Difference between revisions of "ProvenanceContextEntity"
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PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki><br/> | PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki><br/> | ||
SELECT ?year count(*)<br/> | SELECT ?year count(*)<br/> | ||
− | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_context1</nowiki | + | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_context1></nowiki><br/> |
FROM <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki><br/> | FROM <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki><br/> | ||
FROM <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki><br/> | FROM <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki><br/> | ||
Line 243: | Line 243: | ||
PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki><br/> | PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki><br/> | ||
SELECT ?year count(*)<br/> | SELECT ?year count(*)<br/> | ||
− | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_context2</nowiki | + | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_context2></nowiki><br/> |
FROM <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki><br/> | FROM <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki><br/> | ||
FROM <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki><br/> | FROM <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki><br/> | ||
Line 380: | Line 380: | ||
PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki><br/> | PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki><br/> | ||
SELECT ?year count(*)<br/> | SELECT ?year count(*)<br/> | ||
− | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_context3</nowiki | + | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_context3></nowiki><br/> |
FROM <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki><br/> | FROM <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki><br/> | ||
FROM <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki><br/> | FROM <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki><br/> | ||
Line 404: | Line 404: | ||
} | } | ||
order by ?year | order by ?year | ||
+ | |||
+ | === Queries for Reification (R) Dataset === | ||
+ | '''Query 1''': All statements for a given PMID (e.g., 17209178) | ||
+ | |||
+ | PREFIX bkr: <nowiki> <http://mor.nlm.nih.gov/bkr/></nowiki> <br/> | ||
+ | PREFIX dc: <nowiki><http://purl.org/dc/elements/1.1/></nowiki> <br/> | ||
+ | PREFIX provenir: <nowiki><http://knoesis.wright.edu/provenir/></nowiki> <br/> | ||
+ | PREFIX rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki> <br/> | ||
+ | PREFIX rdfs: <nowiki><http://www.w3.org/2000/01/rdf-schema#></nowiki> <br/> | ||
+ | PREFIX umls: <nowiki><http://mor.nlm.nih.gov/umls/></nowiki> <br/> | ||
+ | PREFIX meta: <nowiki><http://mor.nlm.nih.gov/umls/META_></nowiki> <br/> | ||
+ | PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki> <br/> | ||
+ | SELECT ?st_s_inst ?st_p_inst ?st_o_inst <br/> | ||
+ | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_reification></nowiki> <br/> | ||
+ | WHERE {<blockquote> | ||
+ | ?bn rdf:subject ?st_s_inst .<br/> | ||
+ | ?bn rdf:predicate ?st_p_inst .<br/> | ||
+ | ?bn rdf:object ?st_o_inst . | ||
+ | ?bn provenir:derives_from bkr:PUBMED_17209178-INST .</blockquote> | ||
+ | } <br/> | ||
+ | |||
+ | '''Query 2''': All sources for a given statement (Lipoproteins AFFECTS Inflammatory cell) | ||
+ | |||
+ | PREFIX bkr: <nowiki><http://mor.nlm.nih.gov/bkr/></nowiki><br/> | ||
+ | PREFIX dc: <nowiki><http://purl.org/dc/elements/1.1/></nowiki><br/> | ||
+ | PREFIX provenir: <nowiki><http://knoesis.wright.edu/provenir/></nowiki><br/> | ||
+ | PREFIX rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki><br/> | ||
+ | PREFIX rdfs: <nowiki><http://www.w3.org/2000/01/rdf-schema#></nowiki><br/> | ||
+ | PREFIX umls: <nowiki><http://mor.nlm.nih.gov/umls/></nowiki><br/> | ||
