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PennTURBO / semantic-engine

TURBO semantic engine (Drivetrain). Transforms source-dependent RDF data into a source-independent, semantically rich RDF model.
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data item part-hood shouldn't use OMOP specific terms in the valid graph specification #69

Open turbomam opened 4 years ago

turbomam commented 4 years ago

For example. @greenguy33 changed 

drivetrain:GidPartOfColumn
  a drivetrain:InstanceToTermRecipe ;
  drivetrain:multiplicity drivetrain:1-1 ;
  drivetrain:subject drivetrain:GidToBeTyped ;
  drivetrain:predicate obo:BFO_0000050 ;
  drivetrain:object drivetrain:GidColumnTerm ;
.

to use 

drivetrain:GidColumnTerm
  a drivetrain:MultiObjectDescriber ;
.
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX drivetrain: <https://github.com/PennTURBO/Drivetrain/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
insert  {
    graph drivetrain:forTVGS {
        ?recipe drivetrain:object ?modUri .
        ?modUri a drivetrain:MultiObjectDescriber .
    } 
    graph drivetrain:forSOTI {
        ?modUri drivetrain:range ?column .
    } 
}
where 
{
    graph <https://raw.githubusercontent.com/PennTURBO/Drivetrain/master/drivetrain/ontologies/turbo_valid_graph_specification.ttl> {
        ?recipe drivetrain:subject ?s ;
                drivetrain:predicate obo:BFO_0000050 ;
                drivetrain:object ?column .
    }
    graph <https://raw.githubusercontent.com/PennTURBO/Turbo-Ontology/master/ontologies/turbo_merged.owl> {
        ?column a ?t .
        ?t rdfs:subClassOf* <http://transformunify.org/ontologies/TURBO_0010409> ;
                          rdfs:label ?l .
    }
    bind(uri(concat("https://github.com/PennTURBO/Drivetrain/", replace(?l, " ", "_"))) as ?modUri)
}
turbomam commented 4 years ago

Added 90 statements. Update took 0.2s, moments ago.

https://github.com/PennTURBO/Drivetrain/forTVGS

prefix drivetrain: <https://github.com/PennTURBO/Drivetrain/> 
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 

drivetrain:DiagAboutnessAxiomDbXref_person_id_column a drivetrain:MultiObjectDescriber .
drivetrain:DiagParthoodAxiomDbXref_visit_occurrence_id_column a drivetrain:MultiObjectDescriber .
drivetrain:DiagTmd_condition_start_datetime_column a drivetrain:MultiObjectDescriber .
drivetrain:EncCridSym_visit_source_value_column a drivetrain:MultiObjectDescriber .
drivetrain:EncId_visit_occurrence_id_column a drivetrain:MultiObjectDescriber .
drivetrain:EncParticipationAxiomDbXref_person_id_column a drivetrain:MultiObjectDescriber .
drivetrain:EncStartDate_visit_start_date_column a drivetrain:MultiObjectDescriber .
drivetrain:EncTypeAxiomDbXref_visit_concept_id_column a drivetrain:MultiObjectDescriber .
drivetrain:EndDate_visit_end_date_column a drivetrain:MultiObjectDescriber .
drivetrain:Key_person_id_column a drivetrain:MultiObjectDescriber .
drivetrain:MeasAboutnessAxiomDbXref_person_id_column a drivetrain:MultiObjectDescriber .
drivetrain:MeasKeySymb_measurement_id_column a drivetrain:MultiObjectDescriber .
drivetrain:MeasMentionAxiomDbXref_measurement_source_value_column a drivetrain:MultiObjectDescriber .
drivetrain:MeasParthoodAxiomDbXref_visit_occurrence_id_column a drivetrain:MultiObjectDescriber .
drivetrain:MeasTmdPartOfQueryResult_measurement_datetime_column a drivetrain:MultiObjectDescriber .
drivetrain:MeasTypeAxiomDbXref_measurement_source_concept_id_column a drivetrain:MultiObjectDescriber .
drivetrain:MeasValspecPartOfQueryResult_value_as_number_column a drivetrain:MultiObjectDescriber .
drivetrain:MentioningProvPartOfCol_procedure_source_value_column a drivetrain:MultiObjectDescriber .
drivetrain:MulAxiomDbXref_data_column a drivetrain:MultiObjectDescriber .
drivetrain:PatKeySymb_person_source_value_column a drivetrain:MultiObjectDescriber .
drivetrain:PrecedenceAxiomDbXref_preceding_visit_occurrence_id_column a drivetrain:MultiObjectDescriber .
drivetrain:ProcKeySymbPartOfCol_procedure_occurrence_id_column a drivetrain:MultiObjectDescriber .
drivetrain:ProcParthoodAxiomDbXref_visit_occurrence_id_column a drivetrain:MultiObjectDescriber .
drivetrain:ProcParticipationAxiomDbXref_person_id_column a drivetrain:MultiObjectDescriber .
drivetrain:ProcStartDate_procedure_date_column a drivetrain:MultiObjectDescriber .
drivetrain:ProcTypeAxiomDbXref_procedure_source_concept_id a drivetrain:MultiObjectDescriber .
drivetrain:Rid_race_concept_id_column a drivetrain:MultiObjectDescriber .
drivetrain:RxAboutnessAxiomDbXref_person_id_column a drivetrain:MultiObjectDescriber .
drivetrain:RxParthoodAxiomDbXref_visit_occurrence_id_column a drivetrain:MultiObjectDescriber .
drivetrain:RxTmd_drug_exposure_start_datetime_column a drivetrain:MultiObjectDescriber .

