I have a RDF/XML data which I'd like to parse and access the node. It looks like this:
<!-- http://purl.obolibrary.org/obo/VO_0000185 -->
<owl:Class rdf:about="&obo;VO_0000185">
<rdfs:label>Influenza virus gene</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;VO_0000156"/>
<obo:IAO_0000117>YH</obo:IAO_0000117>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/VO_0000186 -->
<owl:Class rdf:about="&obo;VO_0000186">
<rdfs:label>RNA vaccine</rdfs:label>
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&obo;VO_0000001"/>
<owl:Restriction>
<owl:onProperty rdf:resource="&obo;BFO_0000161"/>
<owl:someValuesFrom rdf:resource="&obo;VO_0000728"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="&obo;VO_0000001"/>
<obo:IAO_0000116>Using RNA may eliminate the problem of having to tailor a vaccine for each individual patient with their specific immunity. The advantage of RNA is that it can be used for all immunity types and can be taken from a single cell. DNA vaccines need to produce RNA which then prompts the manufacture of proteins. However, RNA vaccine eliminates the step from DNA to RNA.</obo:IAO_0000116>
<obo:IAO_0000115>A vaccine that uses RNA(s) derived from a pathogen organism.</obo:IAO_0000115>
<obo:IAO_0000117>YH</obo:IAO_0000117>
</owl:Class>
The complete RDF/XML file can be found here.
What I want to do is to do the following:
<rdfs:subClassOf rdf:resource="&obo;VO_0000001"/><rdfs:label>...</rdfs:label>So in the above example the code would go through second chunk and output: "RNA vaccine".
I'm currently stuck with the following code. Where I couldn't access the node. What's the right way to do it? Solutions other than using XML::LibXML are welcomed.
#!/usr/bin/perl -w
use strict;
use Data::Dumper;
use Carp;
use File::Basename;
use XML::LibXML 1.70;
my $filename = "VO.owl";
# Obtained from http://svn.code.sf.net/p/vaccineontology/code/trunk/src/ontology/VO.owl
my $parser = XML::LibXML->new();
my $doc = $parser->parse_file( $filename );
foreach my $chunk ($doc->findnodes('/owl:Class')) {
my ($label) = $chunk->findnodes('./rdfs:label');
my ($subclass) = $chunk->findnodes('./rdfs:subClassOf');
print $label->to_literal;
print $subclass->to_literal;
}
Parsing RDF as if it were XML is a folly. The exact same data can appear in many different ways. For example, all of the following RDF files carry the same data. Any conforming RDF implementation MUST handle them identically...
<!-- example 1 -->
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#me">
<rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Person" />
<foaf:name>Toby Inkster</foaf:name>
</rdf:Description>
</rdf:RDF>
<!-- example 2 -->
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:foaf="http://xmlns.com/foaf/0.1/">
<foaf:Person rdf:about="#me">
<foaf:name>Toby Inkster</foaf:name>
</foaf:Person>
</rdf:RDF>
<!-- example 3 -->
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:foaf="http://xmlns.com/foaf/0.1/">
<foaf:Person rdf:about="#me" foaf:name="Toby Inkster" />
</rdf:RDF>
<!-- example 4 -->
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:foaf="">
<rdf:Description rdf:about="#me"
rdf:type="http://xmlns.com/foaf/0.1/Person"
foaf:name="Toby Inkster" />
</rdf:RDF>
<!-- example 5 -->
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:ID="me">
<rdf:type>
<rdf:Description rdf:about="http://xmlns.com/foaf/0.1/Person" />
</rdf:type>
<foaf:name>Toby Inkster</foaf:name>
</rdf:Description>
</rdf:RDF>
<!-- example 6 -->
<foaf:Person
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
rdf:about="#me"
foaf:name="Toby Inkster" />
I could easily list half a dozen other variations too, but I'll stop there. And this RDF file contains just two statements - I'm a Person; my name is "Toby Inkster" - the OP's data contains over 50,000 statements.
And this is just the XML serialization of RDF; there are other serializations too.
If you try handling all that with XPath, you're likely to end up becoming a lunatic locked away in a tower somewhere, muttering in his sleep about the triples; the triples...
Luckily, Greg Williams has taken that mental health bullet for you. RDF::Trine and RDF::Query are not only the best RDF frameworks for Perl; they're amongst the best in any programming language.
Here is how the OP's task could be achieved using RDF::Trine and RDF::Query:
#!/usr/bin/env perl
use v5.12;
use RDF::Trine;
use RDF::Query;
my $model = 'RDF::Trine::Model'->new(
'RDF::Trine::Store::DBI'->new(
'vo',
'dbi:SQLite:dbname=/tmp/vo.sqlite',
'', # no username
'', # no password
),
);
'RDF::Trine::Parser::RDFXML'->new->parse_url_into_model(
'http://svn.code.sf.net/p/vaccineontology/code/trunk/src/ontology/VO.owl',
$model,
) unless $model->size > 0;
my $query = RDF::Query->new(<<'SPARQL');
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?super_label ?sub_label
WHERE {
?sub rdfs:subClassOf ?super .
?sub rdfs:label ?sub_label .
?super rdfs:label ?super_label .
}
LIMIT 5
SPARQL
print $query->execute($model)->as_string;
Sample output:
+----------------------------+----------------------------------+
| super_label | sub_label |
+----------------------------+----------------------------------+
| "Aves vaccine" | "Ducks vaccine" |
| "route of administration" | "intravaginal route" |
| "Shigella gene" | "aroA from Shigella" |
| "Papillomavirus vaccine" | "Bovine papillomavirus vaccine" |
| "virus protein" | "Feline leukemia virus protein" |
+----------------------------+----------------------------------+
UPDATE: Here's a SPARQL query that can be plugged into the script above to retrieve the data you wanted:
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
SELECT ?subclass ?label
WHERE {
?subclass
rdfs:subClassOf obo:VO_0000001 ;
rdfs:label ?label .
}