+ | PREFIX meta: <nowiki><http://mor.nlm.nih.gov/umls/META_></nowiki><br/> | ||
+ | PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki><br/> | ||
+ | SELECT ?source_inst<br/> | ||
+ | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_reification></nowiki><br/> | ||
+ | WHERE {<blockquote> | ||
+ | ?bn rdf:subject ?st_s_inst .<br/> | ||
+ | ?bn rdf:predicate ?st_p_inst .<br/> | ||
+ | ?bn rdf:object ?st_o_inst .<br/> | ||
+ | ?st_s_inst rdf:type meta:C0023820 .<br/> | ||
+ | ?st_p_inst rdfs:subPropertyOf sn:AFFECTS .<br/> | ||
+ | ?st_o_inst rdf:type meta:C0440752 .<br/> | ||
+ | ?bn provenir:derives_from ?source_inst .</blockquote> | ||
+ | }<br/> | ||
+ | |||
+ | '''Query 3''': Frequency by source for 1 statement (Thalidomide treats disease) | ||
+ | |||
+ | PREFIX bkr: <nowiki><http://mor.nlm.nih.gov/bkr/></nowiki><br/> | ||
+ | PREFIX dc: <nowiki><http://purl.org/dc/elements/1.1/></nowiki><br/> | ||
+ | PREFIX provenir: <nowiki><http://knoesis.wright.edu/provenir/></nowiki><br/> | ||
+ | PREFIX rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki><br/> | ||
+ | PREFIX rdfs: <nowiki><http://www.w3.org/2000/01/rdf-schema#></nowiki><br/> | ||
+ | PREFIX umls: <nowiki><http://mor.nlm.nih.gov/umls/></nowiki><br/> | ||
+ | PREFIX meta: <nowiki><http://mor.nlm.nih.gov/umls/META_></nowiki><br/> | ||
+ | PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki><br/> | ||
+ | SELECT ?source_name count(?source_name)<br/> | ||
+ | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_reification></nowiki><br/> | ||
+ | FROM <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki><br/> | ||
+ | WHERE {<blockquote> | ||
+ | graph <nowiki><http://mor.nlm.nih.gov/bkr_instances_reification></nowiki> {<blockquote> | ||
+ | ?bn rdf:subject ?st_s_inst .<br/> | ||
+ | ?bn rdf:predicate ?st_p_inst .<br/> | ||
+ | ?bn rdf:object ?st_o_inst .<br/> | ||
+ | ?st_s_inst rdf:type meta:C0039736 .<br/> | ||
+ | ?st_p_inst rdfs:subPropertyOf ?st_p_cl .<br/> | ||
+ | ?st_s_inst provenir:derives_from ?source_inst .<br/> | ||
+ | ?source_inst rdf:type ?source_cl .</blockquote> | ||
+ | } .<br/> | ||
+ | graph <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki> {<blockquote> | ||
+ | ?source_cl rdfs:label ?source_name .<br/> | ||
+ | ?st_p_cl rdfs:subPropertyOf ?st_p_cl_top .<br/> | ||
+ | ?st_p_cl_top rdfs:label 'treats' .</blockquote> | ||
+ | } .</blockquote> | ||
+ | } | ||
+ | |||
+ | '''Query 4''': Count the number of journal articles published between two dates (e.g., 2000-01-01 and 2000-12-31) for a given triple (e.g. Thalidomide treats multiple_myeloma) | ||
+ | |||
+ | PREFIX bkr: <nowiki><http://mor.nlm.nih.gov/bkr/></nowiki><br/> | ||
+ | PREFIX dc: <nowiki><http://purl.org/dc/elements/1.1/></nowiki><br/> | ||
+ | PREFIX provenir: <nowiki><http://knoesis.wright.edu/provenir/></nowiki><br/> | ||
+ | PREFIX rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki><br/> | ||
+ | PREFIX rdfs: <nowiki><http://www.w3.org/2000/01/rdf-schema#></nowiki><br/> | ||
+ | PREFIX umls: <nowiki><http://mor.nlm.nih.gov/umls/></nowiki><br/> | ||
+ | PREFIX meta: <nowiki><http://mor.nlm.nih.gov/umls/META_></nowiki><br/> | ||
+ | PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki><br/> | ||
+ | SELECT count(*)<br/> | ||
+ | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_reification></nowiki><br/> | ||
+ | FROM <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki><br/> | ||
+ | WHERE {<blockquote> | ||
+ | graph <nowiki><http://mor.nlm.nih.gov/bkr_instances_reification></nowiki> {<blockquote> | ||
+ | ?bn rdf:subject ?st_s_inst .<br/> | ||
+ | ?bn rdf:predicate ?st_p_inst .<br/> | ||
+ | ?bn rdf:object ?st_o_inst .<br/> | ||
+ | ?st_s_inst rdf:type meta:C0039736 .<br/> | ||
+ | ?st_p_inst rdfs:subPropertyOf sn:TREATS .<br/> | ||
+ | ?st_o_inst rdf:type meta:C0026764 .<br/> | ||