drivetrain:DiagAboutnessAxiomDbXrefPartOfColumn drivetrain:object drivetrain:DiagAboutnessAxiomDbXref_person_id_column .
drivetrain:DiagParthoodAxiomDbXrefPartOfColumn drivetrain:object drivetrain:DiagParthoodAxiomDbXref_visit_occurrence_id_column .
drivetrain:DiagTmdPartOfColumn drivetrain:object drivetrain:DiagTmd_condition_start_datetime_column .
drivetrain:EncCridSymPartOfColumn drivetrain:object drivetrain:EncCridSym_visit_source_value_column .
drivetrain:EncIdPartOfColumn drivetrain:object drivetrain:EncId_visit_occurrence_id_column .
drivetrain:EncParticipationAxiomDbXrefPartOfColumn drivetrain:object drivetrain:EncParticipationAxiomDbXref_person_id_column .
drivetrain:EncStartDatePartOfColumn drivetrain:object drivetrain:EncStartDate_visit_start_date_column .
drivetrain:EncTypeAxiomDbXrefPartOfColumn drivetrain:object drivetrain:EncTypeAxiomDbXref_visit_concept_id_column .
drivetrain:EndDatePartOfColumn drivetrain:object drivetrain:EndDate_visit_end_date_column .
drivetrain:KeyPartOfColumn drivetrain:object drivetrain:Key_person_id_column .
drivetrain:MeasAboutnessAxiomDbXrefPartOfColumn drivetrain:object drivetrain:MeasAboutnessAxiomDbXref_person_id_column .
drivetrain:MeasKeySymbPartOfColumn drivetrain:object drivetrain:MeasKeySymb_measurement_id_column .
drivetrain:MeasMentionAxiomDbXrefPartOfColumn drivetrain:object drivetrain:MeasMentionAxiomDbXref_measurement_source_value_column .
drivetrain:MeasParthoodAxiomDbXrefPartOfColumn drivetrain:object drivetrain:MeasParthoodAxiomDbXref_visit_occurrence_id_column .
drivetrain:MeasTmdPartOfQueryResult drivetrain:object drivetrain:MeasTmdPartOfQueryResult_measurement_datetime_column .
drivetrain:MeasTypeAxiomDbXrefPartOfColumn drivetrain:object drivetrain:MeasTypeAxiomDbXref_measurement_source_concept_id_column .
drivetrain:MeasValspecPartOfQueryResult drivetrain:object drivetrain:MeasValspecPartOfQueryResult_value_as_number_column .
drivetrain:MentioningProvPartOfCol drivetrain:object drivetrain:MentioningProvPartOfCol_procedure_source_value_column .
drivetrain:MulAxiomDbXrefPartOfColumn drivetrain:object drivetrain:MulAxiomDbXref_data_column .
drivetrain:PatKeySymbPartOfColumn drivetrain:object drivetrain:PatKeySymb_person_source_value_column .
drivetrain:PrecedenceAxiomDbXrefPartOfColumn drivetrain:object drivetrain:PrecedenceAxiomDbXref_preceding_visit_occurrence_id_column .
drivetrain:ProcKeySymbPartOfCol drivetrain:object drivetrain:ProcKeySymbPartOfCol_procedure_occurrence_id_column .
drivetrain:ProcParthoodAxiomDbXrefPartOfColumn drivetrain:object drivetrain:ProcParthoodAxiomDbXref_visit_occurrence_id_column .
drivetrain:ProcParticipationAxiomDbXrefPartOfColumn drivetrain:object drivetrain:ProcParticipationAxiomDbXref_person_id_column .
drivetrain:ProcStartDatePartOfColumn drivetrain:object drivetrain:ProcStartDate_procedure_date_column .
drivetrain:ProcTypeAxiomDbXrefPartOfColumn drivetrain:object drivetrain:ProcTypeAxiomDbXref_procedure_source_concept_id .
drivetrain:RidPartOfColumn drivetrain:object drivetrain:Rid_race_concept_id_column .
drivetrain:RxAboutnessAxiomDbXrefPartOfColumn drivetrain:object drivetrain:RxAboutnessAxiomDbXref_person_id_column .
drivetrain:RxParthoodAxiomDbXrefPartOfColumn drivetrain:object drivetrain:RxParthoodAxiomDbXref_visit_occurrence_id_column .
drivetrain:RxTmdPartOfColumn drivetrain:object drivetrain:RxTmd_drug_exposure_start_datetime_column .

