Getting Started with GDI Queries

This topic provides details about the structure to use when writing GDI queries. It focuses on the properties that are common to all types of data sources. It also includes example queries that demonstrate the data integration capabilities for different types of sources.

• GDI Query Syntax
• GDI Query Examples

GDI Query Syntax

The following query syntax shows the structure of a GDI query. The clauses, patterns, and placeholders that are links are described below.

# PREFIX Clause
PREFIX s:     <http://cambridgesemantics.com/ontologies/DataToolkit#>
PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs:  <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd:   <http://www.w3.org/2001/XMLSchema#>
PREFIX owl:   <http://www.w3.org/2002/07/owl#>
PREFIX anzo:  <http://openanzo.org/ontologies/2008/07/Anzo#>
PREFIX zowl:  <http://openanzo.org/ontologies/2009/05/AnzoOwl#>
PREFIX dc:    <http://purl.org/dc/elements/1.1/>

# Result Clause
{ 
   [ GRAPH ${targetGraph} { ] 
   triple_patterns
 [ } ]
}
[ ${usingSources} ]

WHERE
{
   # SERVICE Clause: Include the following service call when reading or inserting data.
    SERVICE [ TOPDOWN ] <http://cambridgesemantics.com/services/DataToolkit>

   # View SERVICE Clause: Or use the service call below when constructing a view.
    SERVICE <http://cambridgesemantics.com/services/DataToolkitView>(${targetGraph})

    { 
      ?data a s:source_type ; 
# Based on the source_type, additional connection and input parameters are
# available. The options below are valid for all sources. For source-related
# options, see Source-Specific Properties in the GDI property reference. 
        s:url "string" ;
        [ s:username "string" ; ]
        [ s:password "string" ; ]
        [ s:timeout int ; ]
        [ s:batching boolean | int ; ]
        [ s:paging [ pagination_options ; ]
        [ s:concurrency int | [ list_of_properties ] ; ]
        [ s:rate int | "string" ; ]
        [ s:locale "string" ; ]
        [ s:sampling int ; ]
        [ s:selector "string" | [ list ] ; ]
        [ s:model "string" ; ]
        [ s:key ("string") ; ]
        [ s:reference [ s:model "string" ; s:using ("string") ]
        [ s:formats [ datatype_formatting_options ] ; ]
        [ s:normalize boolean | [ normalization_rules ] ; ]
        [ s:count ?variable ; ]
        [ s:offset int ; ]
        [ s:limit int ; ]
        # Mapping variables
        ?mapping_variable ( [ "binding" ] [ datatype ] [ "datetime_format" ] ) ;
        ... ;
        .
     # Additional clauses such as BIND, VALUES, FILTER
   }
}

PREFIX s:      <http://cambridgesemantics.com/ontologies/DataToolkit#>
PREFIX rdf:    <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs:   <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd:    <http://www.w3.org/2001/XMLSchema#>
PREFIX owl:    <http://www.w3.org/2002/07/owl#>
PREFIX anzo:   <http://openanzo.org/ontologies/2008/07/Anzo#>
PREFIX zowl:   <http://openanzo.org/ontologies/2009/05/AnzoOwl#>
PREFIX dc:     <http://purl.org/dc/elements/1.1/>

?data a s:DbSource ;
  s:url "{{@db.eca4bfa83481f3638b93ab5fdf93ff9a.url}}" ;
  s:username "{{@db.eca4bfa83481f3638b93ab5fdf93ff9a.user}}" ;
  s:password "{{@db.eca4bfa83481f3638b93ab5fdf93ff9a.password}}" ;

s:concurrency [
  s:limit 24 ;
  s:nodes 4 ;
  s:executorsPerNode 8 ;
] ;

s:rate "90/minute" ;
s:rate "90 per minute" ;
s:rate "200000 every week" ;
s:rate "10000 every 6 hours" ;

GDI Query Examples

The query below reads data from a sample HTTP source that compiles worldwide weather statistics. The source has several models available for retrieving data that is current, daily, historical, etc. To target current data, the query includes s:selector "currently" as an input parameter. In addition, the query demonstrates the use of the "topdown" functionality, where the query sends values to the source to narrow the results. The query includes the TOPDOWN keyword in the GDI service call, and the VALUES clause specifies the latitude and longitude values for the cities to return data for. In addition, since this sample source requires parameters to be specified in the connection URL, the s:url value includes ?lat and ?long as parameters as part of the value.