+ | ?st_s_inst provenir:derives_from ?source_inst .<br/> | ||
+ | ?source_inst rdf:type ?source_cl .</blockquote> | ||
+ | } . | ||
+ | graph <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki> {<blockquote> | ||
+ | ?source_inst dc:date ?source_date .<br/> | ||
+ | FILTER(?source_date >= xsd:date("2000-01-01") && ?source_date < xsd:date("2000-12-31"))</blockquote> | ||
+ | }</blockquote> | ||
+ | } | ||
+ | |||
+ | '''Query 5''': Time profile the number of journal articles published over 10 years that mention the therapeutic use of the drug Thalidomide | ||
+ | |||
+ | PREFIX bkr: <nowiki><http://mor.nlm.nih.gov/bkr/></nowiki><br/> | ||
+ | PREFIX dc: <nowiki><http://purl.org/dc/elements/1.1/></nowiki><br/> | ||
+ | PREFIX provenir: <nowiki><http://knoesis.wright.edu/provenir/></nowiki><br/> | ||
+ | PREFIX rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki><br/> | ||
+ | PREFIX rdfs: <nowiki><http://www.w3.org/2000/01/rdf-schema#></nowiki><br/> | ||
+ | PREFIX umls: <nowiki><http://mor.nlm.nih.gov/umls/></nowiki><br/> | ||
+ | PREFIX meta: <nowiki><http://mor.nlm.nih.gov/umls/META_></nowiki><br/> | ||
+ | PREFIX sn: <nowiki><http://mor.nlm.nih.gov/umls/SEMNET_></nowiki><br/> | ||
+ | SELECT ?year count(*)<br/> | ||
+ | FROM <nowiki><http://mor.nlm.nih.gov/bkr_instances_reification></nowiki><br/> | ||
+ | FROM <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki><br/> | ||
+ | FROM <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki><br/> | ||
+ | where {<blockquote> | ||
+ | {<blockquote> | ||
+ | select (bif:year(?source_date)) as ?year | ||
+ | WHERE {<blockquote> | ||
+ | graph <nowiki><http://mor.nlm.nih.gov/bkr_instances_reification></nowiki> {<blockquote> | ||
+ | ?bn rdf:subject ?st_s_inst .<br/> | ||
+ | ?bn rdf:predicate ?st_p_inst .<br/> | ||
+ | ?bn rdf:object ?st_o_inst .<br/> | ||
+ | ?st_s_inst rdf:type meta:C0039736 .<br/> | ||
+ | ?st_p_inst rdfs:subPropertyOf sn:TREATS .<br/> | ||
+ | ?st_o_inst rdf:type meta:C0026764 .<br/> | ||
+ | ?st_s_inst provenir:derives_from ?source_inst .<br/> | ||
+ | ?source_inst rdf:type ?source_cl .</blockquote> | ||
+ | } . | ||
+ | graph <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki> {<blockquote> | ||
+ | ?source_inst dc:date ?source_date .</blockquote> | ||
+ | }</blockquote> | ||
+ | }</blockquote> | ||
+ | }</blockquote> | ||
+ | } | ||
+ | order by ?year | ||
+ | |||
== Result Set == | == Result Set == | ||
+ | The Evaluation results for the two phase evaluation of the PaCE approach versus the RDF reification approach can be downloaded [http://knoesis.wright.edu/library/download/ProvenanceContextEntity_ResultSet.zip '''here'''] (in .zip format). |
Latest revision as of 20:07, 6 February 2010
Contents
Provenance Context Entity (PaCE) Resource Page
The Provenance Context Entity (PaCE) is a new approach for provenance tracking in RDF datasets using the notion of provenance context to create provenance-aware RDF triples without the use of RDF reification or blank nodes.
This is a resource page for PaCE featuring the queries used in evaluating the PaCE approach.
SPARQL Query Set
The following queries were used in the evaluations.
Queries for M_PaCE Dataset
Query 1: All statements for a given PMID (e.g., 17209178)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?st_s_inst ?st_p_inst ?st_o_inst
FROM <http://mor.nlm.nih.gov/bkr_instances_context1>
?st_s_inst ?st_p_inst ?st_o_inst .
?st_s_inst provenir:derives_from bkr:PUBMED_17209178-INST .
}
Query 2: All sources for a given statement (Lipoproteins AFFECTS Inflammatory cell)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?source_inst
FROM <http://mor.nlm.nih.gov/bkr_instances_context1>
?st_s_inst ?st_p_inst ?st_o_inst .
?st_s_inst provenir:derives_from ?source_inst .
?st_s_inst rdf:type meta:C0023820 .
?st_p_inst rdfs:subPropertyOf sn:AFFECTS .
?st_o_inst rdf:type meta:C0440752 .
