Shared model of clinical study design and outcome
- Giovanni Nisato
In the sections above, we explored different common ways to store and exchange clinical trial and RWD data, namely CDISC, OHDSI and FHIR respectively. They all serve a different purpose and come with different advantages and limitations. However, each model does contain similar and often identical concepts, expressed, stored and handled in different ways. If one takes a step back, there is a shared semantic model, which could greatly help align data sets coming from different sources. As interoperability is a major aspect of FAIR, so is alignment between different approaches.
The BRIDG initiative
One such effort is the BRIDG initiative, see figure 8 for the high level concept map that is used to convert to a common semantic model. For the scope of this guide, concepts related to the study are most relevant, e.g. study site, organisation, protocol, eligibility criteria, arm.
Figure 8: Taken from BRIDG High Level Concept Map | Biomedical Research Integrated Domain Group - showing the BRIDG High Level Concept Map.
BRIDG stands for Biomedical Research Integrated Domain Group and tries to map different domain data models (aka common data models or CDMs) to higher level concepts and align those via the BRIDG model. The BRIDG Domain Information Model can be searched and studied in great detail, e.g. see figure 8 for the BRIDG view for “Structured Protocol - Backbone”.
Figure 9: View of the “Structured Protocol - Backbone” in the BRIDG Browser
Table 3: Semantic mappings using NCIT to CDISC, OMOP and FHIR. Please note that OMOP tables are very patient centric and study elements are not modelled per se in the CDM.
Semantic Concept | NCIT definition | NCIT URI | CDISC domain & data element | OMOP table & data element | FHIR resource & data element |
Study Identifier | A sequence of characters used to identify, name, or characterise the study. | ODM/Study OID | ? | ResearchStudyidentifier | |
Study Name | The name applied to a scientific investigation. | NCIT_C68631 | ODM/StudyName | ? | ResearchStudyname/title |
Study Start | The official beginning of a clinical study, as specified in the clinical study report | NCIT_C142714 | SDM/StudyStart | ? | ResearchStudyperiod |
Study Site Identifier | A sequence of characters used to identify, name, or characterize the study site. | NCIT_C83081 | DM/SITEID | care sitecare_site_id | OrganizationIdentifier |
Ethnic Group | A social group characterized by a distinctive social and cultural tradition that is maintained from generation to generation… | NCIT_C16564 | DM/ETHNIC | Personethnicity_concept_id | Patientextension: us-core-ethnicity |
Sex | The assemblage of physical properties or qualities by which male is distinguished from female; the physical difference between male and female; the distinguishing peculiarity of male or female. | NCIT_C28421 | DM/Sex | Persongender_concept_id | Patientgender |
Normalisation and overlaps FHIR/OHDSI/CDISC
Besides the discussed BRDIG efforts described above, there are a few other initiatives going on trying to map between OHDSI, FHIR and CDISC which we shall mention here briefly. The IMI EHDEN project looks at the OMOP interoperability to different systems (See EHDEN roadmap). Working groups were established, e.g ODHSI/FHIR (link, OMOP2FHIR mappings gsheet) or a OMOP/CDSIC working group (link).
Also HL7 FHIR looks into mapping to other approaches (link), besides OMOP e.g. to PCORNet, i2b2/ACT. See the detailed specifications of the mappings here.
CDISC released the “FHIR to CDISC Joint Mapping Implementation Guide v1.0”, which can be found here.
Semantic integration with Semantic Web standards
Semantic integration with SemWeb standardsAs more and more systems serve data through application programmatic interface delivering JSON payloads, this opens the possibility of semantic integration by mapping the entities and objects served to a common semantic framework.
Projects such as FHIR/RDF (FHIR JSON-LD Playground ), CDISC Phuse RDF (GitHub - phuse-org/rdf.cdisc.org: PhUSE Semantic Technology Working Group CDISC Standards ) offer the possibility of building JSON-LD context file which would provide the semantic context needed to turn JSON message into a JSON-LD one. While the technology is available and grows better supported every day, the availability of an overarching semantic model/ontology that would serve the same purpose as the BRIDG model did in the UML world remains to be established.