I've included below the SQL queries that were used in the VLDB paper for
testing the performance of the Oracle RDF Data Model.
Please note that we simply took some of the examples given on Eric Jain's
Uniprot RDF website and rewrote them to work with our system. It seems the
document with example queries is no longer available via Eric's site, but is
available via archive.org:
http://web.archive.org/web/20041011125430/http://www.isb-sib.ch/~ejain/rdf/s
tore.html#queries
Susie
-- Q1
SELECT AVG(LENGTH(protein)),
AVG(LENGTH(begin)),
AVG(LENGTH(end))
FROM TABLE(RDF_MATCH('(?protein rdf:type :Protein)
(?protein :annotation ?annotation)
(?annotation rdf:type :Transmembrane_Annotation)
(?annotation :range ?range)
(?range :begin ?begin)
(?range :end ?end)',
RDFModels('UniProt'), NULL,
RDFAliases(RDFAlias('', 'urn:lsid:uniprot.org:ontology:'))))
WHERE rownum <= 15000;
-- Q2
SELECT AVG(LENGTH(protein)),
AVG(LENGTH(author)),
AVG(LENGTH(title))
FROM TABLE(RDF_MATCH('(?protein rdf:type :Protein)
(?protein :modified ?modified)
(?protein :citation ?citation)
(?citation :author ?author)
(?citation :title ?title)',
RDFModels('UniProt'), NULL,
RDFAliases(RDFAlias('', 'urn:lsid:uniprot.org:ontology:'))))
WHERE author LIKE 'Bairoch %' AND rownum <= 16
-- Q3
SELECT count(*)
FROM TABLE(RDF_MATCH('(?protein rdf:type :Protein)
(?protein :citation ?citation)
(?citation :author "Bairoch A.")',
RDFModels('UniProt'), NULL,
RDFAliases(RDFAlias('', 'urn:lsid:uniprot.org:ontology:'))))
WHERE rownum <= 32;
-- Q4
SELECT AVG(LENGTH(related))
FROM TABLE(RDF_MATCH('(?protein rdf:type :Protein)
(?protein :keyword
<urn:lsid:uniprot.org:keywords:48>)
(?protein rdfs:seeAlso ?related)',
RDFModels('UniProt'), NULL,
RDFAliases(RDFAlias('', 'urn:lsid:uniprot.org:ontology:'))))
WHERE rownum <= 3000;
-- Q5
SELECT AVG(LENGTH(gene)),
AVG(LENGTH(name)),
AVG(LENGTH(text))
FROM TABLE(RDF_MATCH('(?protein rdf:type :Protein)
(?protein :gene ?gene)
(?gene :name ?name)
(?protein :organism
<urn:lsid:uniprot.org:taxonomy:9606>)
(?protein :annotation ?annotation)
(?annotation rdf:type :Disease_Annotation)
(?annotation rdfs:comment ?text)',
RDFModels('UniProt'), NULL,
RDFAliases(RDFAlias('', 'urn:lsid:uniprot.org:ontology:'))))
WHERE rownum <= 750;
-- Q6
SELECT AVG(LENGTH(protein)),
AVG(LENGTH(mod_date))
FROM TABLE(RDF_MATCH('(?protein rdf:type :Protein)
(?protein :modified ?mod_date)',
RDFModels('UniProt'), NULL,
RDFAliases(RDFAlias('', 'urn:lsid:uniprot.org:ontology:'))))
WHERE mod_date > '2004-08' AND rownum <= 8000;