}
Query 3: Frequency by source for 1 statement (Thalidomide treats disease)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?source_name count(?source_name)
FROM <http://mor.nlm.nih.gov/bkr_instances_context1>
FROM <http://mor.nlm.nih.gov/bkr_schema>
graph <http://mor.nlm.nih.gov/bkr_instances_context1> {?st_s_inst ?st_p_inst ?st_o_inst .
?source_inst rdf:type ?source_cl .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf ?st_p_cl .
?st_s_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_schema> {
} .?source_cl rdfs:label ?source_name .
?st_p_cl_top rdfs:label 'treats' .
?st_p_cl rdfs:subPropertyOf ?st_p_cl_top .
}
Query 4: Count the number of journal articles published between two dates (e.g., 2000-01-01 and 2000-12-31) for a given triple (e.g. Thalidomide treats multiple_myeloma)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT count(*)
FROM <http://mor.nlm.nih.gov/bkr_instances_context1>
FROM <http://mor.nlm.nih.gov/bkr_metadata>
graph <http://mor.nlm.nih.gov/bkr_instances_context1> {?st_s_inst ?st_p_inst ?st_o_inst .
?source_inst rdf:type ?source_cl .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf sn:TREATS .
?st_o_inst rdf:type meta:C0026764 .
?st_s_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_metadata> {}?source_inst dc:date ?source_date .
FILTER(?source_date >= xsd:date("2000-01-01") && ?source_date < xsd:date("2000-12-31"))
}
Query 5: Time profile the number of journal articles published over 10 years that mention the therapeutic use of the drug Thalidomide
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?year count(*)
FROM <http://mor.nlm.nih.gov/bkr_instances_context1>
FROM <http://mor.nlm.nih.gov/bkr_schema>
FROM <http://mor.nlm.nih.gov/bkr_metadata>
{}select (bif:year(?source_date)) as ?year
WHERE {graph <http://mor.nlm.nih.gov/bkr_instances_context1> {}?st_s_inst ?st_p_inst ?st_o_inst .
?source_inst rdf:type ?source_cl .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf sn:TREATS .
?st_o_inst rdf:type meta:C0026764 .
?st_s_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_metadata> {?source_inst dc:date ?source_date .}
} order by ?year
Queries for I_PaCE Dataset
Query 1: All statements for a given PMID (e.g., 17209178)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?st_s_inst ?st_p_inst ?st_o_inst
FROM <http://mor.nlm.nih.gov/bkr_instances_context2>
?st_s_inst ?st_p_inst ?st_o_inst .
?st_p_inst provenir:derives_from bkr:PUBMED_17209178-INST .
?st_s_inst provenir:derives_from bkr:PUBMED_17209178-INST .
}
Query 2: All sources for a given statement (Lipoproteins AFFECTS Inflammatory cell)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?source_inst
FROM <http://mor.nlm.nih.gov/bkr_instances_context2>
?st_s_inst ?st_p_inst ?st_o_inst .
?st_p_inst provenir:derives_from ?source_inst .
?st_s_inst rdf:type meta:C0023820 .
?st_p_inst rdfs:subPropertyOf sn:AFFECTS .
?st_o_inst rdf:type meta:C0440752 .
?st_s_inst provenir:derives_from ?source_inst .
}
Query 3: Frequency by source for 1 statement (Thalidomide treats disease)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?source_name count(?source_name)
FROM <http://mor.nlm.nih.gov/bkr_instances_context2>
FROM <http://mor.nlm.nih.gov/bkr_schema>
graph <http://mor.nlm.nih.gov/bkr_instances_context2> {?st_s_inst ?st_p_inst ?st_o_inst .
?source_inst rdf:type ?source_cl .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf ?st_p_cl .
?st_s_inst provenir:derives_from ?source_inst .
?st_p_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_schema> {
} .?source_cl rdfs:label ?source_name .
?st_p_cl_top rdfs:label 'treats' .
?st_p_cl rdfs:subPropertyOf ?st_p_cl_top .
}
Query 4: Count the number of journal articles published between two dates (e.g., 2000-01-01 and 2000-12-31) for a given triple (e.g. Thalidomide treats multiple_myeloma)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT count(*)
FROM <http://mor.nlm.nih.gov/bkr_instances_context2>
FROM <http://mor.nlm.nih.gov/bkr_metadata>
graph <http://mor.nlm.nih.gov/bkr_instances_context2> {?st_s_inst ?st_p_inst ?st_o_inst .
?source_inst rdf:type ?source_cl .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf sn:TREATS .
?st_o_inst rdf:type meta:C0026764 .
