Web services for data warehouses: OMOP and PCORnet on i2b2. (30th July 2018)

• Record Type: Journal Article
• Authors: Klann, Jeffrey G; Phillips, Lori C; Herrick, Christopher; Joss, Matthew A H; Wagholikar, Kavishwar B; Murphy, Shawn N
• Is Part Of: Journal of the American Medical Informatics Association. Volume 25:Number 10(2018)
• Page Start: 1331
• Page End: 1338
• Publication Date: 2018-07-30
• Subjects: medical informatics -- data integration -- data models -- ontology-driven data representation -- Patient Centered Outcomes Research Institute -- Observational Health Data Sciences and Informatics -- Informatics for Integrating Biology and the Bedside; Medical informatics -- Periodicals; Information Services -- Periodicals; Medical Informatics -- Periodicals; Médecine -- Informatique -- Périodiques; Informatica; Geneeskunde; Informatique médicale; Computer network resources; Electronic journals; 610.285
• DOI: 10.1093/jamia/ocy093
• Languages: English
• ISSNs: 1067-5027

Abstract

Abstract: Objective: Healthcare organizations use research data models supported by projects and tools that interest them, which often means organizations must support the same data in multiple models. The healthcare research ecosystem would benefit if tools and projects could be adopted independently from the underlying data model. Here, we introduce the concept of a reusable application programming interface (API) for healthcare and show that the i2b2 API can be adapted to support diverse patient-centric data models. Materials and Methods: We develop methodology for extending i2b2's pre-existing API to query additional data models, using i2b2's recent "multi-fact-table querying" feature. Our method involves developing data-model-specific i2b2 ontologies and mapping these to query non-standard table structure. Results: We implement this methodology to query OMOP and PCORnet models, which we validate with the i2b2 query tool. We implement the entire PCORnet data model and a five-domain subset of the OMOP model. We also demonstrate that additional, ancillary data model columns can be modeled and queried as i2b2 "modifiers." Discussion: i2b2's REST API can be used to query multiple healthcare data models, enabling shared tooling to have a choice of backend data stores. This enables separation between data model and software tooling for some of the more popular open analytic data models in healthcare. Conclusion: This methodology immediately allows querying OMOP and PCORnet using the i2b2 API. It is released as an open-source set of Docker images, and also on the i2b2 community wiki.