Making Study Populations Visible through Knowledge Graphs

A website to navigate resources open-sourced via the associated ISWC 2019 paper



*This image was taken from: https://www.policyschool.ca/background-banner/health-policy/health-banner/

Concept Map Ontology File Ontologies Reused

Conceptual Model

An overview of the main classes and their property associations. Some property associations exist only upon representation of the Table 1 data, and so we highlight instances in pink

Ontologies

    Study Cohort Ontology (SCO)

    Link: https://raw.githubusercontent.com/tetherless-world/study-cohort-ontology/master/Ontologies/studycohort.owl

    View the ontology documentation at: https://tetherless-world.github.io/study-cohort-ontology/WidocoDocumentation/doc/index-en.html

    Primary Classes and Definitions

    1. Research Study
      • Definition: A scientific investigation that involves testing a hypothesis
      • Immediate Superclass: None
      • Example: "10-Year Follow-up of Intensive Glucose Control in Type 2 Diabetes"
      • Reused From: Hasco
    2. Clinical Trial
      • Definition: A prospective study designed to evaluate whether one or more interventions are associated with an outcome
      • Immediate Superclass: Research Study
      • Example: "10-Year Follow-up of Intensive Glucose Control in Type 2 Diabetes"
      • Reused From: National Cancer Institute Thesarus (NCIT)
    3. Cohort
      • Definition: A cohort is the group of subjects enrolled in a study
      • Immediate Superclass: None
      • Example: Randomized Cohort in "10-Year Follow-up of Intensive Glucose Control in Type 2 Diabetes"
      • Reused From: The Statistical Methods Ontology (STATO)
    4. Study Arm
      • Definition: A group or subgroup of participants in a clinical trial that receives a specific intervention/treatment, or no intervention, according to the trial's protocol
      • Immediate Superclass: Cohort
      • Example: Metformin Conventional Therapy Arm
      • Reused From: None
    5. Study Subject
      • Definition: A person who receives medical attention, care, or treatment, or who is registered with medical professional or institution with the purpose to receive medical care when necessary
      • Immediate Superclass: None
      • Example: African American Male Subject in "10-Year Follow-up of Intensive Glucose Control in Type 2 Diabetes"
      • Reused From: SemanticScience Integrated Ontology (SIO)
    6. Study Intervention
      • Definition: A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available
      • Immediate Superclass: None
      • Example: Metformin
      • Reused From: ProvCaRe
    7. Subject Characteristic
      • Definition: Property that summarizes important attributes of the participants enrolled in a study
      • Immediate Superclass: None
      • Example: Age
      • Reused From: None
    8. Statistical Measure
      • Definition: a standard unit used to express the size, amount, or degree of something
      • Immediate Superclass: None
      • Example: Mean
      • Reused From: ProvCaRe

    Accompanying Suite of Ontologies

Ontologies Reused

We group the ontologies we reuse by the purpose and the use-cases they are intended to serve, as vocabularies for.

Study Design Ontologies

Medical Ontologies

Mid-Level Ontologies

Statistical Ontologies

MIREOT Script

Below we present a small Python script that can be used to fetch the child and parent hierarchy for a class, given its IRI. This script pulls in all the axioms defined on the classes as well. We leverage the powerful constructs of the SPARQL DESCRIBE functionality to achieve this. This script outputs the RDF/XML version of the subset class tree.

 from SPARQLWrapper import *
from owlready2 import *
import os

sparql_endpoint = "http://localhost:9999/bigdata/sparql"

query = '''
describe ?child ?superParent 
where {
   hint:Query hint:describeMode "CBD".
  ?child rdfs:subClassOf* ?super .
  ?super rdfs:subClassOf* ?superParent .
}
values ?super {<http://hadatac.org/ont/chear#ATIDU>}
'''

sparql_wrapper = SPARQLWrapper(sparql_endpoint)
sparql_wrapper.setQuery(query)
sparql_wrapper.setReturnFormat(RDF)
results = sparql_wrapper.query().convert()
results.serialize('output.owl', format="pretty-xml")
print("Writing results to a rdf-xml file")

Ontology Prefixes

Prefix Links
rdf Resource Description Framework
rdfs RDF Schema
owl Web Ontology Language
xsd XML Schema Definition
dct Dublin Core Term
skos Simple Knowledge Organization System
sco Study Cohort Ontology
chear Children’s Health Exposure Analysis Resource
hasco Human-Aware Science Ontology
fibo-fnd-utl-av Financial Industry Business Ontology
sio SemanticScience Integrated Ontology
obo OBO Foundry
stato The Statistical Methods Ontolgy
uo Units of Measurement Ontology
pato Human Phenotypic Quality Ontology
ncit National Cancer Institute Thesarus
provcare Provenance for Clinical + Healthcare Research
ocre Ontology of Clinical Research
</ul>