Summary

Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler

Package variables

Included modules

Inherit

Bio::OntologyIO::Handlers::BaseSAXHandler

Synopsis

   # see load_interpro.pl in bioperl-db/scripts/biosql/

Description

This module take the advantage of SAX, a stream-based XML parser
technology, to keep the used memory as small as possible.
InterProHandler in the same directory use another scheme to keep all
interpro record in the engine and keep the ontology data in memory,
almost impossible to operate it!

Methods

Methods description

None available.

Methods code

sub _initialize {

    my($self,@args)=@_;
    $self->SUPER::_initialize(@args);
    my ($db, $version) = $self->_rearrange(
        [qw(DB  VERSION)], @args);
    defined $db or $self->throw('db must be assigned');
    $self->_db($db);
    my $ontology = Bio::Ontology::Ontology->new(
        -name => 'InterPro',
        -definition => "InterPro, $version"
    );
    $self->_ontology($ontology);
    $is_a_rel = Bio::Ontology::RelationshipType->get_instance('IS_A');
    $is_a_rel->ontology($ontology);

}

sub start_document {

    my $self = shift;
    my $ont = $self->_ontology;
    my $db = $self->_db;
    $ont->add_term($self->create_term(-identifier=>'Family', -name=>'Family'));
    $ont->add_term($self->create_term(-identifier=>'Domain', -name=>'Domain'));
    $ont->add_term($self->create_term(-identifier=>'Repeat', -name=>'Repeat'));
    $ont->add_term($self->create_term(-identifier=>'PTM', 
        -name=>'post-translational modification'));
    $ont->add_term($self->create_term(
        -identifier=>'Active_site', -name=>'Active_site'));
    $ont->add_term($self->create_term(
        -identifier=>'Binding_site', -name=>'Binding_site'));

}

sub start_element {

    my $self=shift;
    my $tag=$_[0]->{Name};
    my %args=%{$_[0]->{Attributes}};
    my $ont = $self->_ontology;

    if($tag eq 'interpro'){
        my $id = $args{id};
        my $term = $self->create_term(-identifier=>$id);
        $term->ontology($ont);
        $term->add_synonym($args{short_name});
        $term->definition();
        
        my $object_term =
            ($ont->engine->get_term_by_identifier($args{type}))[0];
        
        my $rel = Bio::Ontology::Relationship->new(
            -subject_term => $term,
            -predicate_term => $is_a_rel,
            -object_term => $object_term,
            -ontology => $ont
        );
        $self->_relationship($rel);
    }elsif($tag eq 'example'){
        my $example = Bio::Annotation::DBLink->new;
        $self->_current_hash->{example} = $example;
    }elsif($tag eq 'db_xref'){
        my $top = $self->_top_tag;
        if($top eq 'example'){
            my $example = $self->_current_hash->{example};
            $example->database($args{db});
            $example->primary_id($args{dbkey});
            print "EXAmPLE:\t", $example->database, '|', $example->primary_id, "\n";
        }elsif($top eq 'child'){
            ;
        }elsif($top eq 'member_list'){
            my $dblink=Bio::Annotation::DBLink->new(
                -dbname => $args{id},
                -primary_id => $args{dbkey},
                -comment => $args{name}
            );
        }elsif($top eq 'external_doc_list'){
            ;
        }elsif($top eq 'publication'){
            if($args{db} eq 'MEDLINE'){
                $self->_current_hash->{medline} =$args{dbkey};
            }else{
                print "Anywhere else??!!\n";
            }
        }elsif($top eq 'structure_db_links'){
            ;
        }elsif($top eq 'abstract'){
            ;
        }else{
            print "Possible??--$top\n";
        }
    }elsif($tag eq 'publication'){
        my $publication = Bio::Annotation::Reference->new(
            -medline => $args{id});
        $self->_current_hash->{publication} = $publication;
    }elsif($tag eq 'author_list'){
        ;
    }elsif($tag eq 'journal'){
        ;
    }elsif($tag eq 'location'){
        ;
    }elsif($tag eq 'year'){
        ;
    }else{
        ;
    }
        
