caDSR RDF Graphs - fhircat/FHIRCat GitHub Wiki

Display Object Class Main Concept

PREFIX cmdr: <http://cbiit.nci.nih.gov/caDSR#>
PREFIX isomdr: <http://www.iso.org/11179/MDR#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

CONSTRUCT {
  ?DE isomdr:Object_Class_Main_Concept ?main_concept . 
} WHERE {
	?DE isomdr:Object_Class ?object_class .
    ?object_class cmdr:main_concept ?main_concept .
  
} LIMIT 100

Display Permitted Value Main Concept

PREFIX isomdr: <http://www.iso.org/11179/MDR#>
PREFIX cmdr: <http://cbiit.nci.nih.gov/caDSR#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
construct {
    ?DE isomdr:permitted_value_main_concept ?main_concept .
} where { 
        ?DE isomdr:permitted_value ?permitted_value .
        ?permitted_value cmdr:has_concept ?concept .
        ?concept cmdr:main_concept ?main_concept .
        ?main_concept rdfs:label ?label .



} limit 100 

Data Elements having object class defined in BRIDG model

SPARQL Query Group by Label

PREFIX isomdr: <http://www.iso.org/11179/MDR#>
PREFIX cmdr: <http://cbiit.nci.nih.gov/caDSR#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
select distinct ?label (count(?label) as ?count) where { 

    ?DE isomdr:Object_Class ?object_class .
    ?object_class cmdr:main_concept ?concept .
    ?concept ncit:A8 ncit:C159501 .
    ?concept ncit:P106 ?semantic_type .
    ?concept rdfs:label ?label .
 

} group by ?label order by DESC(?count)

Results

?label	?count
Person	1453
Activity	1207
Adverse Event	540
Outcome	454
Biospecimen	400
Document	210
Clinical Study Protocol	205
Material	176
Intervention or Procedure	166
Professional Organization or Group	128
Dose	123
Identifier	106
Address	90
Pharmacologic Substance	90
Medical Device	89
Healthcare Facility	86
Investigator	85
Description	81
Summary	78
Quantity	70
Product	66
Name	54
Laboratory	50
Research Personnel	44
Age	40
Text	37
Principal Investigator	36
Research Resource	34
Study Subject	34
Organism	33
Health Care Provider	32
Reference	29
Postal Address	19
Study Site	19
Organism Strain	17
Concomitant Agent	16
Service	16
Accession Number	15
Birth Date	12
Comment	12
Protocol Treatment Arm	11
Message	10
Duration	9
Subject	9
Capacity	8
Package	8
Performing Laboratory	8
Clinical Trial Epoch	7
Concept Descriptor	7
Manufacturer	7
Performed Clinical Study Activity	7
Animal	6
Author	6
Signature	6
Keyword	5
Performed By	5
Place	5
Uniform Resource Locator	5
Funding	4
Adverse Event Outcome	3
Code	3
Evaluator	3
Person Name	3
Purpose	3
Boolean	2
Clinical Research Associate	2
Distributor	2
Food or Food Product	2
Lot Number	2
Telecommunication Address	2
Clinical Trials Cooperative Group	1
Enhancement Description	1
Performed Imaging	1
Performed Specimen Collection	1
Probability	1
Reviewable Unit	1
Study Activity	1
Study Site Personnel	1
Title	1
Treating Site	1

SPARQL Query Group by Semantic Type

PREFIX isomdr: <http://www.iso.org/11179/MDR#>
PREFIX cmdr: <http://cbiit.nci.nih.gov/caDSR#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
select distinct ?semantic_type (count(?semantic_type) as ?count) where { 

    ?DE isomdr:Object_Class ?object_class .
    ?object_class cmdr:main_concept ?concept .
    ?concept ncit:A8 ncit:C159501 .
    ?concept ncit:P106 ?semantic_type .
    ?concept rdfs:label ?label .
 

} group by ?semantic_type order by DESC(?count)

Results

?semantic_type	?count
Human	1461
Activity	1224
Finding	997
Intellectual Product	721
Body Substance	400
Professional or Occupational Group	332
Conceptual Entity	204
Substance	176
Health Care Activity	166
Spatial Concept	114
Pharmacologic Substance	90
Medical Device	89
Health Care Related Organization	87
Quantitative Concept	79
Entity	66
Idea or Concept	66
Organization	58
Organism	50
Manufactured Object	45
Functional Concept	43
Organism Attribute	43
Classification	36
Temporal Concept	21
Research Activity	20
Qualitative Concept	15
Occupational Activity	7
Animal	6
Governmental or Regulatory Activity	4
Food	2