Experimental/unified design

Created by: avullo

This is introducing RDF writers for features (non ensembl) and corresponding xrefs.

modules/Bio/EnsEMBL/IO/Object/RDF.pm

+=head1 LICENSE
+
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+Copyright [2016] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=head1 NAME
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+=cut
+
+package Bio::EnsEMBL::IO::Object::RDF;
+
+use strict;
+use warnings;
+use Carp;
+
+use Bio::EnsEMBL::Utils::RDF qw/u triple/;
+
+sub new {
+  my ($class) = @_;
+  
+  my $self = {};
+  bless $self, $class;
+  
+  return $self;
+}
+
+=head2 namespaces
+
+=cut
+
+sub namespaces {
+  my ($class, %prefix) = @_;
+  %prefix = %Bio::EnsEMBL::Utils::RDF::prefix unless %prefix;
+    
+  return bless { type => 'namespaces', prefix => \%prefix }, $class;
+}
+
+=head2 species
+
+=cut
+
+sub species {
+    my $class = shift;
+    my %args = @_;
+    exists $args{taxon_id} or croak "Undefined species taxon_id";
+    exists $args{scientific_name} or croak "Undefined species scientific name";
+    exists $args{common_name} or croak "Undefined species common name";
+    
+    return bless { type => 'species', %args }, $class;
+  }
+
+sub create_record {
+  my $self = shift;
+
+  my $line;
+
+  if($self->{type} eq 'namespaces') {
+    return unless scalar keys %{$self->{prefix}};
+    
+    $line = join("\n", map { sprintf "\@prefix %s: %s .", $_, u($self->{prefix}{$_}) } sort keys %{$self->{prefix}});
+  } elsif($self->{type} eq 'species') {
+    my $taxon_id = $self->{taxon_id};
+    my $scientific_name = $self->{scientific_name};
+    my $common_name = $self->{common_name};
+
+    # return global triples about the organism  
+    $line = sprintf "%s\n%s\n%s\n%s",
+      triple('taxon:'.$taxon_id, 'rdfs:subClassOf', 'obo:OBI_0100026'),
+      triple('taxon:'.$taxon_id, 'skos:prefLabel', qq("$scientific_name")),
+      triple('taxon:'.$taxon_id, 'skos:altLabel', qq("$common_name")),
+      triple('taxon:'.$taxon_id, 'dc:identifier', qq("$taxon_id"));
+  } else {
+    croak "Unrecognised RDF object type";
+  }
+
+  return $line;
+}
+
+1;