https://github.com/PennTURBO/Drivetrain/forSOTI

prefix drivetrain: <https://github.com/PennTURBO/Drivetrain/> 
prefix turbo: <http://transformunify.org/ontologies/> 

drivetrain:DiagAboutnessAxiomDbXref_person_id_column drivetrain:range turbo:TURBO_0010701 .
drivetrain:DiagParthoodAxiomDbXref_visit_occurrence_id_column drivetrain:range turbo:TURBO_0010704 .
drivetrain:DiagTmd_condition_start_datetime_column drivetrain:range turbo:TURBO_0010604 .
drivetrain:EncCridSym_visit_source_value_column drivetrain:range turbo:TURBO_0010455 .
drivetrain:EncId_visit_occurrence_id_column drivetrain:range turbo:TURBO_0010453 .
drivetrain:EncParticipationAxiomDbXref_person_id_column drivetrain:range turbo:TURBO_0010447 .
drivetrain:EncStartDate_visit_start_date_column drivetrain:range turbo:TURBO_0010457 .
drivetrain:EncTypeAxiomDbXref_visit_concept_id_column drivetrain:range turbo:TURBO_0010449 .
drivetrain:EndDate_visit_end_date_column drivetrain:range turbo:TURBO_0010451 .
drivetrain:Key_person_id_column drivetrain:range turbo:TURBO_0010442 .
drivetrain:MeasAboutnessAxiomDbXref_person_id_column drivetrain:range turbo:TURBO_0010483 .
drivetrain:MeasKeySymb_measurement_id_column drivetrain:range turbo:TURBO_0010482 .
drivetrain:MeasMentionAxiomDbXref_measurement_source_value_column drivetrain:range turbo:TURBO_0010487 .
drivetrain:MeasParthoodAxiomDbXref_visit_occurrence_id_column drivetrain:range turbo:TURBO_0010486 .
drivetrain:MeasTmdPartOfQueryResult_measurement_datetime_column drivetrain:range turbo:TURBO_0010484 .
drivetrain:MeasTypeAxiomDbXref_measurement_source_concept_id_column drivetrain:range turbo:TURBO_0010488 .
drivetrain:MeasValspecPartOfQueryResult_value_as_number_column drivetrain:range turbo:TURBO_0010411 .
drivetrain:MentioningProvPartOfCol_procedure_source_value_column drivetrain:range turbo:TURBO_0010470 .
drivetrain:MulAxiomDbXref_data_column drivetrain:range turbo:TURBO_0010423 .
drivetrain:PatKeySymb_person_source_value_column drivetrain:range turbo:TURBO_0010444 .
drivetrain:PrecedenceAxiomDbXref_preceding_visit_occurrence_id_column drivetrain:range turbo:TURBO_0010459 .
drivetrain:ProcKeySymbPartOfCol_procedure_occurrence_id_column drivetrain:range turbo:TURBO_0010465 .
drivetrain:ProcParthoodAxiomDbXref_visit_occurrence_id_column drivetrain:range turbo:TURBO_0010466 .
drivetrain:ProcParticipationAxiomDbXref_person_id_column drivetrain:range turbo:TURBO_0010464 .
drivetrain:ProcStartDate_procedure_date_column drivetrain:range turbo:TURBO_0010472 .
drivetrain:ProcTypeAxiomDbXref_procedure_source_concept_id drivetrain:range turbo:TURBO_0010469 .
drivetrain:Rid_race_concept_id_column drivetrain:range turbo:TURBO_0010441 .
drivetrain:RxAboutnessAxiomDbXref_person_id_column drivetrain:range turbo:TURBO_0010702 .
drivetrain:RxParthoodAxiomDbXref_visit_occurrence_id_column drivetrain:range turbo:TURBO_0010703 .
drivetrain:RxTmd_drug_exposure_start_datetime_column drivetrain:range turbo:TURBO_0010706 .
turbomam commented 4 years ago

Additionally, need to remove existing drivetrain:object triples where the object is an OMOP column term.

Will do manually to preserve line ordering in file (SPARQL update and re-save -> random ordering)