PREFIX s:      <http://cambridgesemantics.com/ontologies/DataToolkit#>
PREFIX rdf:    <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs:   <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd:    <http://www.w3.org/2001/XMLSchema#>
PREFIX owl:    <http://www.w3.org/2002/07/owl#>
PREFIX anzo:   <http://openanzo.org/ontologies/2008/07/Anzo#>
PREFIX zowl:   <http://openanzo.org/ontologies/2009/05/AnzoOwl#>
PREFIX dc:     <http://purl.org/dc/elements/1.1/>
PREFIX ex:     <http://example.org/ontologies/City#>

SELECT  
	?city ?state ?summary ?temp ?rainChance
	?humidity ?pressure ?windSpeed
WHERE
{
	SERVICE TOPDOWN <http://cambridgesemantics.com/services/DataToolkit>
    {
	  ?data a s:HttpSource ;
	  s:url "https://sampleEndpoint.com/forecast/{{?lat}},{{?long}}" ;
	  s:selector "currently" ;
	  ?lat ("latitude") ;
	  ?long ("longitude") ;
	  ?temp ("temperature") ;
	  ?rainChance ( "precipProbability" ) ;
	  ?humidity () ;
	  ?pressure () ;
	  ?windSpeed () .
    }
    VALUES( ?city ?state ?lat ?long )
    {
	  ( "Lakeway" "TX" 30.374563 -97.975892 )
	  ( "Boston" "MA" 42.358043 -71.060415 )
	  ( "Seattle" "WA" 47.590720 -122.307053 )
	  ( "Chicago" "IL" 41.837741 -87.823296 )
	  ( "Hilo" "HI" 19.702040 -155.090312 )
    }
}
ORDER BY ?city

The query returns the following results:

city    | state | summary       | temp  | rainChance | humidity | pressure | windSpeed
--------+-------+---------------+-------+------------+----------+----------+-----------
Boston  | MA    | Overcast      | 79.81 |          0 |      0.6 |   1018.7 |      7.71
Chicago | IL    | Clear         |  81.7 |          0 |     0.52 |   1021.1 |      5.13
Hilo    | HI    | Partly Cloudy |  72.6 |       0.13 |     0.79 |   1018.6 |      4.86
Lakeway | TX    | Partly Cloudy | 92.43 |          0 |     0.48 |   1013.3 |     10.85
Seattle | WA    | Mostly Cloudy | 61.82 |          0 |     0.76 |   1018.2 |      4.57
5 rows

The example below ingests data into a data layer from a database source using an INSERT query in a Direct Load Step.

PREFIX s:       <http://cambridgesemantics.com/ontologies/DataToolkit#>
PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
PREFIX owl:     <http://www.w3.org/2002/07/owl#>
PREFIX anzo:    <http://openanzo.org/ontologies/2008/07/Anzo#>
PREFIX zowl:    <http://openanzo.org/ontologies/2009/05/AnzoOwl#>
PREFIX dc:      <http://purl.org/dc/elements/1.1/>
PREFIX :        <http://example.com/ontologies/kl_hosp#>

INSERT
{
	GRAPH ${targetGraph}
    {
	?InputEvent_cv a :InputEvent_cv ;
	    :row_id ?row_id ;
	    :subject_id ?subject_id ;
	    :hadm_id ?hadm_id ;
	    :icustay_id ?icustay_id ;
	    :charttime ?charttime ;
	    :itemid ?itemid ;
	    :amount ?amount ;
	    :amountuom ?amountuom ;
	    :rate ?rate ;
	    :rateuom ?rateuom ;
	    :storetime ?storetime ;
	    :cgid ?cgid ;
	    :orderid ?orderid ;
	    :linkorderid ?linkorderid ;
	    :stopped ?stopped ;
	    :newbottle ?newbottle ;
	    :originalamount ?originalamount ;
	    :originalamountuom ?originalamountuom ;
	    :originalroute ?originalroute ;
	    :originalrate ?originalrate ;
	    :originalrateuom ?originalrateuom ;
	    :originalsite ?originalsite .
    }
}
WHERE
{
	SERVICE <http://cambridgesemantics.com/services/DataToolkit>
    {
	?data a s:DbSource ;
	    s:url "{{@db.eca4bfa83481f3638b93ab5fdf93ff9a.url}}" ;
            s:username "{{@db.eca4bfa83481f3638b93ab5fdf93ff9a.user}}"
            s:password "{{@db.eca4bfa83481f3638b93ab5fdf93ff9a.password}}"
	    s:selector "kl_hosp_schema.inputevents_cv" ;
	    ?row_id (xsd:int) ;
	    ?subject_id (xsd:int) ;
	    ?hadm_id (xsd:int) ;
	    ?icustay_id (xsd:int) ;
	    ?charttime (xsd:dateTime) ;
	    ?itemid (xsd:int) ;
	    ?amount (xsd:float) ;
	    ?amountuom (xsd:string) ;
	    ?rate (xsd:float) ;
	    ?rateuom (xsd:string) ;
	    ?storetime (xsd:dateTime) ;
	    ?cgid (xsd:int) ;
	    ?orderid (xsd:int) ;
	    ?linkorderid (xsd:int) ;
	    ?stopped (xsd:string) ;
	    ?newbottle (xsd:int) ;
	    ?originalamount (xsd:float) ;
	    ?originalamountuom (xsd:string) ;
	    ?originalroute (xsd:string) ;
	    ?originalrate (xsd:float) ;
	    ?originalrateuom (xsd:string) ;
	    ?originalsite (xsd:string) ;
	BIND(IRI("http://example.com/inputevent_cv/{{?row_id}}") AS ?InputEvent_cv)
	BIND(IRI("http://example.com/patients/{{?subject_id}}") AS ?patient)
	BIND(IRI("http://example.com/admissions/{{?hadm_id}}") AS ?admission) 
    }
}

