Difference between revisions of "ProvenanceContextEntity"

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The following queries were used in the evaluations.
 
The following queries were used in the evaluations.
  
−
=== 1. Queries for M_PaCE Dataset ===
+
=== Queries for M_PaCE Dataset ===
 
'''Query 1''': All statements for a given PMID (e.g., 17209178)
 
'''Query 1''': All statements for a given PMID (e.g., 17209178)
  
Line 111: Line 111:
 
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>><br/>
+
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 120: Line 120:
 
graph <nowiki><http://mor.nlm.nih.gov/bkr_instances_context1></nowiki> {<blockquote>
 
graph <nowiki><http://mor.nlm.nih.gov/bkr_instances_context1></nowiki> {<blockquote>
 
?st_s_inst ?st_p_inst ?st_o_inst .<br/>
 
?st_s_inst ?st_p_inst ?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
 +
 +
=== Queries for I_PaCE 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_context2></nowiki> <br/>
 +
WHERE {<blockquote>
 +
        ?st_s_inst ?st_p_inst ?st_o_inst .<br/>
 +
?st_s_inst provenir:derives_from bkr:PUBMED_17209178-INST . <br/>
 +
?st_p_inst 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_context2></nowiki><br/>
 +
WHERE {<blockquote>
 +
?st_s_inst ?st_p_inst ?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/>
 +
?st_s_inst provenir:derives_from ?source_inst .<br/>
 +
?st_p_inst 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_context2></nowiki><br/>
 +
FROM <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki><br/>
 +
WHERE {<blockquote>
 +
graph <nowiki><http://mor.nlm.nih.gov/bkr_instances_context2></nowiki> {<blockquote>
 +
?st_s_inst ?st_p_inst ?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/>
 +
                ?st_p_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_context2></nowiki><br/>
 +
FROM <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki><br/>
 +
WHERE {<blockquote>
 +
graph <nowiki><http://mor.nlm.nih.gov/bkr_instances_context2></nowiki> {<blockquote>
 +
?st_s_inst ?st_p_inst ?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/>
 +
                ?st_p_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_context2></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_context2></nowiki> {<blockquote>
 +
?st_s_inst ?st_p_inst ?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/>
 +
                                ?st_p_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
 +
 +
=== Queries for E_PaCE 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_context3></nowiki> <br/>
 +
WHERE {<blockquote>
 +
        ?st_s_inst ?st_p_inst ?st_o_inst .<br/>
 +
?st_s_inst provenir:derives_from bkr:PUBMED_17209178-INST .
 +
        ?st_p_inst provenir:derives_from bkr:PUBMED_17209178-INST .
 +
?st_o_inst 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_context3></nowiki><br/>
 +
WHERE {<blockquote>
 +
?st_s_inst ?st_p_inst ?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/>
 +
?st_s_inst provenir:derives_from ?source_inst .<br/>
 +
        ?st_p_inst provenir:derives_from ?source_inst .<br/>
 +
?st_o_inst 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_context3></nowiki><br/>
 +
FROM <nowiki><http://mor.nlm.nih.gov/bkr_schema></nowiki><br/>
 +
WHERE {<blockquote>
 +
graph <nowiki><http://mor.nlm.nih.gov/bkr_instances_context3></nowiki> {<blockquote>
 +
?st_s_inst ?st_p_inst ?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/>
 +
                ?st_p_inst provenir:derives_from ?source_inst .<br/>
 +
?st_o_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_context3></nowiki><br/>
 +
FROM <nowiki><http://mor.nlm.nih.gov/bkr_metadata></nowiki><br/>
 +
WHERE {<blockquote>
 +
graph <nowiki><http://mor.nlm.nih.gov/bkr_instances_context3></nowiki> {<blockquote>
 +
?st_s_inst ?st_p_inst ?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/>
 +
                ?st_p_inst provenir:derives_from ?source_inst .<br/>
 +
?st_o_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_context3></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_context3></nowiki> {<blockquote>
 +
?st_s_inst ?st_p_inst ?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/>
 +
                                ?st_p_inst provenir:derives_from ?source_inst .<br/>
 +
                ?st_o_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
 +
 +
=== 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_s_inst rdf:type meta:C0039736 .<br/>
 
?st_p_inst rdfs:subPropertyOf sn:TREATS .<br/>
 
?st_p_inst rdfs:subPropertyOf sn:TREATS .<br/>
Line 135: Line 544:
  
 
== 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

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>

WHERE {

 ?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>

WHERE {

?st_s_inst ?st_p_inst ?st_o_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_context1>
FROM <http://mor.nlm.nih.gov/bkr_schema>

WHERE {
graph <http://mor.nlm.nih.gov/bkr_instances_context1> {

?st_s_inst ?st_p_inst ?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 .

