@_);
}    # _is_a_relationship

# This simply delegates. See OBOEngine
}
_related_to_relationshipdescriptionprevnextTop
sub _related_to_relationship {
    my $self = shift;

    return $self->_ont_engine()->related_to_relationship(@_);
}    # _is_a_relationship


# This simply delegates. See OBOEngine
}
_regulates_relationshipdescriptionprevnextTop
sub _regulates_relationship {
    my $self = shift;

    return $self->_ont_engine()->regulates_relationship(@_);
}    # _part_of_relationship

# This simply delegates. See OBOEngine
}
_positively_regulates_relationshipdescriptionprevnextTop
sub _positively_regulates_relationship {
    my $self = shift;

    return $self->_ont_engine()->positively_regulates_relationship(@_);
}    # _part_of_relationship


# This simply delegates. See OBOEngine
}
_negatively_regulates_relationshipdescriptionprevnextTop
sub _negatively_regulates_relationship {
    my $self = shift;

    return $self->_ont_engine()->negatively_regulates_relationship(@_);
}    # _part_of_relationship

# This simply delegates. See OBOEngine
}
_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 OBOEngine
}
_has_termdescriptionprevnextTop
sub _has_term {
    my $self = shift;

    return $self->_ont_engine()->has_term(@_);
}    # _add_term

# Holds the OBO 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

# Removes the escape chracters from the file
}
_filter_linedescriptionprevnextTop
sub _filter_line {
    my ( $self, $line ) = @_;

    chomp($line);
    $line =~ tr [\200-\377]
          [\000-\177];    # see 'man perlop', section on tr/
                          # weird ascii characters should be excluded
    $line =~ tr/\0-\10//d;     # remove weird characters; ascii 0-8
                               # preserve \11 (9 - tab) and \12 (10-linefeed)
    $line =~ tr/\13\14//d;     # remove weird characters; 11,12
                               # preserve \15 (13 - carriage return)
    $line =~ tr/\16-\37//d;    # remove 14-31 (all rest before space)
    $line =~ tr/\177//d;       # remove DEL character

    $line =~ s/^\!.*//;
    $line =~ s/[^\\]\!.*//;
    $line =~ s/[^\\]\#.*//;
    $line =~ s/^\s+//;
    $line =~ s/\s+$//;

    return $line;
}

# Parses the header
}
_headerdescriptionprevnextTop
sub _header {
    my $self                  = shift;
    my $annotation_collection = Bio::Annotation::Collection->new();
    my ( $tag, $value );
    my $line_counter = 0;
    $self->{'_current_line_no'} = 0;
    my $format_version_header_flag = 0;
    my $default_namespace_header_flag = 0;

    while ( my $line = $self->_readline() ) {
        ++$line_counter;
        my $line = $self->_filter_line($line);
        if ( !$line ) {
            if ( !$format_version_header_flag || !$default_namespace_header_flag) {
                $self->throw(
"OBO File Format Error -\n Cannot find tag format-version and/ default-namespace . These are required header.\n"
                );
            }

            $self->{'_current_line_no'} = $line_counter;
            return $annotation_collection;
        }

        ### CHeck if there is a header
        if($line =~ /\[\w*\]/) {
                $self->throw(
"OBO File Format Error -\n Cannot find tag format-version. Thi ia a required header.\n"
                );
          }


        ### If the line is not null, check it contains atleasdt one colon
        $self->_check_colon( $line, $line_counter );

        ### Thsse ar the allowed headers. Any other headers will be ignored
        if ( $line =~
/^(\[|format-version:|typeref:|version:|date:|saved-by:|auto-generated-by:|default-namespace:|remark:|subsetdef:)/
          )
        {
            if ( $line =~ /^([\w\-]+)\:\s*(.*)/ ) {
                ( $tag, $value ) = ( $1, $2 );
            }

            if ( $tag =~ /format-version/) {
                $format_version_header_flag = 1;
            }elsif( $tag =~ /default-namespace/ ) {
                $default_namespace_header_flag = 1;
            }

            my $header = Bio::Annotation::SimpleValue->new( -value => $value );
            $annotation_collection->add_Annotation( $tag, $header );

            #### Assign the Ontology name as the value of the default-namespace header
            if ( $tag =~ /default-namespace/i ) {