    $self->_visited_count_inc($tag);
    $self->_push_tag($tag);

}

sub end_element {

    my $self=shift;
    my $tag=shift->{Name};
    my $chars_in=$self->_chars_hash->{$tag};
    if($tag eq 'interpro'){
        my $rel = $self->_relationship;
        my $db = $self->_db;
        my $prel = $db->create_persistent($rel);
        eval {$prel->create};
        if($@){
            my $interpro = $rel->subject_term;
            print STDERR "$@\n\n\n\n";
            print STDERR "$interpro\n\n\n", '-'x80, "\n";
        }
#        print $count++, "\n";
    }elsif($tag eq 'name'){
        my $rel = $self->_relationship;
        $rel->subject_term->name($self->_chars_hash->{name});
        $self->_chars_hash->{name}='';
    }elsif($tag eq 'abstract'){
        my $rel = $self->_relationship;
        my $abstract = $self->_chars_hash->{abstract};
        $abstract =~ s/\n/ /g;
        $rel->subject_term->definition($abstract);
        $self->_chars_hash->{abstract} = '';
    }elsif($tag eq 'example'){
        my $example = $self->_current_hash->{example};
        my $comment = $self->_chars_hash->{example};
        $comment =~ s/^(\s+)//; $comment =~ s/(\s+)$//;
        $example->comment($comment);
        $self->_relationship->subject_term->add_dblink($example);
        $self->_chars_hash->{example}='';
    }elsif($tag eq 'publication'){
        my $publication = $self->_create_publication;
        $self->_relationship->subject_term->add_reference($publication);
    }elsif($tag eq 'author_list'){
        $self->_current_hash->{author} =$chars_in;
    }elsif($tag eq 'title'){
        $self->_current_hash->{title}=$chars_in;
    }
    $self->_pop_tag;
    $self->_visited_count_dec($tag);

}

sub characters {

    my $self=shift;
    my $text = shift->{Data};

    my $top_tag =$self->_top_tag;
    $self->_chars_hash->{$top_tag} .= $text;
    
#    $self->_chars_hash->{abstract} .= $text if $self->_visited_count('abstract');

}

sub create_term {

    my ($self, @args) = @_;
    my $term = Bio::Ontology::Term->new(@args);
    return $term;

}

sub _db {

    my $self=shift;
    if(@_){
        my $db = shift;
        if(exists $self->{_db}){ $self->throw('db can be set only once'); }
        $self->{_db}=$db;
    }
    return $self->{_db};

}

sub _ontology {

    my $self = shift;
    $self->{_ontology}=shift if @_;
    return $self->{_ontology};

}

sub _relationship {

    my $self =shift;
    $self->{_relationship}=shift if @_;
    return $self->{_relationship};

}

sub _create_publication {

    my $self=shift;
    my $publication = $self->_current_hash->{publication};
    my $author = $self->_current_hash->{author};
    my $journal = $self->_current_hash->{journal};
    my $year = $self->_current_hash->{year};
    my $page_location = $self->_current_hash->{page_location};
    my $volumn = $self->_current_hash->{volumn};
    $publication->authors($author);
    $publication->location("$journal, $year, V $volumn, $page_location");
    my $title = $self->_current_hash->{title};
    $publication->title($title);
    my $medline = $self->_current_hash->{medline};
    $publication->medline($medline);
    
# Clear the above in current hash
    $self->_current_hash->{publication} = undef;
    $self->_current_hash->{author}      = undef;
    $self->_current_hash->{journal}     = undef;
    $self->_current_hash->{year}        = undef;
    $self->_current_hash->{page_location}=undef;
    $self->_current_hash->{volumn}      = undef;
    $self->_current_hash->{title}       = undef;
    $self->_current_hash->{medline}     = undef;

}

General documentation

Juguang Xiao, juguang@tll.org.sg

The rest of the documentation details each of the object methods.
Interal methods are usually preceded with a _