?source_inst rdf:type ?source_cl .

} .

graph <http://mor.nlm.nih.gov/bkr_schema> {

?source_cl rdfs:label ?source_name .
?st_p_cl rdfs:subPropertyOf ?st_p_cl_top .

?st_p_cl_top rdfs:label 'treats' .
} .

}

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>

WHERE {
graph <http://mor.nlm.nih.gov/bkr_instances_context1> {

?st_s_inst ?st_p_inst ?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 .

?source_inst rdf:type ?source_cl .

} .

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>

where {
{

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 .
?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 .

?source_inst rdf:type ?source_cl .

} .

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>

WHERE {

 ?st_s_inst ?st_p_inst ?st_o_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_context2>

WHERE {

?st_s_inst ?st_p_inst ?st_o_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_context2>
FROM <http://mor.nlm.nih.gov/bkr_schema>

WHERE {
graph <http://mor.nlm.nih.gov/bkr_instances_context2> {

?st_s_inst ?st_p_inst ?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 .
 ?st_p_inst provenir:derives_from ?source_inst .

?source_inst rdf:type ?source_cl .

} .

graph <http://mor.nlm.nih.gov/bkr_schema> {

?source_cl rdfs:label ?source_name .
?st_p_cl rdfs:subPropertyOf ?st_p_cl_top .

?st_p_cl_top rdfs:label 'treats' .
} .

}

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>

WHERE {
graph <http://mor.nlm.nih.gov/bkr_instances_context2> {

?st_s_inst ?st_p_inst ?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 .
 ?st_p_inst provenir:derives_from ?source_inst .

?source_inst rdf:type ?source_cl .

} .

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>

where {
{

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 .
?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 .

?source_inst rdf:type ?source_cl .

} .

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>

WHERE {

 ?st_s_inst ?st_p_inst ?st_o_inst .
?st_s_inst provenir:derives_from bkr:PUBMED_17209178-INST .  ?st_p_inst provenir:derives_from bkr:PUBMED_17209178-INST .

?st_o_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>

WHERE {

?st_s_inst ?st_p_inst ?st_o_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 .

?st_o_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>

WHERE {
graph <http://mor.nlm.nih.gov/bkr_instances_context3> {

?st_s_inst ?st_p_inst ?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 .
 ?st_p_inst provenir:derives_from ?source_inst .
?st_o_inst provenir:derives_from ?source_inst .

?source_inst rdf:type ?source_cl .

} .

graph <http://mor.nlm.nih.gov/bkr_schema> {

?source_cl rdfs:label ?source_name .
?st_p_cl rdfs:subPropertyOf ?st_p_cl_top .

?st_p_cl_top rdfs:label 'treats' .
} .

}

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>

WHERE {
graph <http://mor.nlm.nih.gov/bkr_instances_context3> {

?st_s_inst ?st_p_inst ?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 .
 ?st_p_inst provenir:derives_from ?source_inst .
?st_o_inst provenir:derives_from ?source_inst .

?source_inst rdf:type ?source_cl .

} .

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>

where {
{

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 .
?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 .

?source_inst rdf:type ?source_cl .

} .

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>

WHERE {

 ?bn rdf:subject ?st_s_inst .
 ?bn rdf:predicate ?st_p_inst .
 ?bn rdf:object ?st_o_inst .

?bn 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_reification>

WHERE {

?bn rdf:subject ?st_s_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 .

?bn 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_reification>
FROM <http://mor.nlm.nih.gov/bkr_schema>

WHERE {
graph <http://mor.nlm.nih.gov/bkr_instances_reification> {

?bn rdf:subject ?st_s_inst .
?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 .

?source_inst rdf:type ?source_cl .

} .

graph <http://mor.nlm.nih.gov/bkr_schema> {

?source_cl rdfs:label ?source_name .
?st_p_cl rdfs:subPropertyOf ?st_p_cl_top .

?st_p_cl_top rdfs:label 'treats' .
} .

}

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>

WHERE {
graph <http://mor.nlm.nih.gov/bkr_instances_reification> {

?bn rdf:subject ?st_s_inst .
?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 .

?source_inst rdf:type ?source_cl .

} .

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>

where {
{

select (bif:year(?source_date)) as ?year

WHERE {
graph <http://mor.nlm.nih.gov/bkr_instances_reification> {

?bn rdf:subject ?st_s_inst .
 ?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 .

?source_inst rdf:type ?source_cl .

} .

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).

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