example AO annotation serialization in RDF using Perl

gistfile1.pl

use Data::UUID;

#use RDF::Trine::Serializer::Turtle;
#use RDF::Trine::Serializer::Notation3;
use RDF::Trine::Serializer::NTriples;

use RDF::Trine::Namespace qw(rdf);



my $foaf = RDF::Trine::Namespace->new('http://xmlns.com/foaf/0.1/' );
my $ao =  RDF::Trine::Namespace->new('http://purl.org/ao/core/');
my $aot = RDF::Trine::Namespace->new('http://purl.org/ao/types/');
my $aos = RDF::Trine::Namespace->new('http://purl.org/ao/selectors/');
my $aof =  RDF::Trine::Namespace->new('http://purl.org/ao/foaf/');

my $pav = RDF::Trine::Namespace->new('http://purl.org/pav/');


my $ex = RDF::Trine::Namespace->new('http://example/');

sub resource {
  return RDF::Trine::Node::Resource->new(shift);
}

sub literal {
  return RDF::Trine::Node::Literal->new(shift);
}

sub literalString {
  return RDF::Trine::Node::Literal->new(shift, shift);
}

sub statement {
  return RDF::Trine::Statement->new(shift, shift, shift);
}

sub newPrefixURI {
  my $ug = new Data::UUID;
  my $name = (shift) . "_" . $ug->create_hex();
  return $ex->$name;
}

sub newAnnotationURI {
  return newPrefixURI("A");
}

sub newSpanURI {
  return newPrefixURI("SPAN");
}

sub addStatementsToModel {
  my $model = shift;
  my $statements = shift;
  foreach my $statement(@$statements) {
    $model->add_statement(statement(@$statement));
  }
  return $model;
}

sub addAnnotation {
  my %params = @_;
  my $model = $params{model};
  my $A = newAnnotationURI();
  addStatementsToModel($model, 
                       [[$A, $rdf->type, $ao->Annotation],
                        [$A, $pav->createdBy, $ex->foo],
                        [$A, $pav->createdOn, $ex->now]]);
  return {model => $model, annotation => $A};
}

sub addDocument {
  my %params = @_;
  my $model = $params{model};
  my $pmid = $params{pmid};
  my $pmidURI = resource("http://www.ncbi.nlm.nih.gov/pubmed/" . $pmid);

print $pmidURI;
  ## my $document = $params{document};

  addStatementsToModel($model, 
                       [[$pmidURI, $rdf->type, $foaf->Document]]);
  return {(%params, document => $pmidURI)};  
}

sub addDocumentVersion {
  my %params = @_;
  my $model = $params{model};
  my $dateAccessed = $params{dateAccessed};
  my $document = $params{document};
  my $DV = newPrefixURI("DocVersion");
  addStatementsToModel($model, 
                       [[$DV, $rdf->type, $ao->SourceDocument],
                        [$DV, $pav->sourceAccessedOn, $ex->now],
                        [$DV, $pav->retrievedFrom, $document]]);
  return {(%params, documentVersion => $DV)};  
}

sub addContext {
  my %params = @_;
  my $model = $params{model};
  my $start = $params{start};
  my $end = $params{end};
  my $A = $params{annotation};
  my $D = $params{document};
  my $DV = $params{documentVersion};
  my $S = newSpanURI();
  addStatementsToModel($model, 
                       [[$A, $ao->hasContext, $S],
                        [$S, $rdf->type, $aos->StartEndTextSelector],
                        [$S, $aos->start, literal($start)],
                        [$S, $aos->end, literal($end)]]);
  if ($DV) {
    addStatementsToModel($model, 
                         [[$S, $ao->onSourceDocument, $DV]]);
  } else {
    addStatementsToModel($model, 
                         [[$S, $aof->onDocument, $D]]);
  }

  return %params;
}


my $RDF;
my $model;
my $progressiveOutput;

my $file_name = 'annotation.ntriple';
open ($RDF, ">>$file_name") || die ("Could not open $file_name!");

my $serializer = RDF::Trine::Serializer::NTriples->new();
#other serializer formats
#RDF::Trine::Serializer::Turtle->new(namespaces => $namespaces);
#RDF::Trine::Serializer::Notation3->new(namespaces => $namespaces);


# TODO LOOP HERE
$model = RDF::Trine::Model->temporary_model;
$progressiveOutput = addAnnotation(model => $model);
$progressiveOutput = addDocument((%$progressiveOutput, pmid=> 18276894));
$progressiveOutput = 
  addDocumentVersion((%$progressiveOutput, dateAccessed=>"now"));
$progressiveOutput = addContext((%$progressiveOutput, start => 5, end => 10));
$serializer->serialize_model_to_file($RDF, $model);

#for test
#print $serializer->serialize_model_to_string($model);

#END LOOP


close ($RDF);