?st_s_inst provenir:derives_from ?source_inst .
?st_p_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_metadata> {}?source_inst dc:date ?source_date .
FILTER(?source_date >= xsd:date("2000-01-01") && ?source_date < xsd:date("2000-12-31"))
}
Query 5: Time profile the number of journal articles published over 10 years that mention the therapeutic use of the drug Thalidomide
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?year count(*)
FROM <http://mor.nlm.nih.gov/bkr_instances_context2>
FROM <http://mor.nlm.nih.gov/bkr_schema>
FROM <http://mor.nlm.nih.gov/bkr_metadata>
{}select (bif:year(?source_date)) as ?year
WHERE {graph <http://mor.nlm.nih.gov/bkr_instances_context2> {}?st_s_inst ?st_p_inst ?st_o_inst .
?source_inst rdf:type ?source_cl .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf sn:TREATS .
?st_o_inst rdf:type meta:C0026764 .
?st_s_inst provenir:derives_from ?source_inst .
?st_p_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_metadata> {?source_inst dc:date ?source_date .}
} order by ?year
Queries for E_PaCE Dataset
Query 1: All statements for a given PMID (e.g., 17209178)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?st_s_inst ?st_p_inst ?st_o_inst
FROM <http://mor.nlm.nih.gov/bkr_instances_context3>
?st_s_inst ?st_p_inst ?st_o_inst .
?st_o_inst provenir:derives_from bkr:PUBMED_17209178-INST .
?st_s_inst provenir:derives_from bkr:PUBMED_17209178-INST . ?st_p_inst provenir:derives_from bkr:PUBMED_17209178-INST .
}
Query 2: All sources for a given statement (Lipoproteins AFFECTS Inflammatory cell)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?source_inst
FROM <http://mor.nlm.nih.gov/bkr_instances_context3>
?st_s_inst ?st_p_inst ?st_o_inst .
?st_o_inst provenir:derives_from ?source_inst .
?st_s_inst rdf:type meta:C0023820 .
?st_p_inst rdfs:subPropertyOf sn:AFFECTS .
?st_o_inst rdf:type meta:C0440752 .
?st_s_inst provenir:derives_from ?source_inst .
?st_p_inst provenir:derives_from ?source_inst .
}
Query 3: Frequency by source for 1 statement (Thalidomide treats disease)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?source_name count(?source_name)
FROM <http://mor.nlm.nih.gov/bkr_instances_context3>
FROM <http://mor.nlm.nih.gov/bkr_schema>
graph <http://mor.nlm.nih.gov/bkr_instances_context3> {?st_s_inst ?st_p_inst ?st_o_inst .
?source_inst rdf:type ?source_cl .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf ?st_p_cl .
?st_s_inst provenir:derives_from ?source_inst .
?st_p_inst provenir:derives_from ?source_inst .
?st_o_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_schema> {
} .?source_cl rdfs:label ?source_name .
?st_p_cl_top rdfs:label 'treats' .
?st_p_cl rdfs:subPropertyOf ?st_p_cl_top .
}
Query 4: Count the number of journal articles published between two dates (e.g., 2000-01-01 and 2000-12-31) for a given triple (e.g. Thalidomide treats multiple_myeloma)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT count(*)
FROM <http://mor.nlm.nih.gov/bkr_instances_context3>
FROM <http://mor.nlm.nih.gov/bkr_metadata>
graph <http://mor.nlm.nih.gov/bkr_instances_context3> {?st_s_inst ?st_p_inst ?st_o_inst .
?source_inst rdf:type ?source_cl .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf sn:TREATS .
?st_o_inst rdf:type meta:C0026764 .
?st_s_inst provenir:derives_from ?source_inst .
?st_p_inst provenir:derives_from ?source_inst .
?st_o_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_metadata> {}?source_inst dc:date ?source_date .
FILTER(?source_date >= xsd:date("2000-01-01") && ?source_date < xsd:date("2000-12-31"))
}
Query 5: Time profile the number of journal articles published over 10 years that mention the therapeutic use of the drug Thalidomide
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?year count(*)
FROM <http://mor.nlm.nih.gov/bkr_instances_context3>
FROM <http://mor.nlm.nih.gov/bkr_schema>
FROM <http://mor.nlm.nih.gov/bkr_metadata>
{}select (bif:year(?source_date)) as ?year
WHERE {graph <http://mor.nlm.nih.gov/bkr_instances_context3> {}?st_s_inst ?st_p_inst ?st_o_inst .