The following query ingests airport-related data from a CSV file.

PREFIX s:       <http://cambridgesemantics.com/ontologies/DataToolkit#>
PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#>
PREFIX owl:     <http://www.w3.org/2002/07/owl#>
PREFIX anzo:    <http://openanzo.org/ontologies/2008/07/Anzo#>
PREFIX zowl:    <http://openanzo.org/ontologies/2009/05/AnzoOwl#>
PREFIX dc:      <http://purl.org/dc/elements/1.1/>

INSERT 
{
  GRAPH ${targetGraph}
  { 
   ?code a <http://anzograph.com/airport> ;
      <http://anzograph.com/airport/name> ?name ;
      <http://anzograph.com/airport/city> ?city ;
      <http://anzograph.com/airport/state> ?state ;
      <http://anzograph.com/airport/latitude> ?lat;
      <http://anzograph.com/airport/longitude> ?long.
  }
}
WHERE
{
	SERVICE <http://cambridgesemantics.com/services/DataToolkit>
    {
	?data a s:FileSource ;
          s:url "/opt/shared-files/airports.csv" ;
          ?iata_code ("IATA_CODE" xsd:string) ;
          ?name ("AIRPORT" xsd:string) ;
          ?city ("CITY" xsd:string) ;
          ?state ("STATE" xsd:string) ;
          ?lat ("LATITUDE" xsd:double) ;
          ?long ("LONGITUDE" xsd:double).
	BIND(IRI("http://anzograph.com/airport/{{?iata_code}}") as ?code)
    }
}

The query below creates a view of a database source.

PREFIX s:    <http://cambridgesemantics.com/ontologies/DataToolkit#>
PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd:  <http://www.w3.org/2001/XMLSchema#>
PREFIX owl:  <http://www.w3.org/2002/07/owl#>
PREFIX anzo: <http://openanzo.org/ontologies/2008/07/Anzo#>
PREFIX zowl: <http://openanzo.org/ontologies/2009/05/AnzoOwl#>
PREFIX dc:   <http://purl.org/dc/elements/1.1/>
PREFIX ont:  <http://cambridgesemantics.com/ont/autogen/Rh/MIMIC-III-Data_Source/mimic_iii_schema#>

CONSTRUCT 
{
   ?caregiversURI a ont:caregivers ;
      ont:caregivers_cgid ?cgid ;
      ont:caregivers_description ?description ;
      ont:caregivers_label ?label .
}
WHERE
{
   GRAPH ?g 
   {
      SERVICE <http://cambridgesemantics.com/services/DataToolkitView>(${targetGraph}) {
    {
        ?data a s:DbSource ;
          s:url "{{@db.eca4bfa83481f3638b93ab5fdf93dd9a.url}}" ;
          s:username "{{@db.eca4bfa83481f3638b93ab5fdf93dd9a.user}}"
          s:password "{{@db.eca4bfa83481f3638b93ab5fdf93dd9a.password}}"
          s:selector "mimic_iii_schema.caregivers" ;
          ?row_id (xsd:int) ;
          ?cgid (xsd:int) ;
          ?label (xsd:string) ;
          ?description (xsd:string) .
      BIND(IRI("http://cambridgesemantics.com/class/caregivers/{{?row_id}}") AS ?caregiversURI) }
    }
  }
}

Related Topics

• General GDI Concepts and Usage
• Generating a Graph and Ontology with a Direct Load Step