                $self->ontology_name($value);
            }

        }

    }

}

### Parses each stanza of the file
}
_next_termdescriptionprevnextTop
sub _next_term {
    my $self             = shift;
    my $term             ;
    my $skip_stanza_flag = 1;
    my $line_counter     = $self->{'_current_line_no'};

    while ( my $line = $self->_readline() ) {
        #print $line."\n";
        ++$line_counter;
        my $line = $self->_filter_line($line);
        if ( !$line && $term ) {
            $self->{'_current_line_no'} = $line_counter;
            return $term;
        }

        if ( ( $line =~ /^\[(\w+)\]\s*(.*)/ ) ) {    #New stanza

            if ( uc($1) eq "TERM" ) {

                $term             = $self->_create_term_object;
                $skip_stanza_flag = 0;
                ### Reset the relationships after each stanza
                $self->{'_relationships'} = {};
                $self->{'_isa_parents'}   = undef;
            }
            elsif ( uc($1) eq "TYPEDEF" ) {
                $skip_stanza_flag = 1;
                ### Check if this typedef is already defined by the relationship
            }
            else {
                $skip_stanza_flag = 1;
                $self->warn(
"OBO File Format Warning on line $line_counter $line\n Unrecognized stanza type found. Skipping this stanza.\n"
                );
            }
            next;
        }

        ### If the line is not null, check it contains atleasdt one colon
        $self->_check_colon( $line, $line_counter );

        ### if there is any tag value other thn the list below move to the next tag
        next
          if (
            (
                $line !~
/^(\[|id:|name:|is_a:|relationship:|namespace:|is_obsolete:|alt_id:|def:|xref_analog:|exact_synonym:|broad_synonym:|related_synonym:|synonym:|comment:|xref:)/
            )
            || $skip_stanza_flag
          );

        if ( $line =~ /^([\w\-]+)\:\s*(.*)/ ) {    #TAg Value pair
            my ( $tag, $val ) = ( $1, $2 );

            ### If no value for the tag thrown a warning
            if ( !$val ) {
                $self->warn(
"OBO File Format Warning on line $line_counter $line\n Tag has no value\n"
                );
            }

            my $qh;
            ( $val, $qh ) = $self->_extract_quals($val);
            my $val2 = $val;
            $val2 =~ s/\\,/,/g;
            $tag = uc($tag);
            if ( $tag eq "ID" ) {

                $term->identifier($val);
                if ( $self->_has_term($term) ) {
                    $term = $self->_ont_engine()->get_terms($val);
                }

            }
            elsif ( $tag eq "NAME" ) {
                $term->name($val);
            }
            elsif ( $tag eq "XREF_ANALOG" ) {
                if ( !$term->has_dbxref($val) ) {
                    $term->add_dbxref(-dbxrefs => $self->_to_annotation([$val]));
                }
            }
            elsif ( $tag eq "XREF_UNKNOWN" ) {
                $term->add_dbxref(-dbxrefs => $self->_to_annotation([$val]));
            }
            elsif ( $tag eq "NAMESPACE" ) {
                $term->namespace($val);
            }
            elsif ( $tag eq "DEF" ) {
                my ( $defstr, $parts ) = $self->_extract_qstr($val);
                $term->definition($defstr);
                my $ann = $self->_to_annotation($parts);
                $term->add_dbxref(-dbxrefs => $ann);
            }
            elsif ( $tag =~ /(\w*)synonym/i ) {
                #$val =~ s/['"\[\]]//g; #NML commented out b/c need quotes
                $term->add_synonym($val);
            }
            elsif ( $tag eq "ALT_ID" ) {
                $term->add_secondary_id($val);
            }
	    elsif ( $tag =~ /XREF/i ) {
		$term->add_secondary_id($val);
	    }
            elsif ( $tag eq "IS_OBSOLETE" ) {

                if ( $val eq 'true' ) {
                    $val = 1;
                }
                if ( $val eq 'false' ) {
                    $val = 0;
                }
                $term->is_obsolete($val);
            }
            elsif ( $tag eq "COMMENT" ) {
                $term->comment($val);
            }
            elsif ( $tag eq "RELATIONSHIP" ) {
                $self->_handle_relationship_tag($val);
            }
            elsif ( $tag eq "IS_A" ) {

                $val =~ s/ //g;
                my $parent_term = $self->_create_term_object();
                $parent_term->identifier($val);

                if ( $self->{'_isa_parents'} ) {
                    my $isa_parents_array_ref = $self->{'_isa_parents'};
                    push( @$isa_parents_array_ref, $parent_term );
                }
                else {
                    my @terms_array;
                    push( @terms_array, $parent_term );
                    $self->{'_isa_parents'} =\@ terms_array;
                }
            }
        }
    }
    return $term;
}