?source_inst rdf:type ?source_cl .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf sn:TREATS .
?st_o_inst rdf:type meta:C0026764 .
?st_s_inst provenir:derives_from ?source_inst .
?st_p_inst provenir:derives_from ?source_inst .
?st_o_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_metadata> {?source_inst dc:date ?source_date .}
} order by ?year
Queries for Reification (R) Dataset
Query 1: All statements for a given PMID (e.g., 17209178)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?st_s_inst ?st_p_inst ?st_o_inst
FROM <http://mor.nlm.nih.gov/bkr_instances_reification>
?bn rdf:subject ?st_s_inst .
?bn provenir:derives_from bkr:PUBMED_17209178-INST .
?bn rdf:predicate ?st_p_inst .
?bn rdf:object ?st_o_inst .
}
Query 2: All sources for a given statement (Lipoproteins AFFECTS Inflammatory cell)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?source_inst
FROM <http://mor.nlm.nih.gov/bkr_instances_reification>
?bn rdf:subject ?st_s_inst .
?bn provenir:derives_from ?source_inst .
?bn rdf:predicate ?st_p_inst .
?bn rdf:object ?st_o_inst .
?st_s_inst rdf:type meta:C0023820 .
?st_p_inst rdfs:subPropertyOf sn:AFFECTS .
?st_o_inst rdf:type meta:C0440752 .
}
Query 3: Frequency by source for 1 statement (Thalidomide treats disease)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?source_name count(?source_name)
FROM <http://mor.nlm.nih.gov/bkr_instances_reification>
FROM <http://mor.nlm.nih.gov/bkr_schema>
graph <http://mor.nlm.nih.gov/bkr_instances_reification> {?bn rdf:subject ?st_s_inst .
?source_inst rdf:type ?source_cl .
?bn rdf:predicate ?st_p_inst .
?bn rdf:object ?st_o_inst .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf ?st_p_cl .
?st_s_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_schema> {
} .?source_cl rdfs:label ?source_name .
?st_p_cl_top rdfs:label 'treats' .
?st_p_cl rdfs:subPropertyOf ?st_p_cl_top .
}
Query 4: Count the number of journal articles published between two dates (e.g., 2000-01-01 and 2000-12-31) for a given triple (e.g. Thalidomide treats multiple_myeloma)
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT count(*)
FROM <http://mor.nlm.nih.gov/bkr_instances_reification>
FROM <http://mor.nlm.nih.gov/bkr_metadata>
graph <http://mor.nlm.nih.gov/bkr_instances_reification> {?bn rdf:subject ?st_s_inst .
?source_inst rdf:type ?source_cl .
?bn rdf:predicate ?st_p_inst .
?bn rdf:object ?st_o_inst .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf sn:TREATS .
?st_o_inst rdf:type meta:C0026764 .
?st_s_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_metadata> {}?source_inst dc:date ?source_date .
FILTER(?source_date >= xsd:date("2000-01-01") && ?source_date < xsd:date("2000-12-31"))
}
Query 5: Time profile the number of journal articles published over 10 years that mention the therapeutic use of the drug Thalidomide
PREFIX bkr: <http://mor.nlm.nih.gov/bkr/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX provenir: <http://knoesis.wright.edu/provenir/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX umls: <http://mor.nlm.nih.gov/umls/>
PREFIX meta: <http://mor.nlm.nih.gov/umls/META_>
PREFIX sn: <http://mor.nlm.nih.gov/umls/SEMNET_>
SELECT ?year count(*)
FROM <http://mor.nlm.nih.gov/bkr_instances_reification>
FROM <http://mor.nlm.nih.gov/bkr_schema>
FROM <http://mor.nlm.nih.gov/bkr_metadata>
{}select (bif:year(?source_date)) as ?year
WHERE {graph <http://mor.nlm.nih.gov/bkr_instances_reification> {}?bn rdf:subject ?st_s_inst .
?source_inst rdf:type ?source_cl .
?bn rdf:predicate ?st_p_inst .
?bn rdf:object ?st_o_inst .
?st_s_inst rdf:type meta:C0039736 .
?st_p_inst rdfs:subPropertyOf sn:TREATS .
?st_o_inst rdf:type meta:C0026764 .
?st_s_inst provenir:derives_from ?source_inst .
} .
graph <http://mor.nlm.nih.gov/bkr_metadata> {?source_inst dc:date ?source_date .}
} order by ?year
Result Set
The Evaluation results for the two phase evaluation of the PaCE approach versus the RDF reification approach can be downloaded here (in .zip format).