# Creates a Bio::Ontology::OBOterm object
}
_create_term_objectdescriptionprevnextTop
sub _create_term_object {
    my ($self) = @_;
    my $term = $self->term_factory->create_object();
    return $term;

}

#
}
_extract_qualsdescriptionprevnextTop
sub _extract_quals {
    my ( $self, $str ) = @_;

    my %q = ();
    if ( $str =~ /(.*)\s+(\{.*\})\s*$/ ) {
        my $return_str = $1;
        my $extr       = $2;
        if ($extr) {
            my @qparts = $self->_split_on_comma($extr);
            foreach (@qparts) {
                if (/(\w+)=\"(.*)\"/) {
                    $q{$1} = $2;
                }
                elsif (/(\w+)=\'(.*)\'/) {
                    $q{$1} = $2;
                }
                else {
                    warn("$_ in $str");
                }
            }
        }
        return ( $return_str,\% q  );
    }
    else {
        return ( $str, {} );
    }
}
#
}
_extract_qstrdescriptionprevnextTop
sub _extract_qstr {
    my ( $self, $str ) = @_;

    my ( $extr, $rem, $prefix ) = extract_quotelike($str);
    my $txt = $extr;
    $txt =~ s/^\"//;
    $txt =~ s/\"$//;
    if ($prefix) {
        warn("illegal prefix: $prefix in: $str");
    }

    my @extra = ();

    # eg synonym: "foo" EXACT [...]
    if ( $rem =~ /(\w+)\s+(\[.*)/ ) {
        $rem = $2;
        push( @extra, split( ' ', $1 ) );
    }

    my @parts = ();
    while ( ( $extr, $rem, $prefix ) = extract_bracketed( $rem, '[]' ) ) {
        last unless $extr;
        $extr =~ s/^\[//;
        $extr =~ s/\]$//;
        push( @parts, $extr ) if $extr;
    }
    @parts =
      map { $self->_split_on_comma($_) } @parts;

    $txt =~ s/\\//g;
    return ( $txt,\@ parts,\@ extra );
}
#
}
_split_on_commadescriptionprevnextTop
sub _split_on_comma {
    my ( $self, $str ) = @_;
    my @parts = ();
    while ( $str =~ /(.*[^\\],\s*)(.*)/ ) {
        $str = $1;
        my $part = $2;
        unshift( @parts, $part );
        $str =~ s/,\s*$//;
    }
    unshift( @parts, $str );
    return map { s/\\//g; $_ } @parts;
}

# This method checks for an existing colon in a line
}
_check_colondescriptionprevnextTop
sub _check_colon {
    my ( $self, $line, $line_no ) = @_;
    if ( $line && !( $line =~ /:/ ) ) {
        $self->throw(
"OBO File Format Error on line $line_no $line -\n Cannot find key-terminating colon\n"
        );
    }
}

# This method handles relationship tags
}
_handle_relationship_tagdescriptionprevnextTop
sub _handle_relationship_tag {
    my ( $self, $val ) = @_;
    my @parts        = split( / /, $val );
    my $relationship = uc($parts[0]);
    my $id           = $parts[1] =~ /\^(w+)\s+\!/ ? $1 : $parts[1];
    my $parent_term  = $self->_create_term_object();
    $parent_term->identifier($id);

    if ( my $realtionships_hash = $self->{'_relationships'} ) {
        my $id_array_ref = $$realtionships_hash{$relationship};
        if ( !$id_array_ref ) {
            my @ids;
            push( @ids, $id );
            $$realtionships_hash{$relationship} =\@ ids;

        }
        else {
            push( @$id_array_ref, $id );
        }

    }

}

# 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
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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
Sohel Merchant
Email: s-merchant@northwestern.edu
Address:
  Northwestern University
  Center for Genetic Medicine (CGM), dictyBase
  Suite 1206,
  676 St. Clair st
  Chicago IL 60611
CONTRIBUTORTop
 Hilmar Lapp, hlapp at gmx.net
 Chris Mungall,   cjm at fruitfly.org
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 => "obo",
                             -file => "gene_ontology.obo");
 Function: Creates a new dagflat parser.
 Returns : A new dagflat parser object, implementing Bio::OntologyIO.
 Args    : -file      => a single ontology flat file holding the
                          terms, descriptions and relationships
           -ontology_name => the name of the ontology; if not specified the
                          parser will assign the name of the ontology as the
                          default-namespace header value from the OBO file.
           -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.