ArticleJournal of the American Medical Informatics Association : JAMIA2018
Web services for data warehouses: OMOP and PCORnet on i2b2.
Article in Journal of the American Medical Informatics Association : JAMIA, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT03911687 (Communicating Narrative Concerns Entered by RNs), which is not on this map. Cited by 23 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Communicating Narrative Concerns Entered by RNs (CONCERN) Clinical Decision Support (CDS) System
Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Common data models and data standards for tabular health data: a systematic review.BMC medical informatics and decision making · 2025Pooled it
- Article
- Causal Inference via Electronic Health Records in the National Clinical Cohort Collaborative: Challenges and Solutions in Long COVID Research.medRxiv : the preprint server for health sciences · 2025Article
- An interactive dashboard for analyzing user interaction patterns in the i2b2 clinical data warehouse.BMC medical informatics and decision making · 2024Article
- Evolution of a Graph Model for the OMOP Common Data Model.Applied clinical informatics · 2024Article
- Automatically pre-screening patients for the rare disease aromatic l-amino acid decarboxylase deficiency using knowledge engineering, natural language processing, and machine learning on a large EHR population.Journal of the American Medical Informatics Association : JAMIA · 2024Article
- Learning across diverse biomedical data modalities and cohorts: Challenges and opportunities for innovation.Patterns (New York, N.Y.) · 2024Review
- Clinical Data Warehousing: A Scoping Review.Journal of the Society for Clinical Data Management · 2024Article
- A broadly applicable approach to enrich electronic-health-record cohorts by identifying patients with complete data: a multisite evaluation.Journal of the American Medical Informatics Association : JAMIA · 2023Article
- Integrating row level security in i2b2: segregation of medical records into data marts without data replication and synchronization.JAMIA open · 2023Article
- A Data Transformation Methodology to Create Findable, Accessible, Interoperable, and Reusable Health Data: Software Design, Development, and Evaluation Study.Journal of medical Internet research · 2023Article
- Synthetic data in health care: A narrative review.PLOS digital health · 2023Article
- I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform.Bioinformatics (Oxford, England) · 2022Article
- Enhancing research data infrastructure to address the opioid epidemic: the Opioid Overdose Network (O2-Net).JAMIA open · 2022Article
- Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration.Journal of biomedical informatics · 2022Article
- Use of automatic SQL generation interface to enhance transparency and validity of health-data analysis.Informatics in medicine unlocked · 2022Article
- A scalable, secure, and interoperable platform for deep data-driven health management.Nature communications · 2021Article
- Automated production of research data marts from a canonical fast healthcare interoperability resource data repository: applications to COVID-19 research.Journal of the American Medical Informatics Association : JAMIA · 2021Article
- Deep-learning-based automated terminology mapping in OMOP-CDM.Journal of the American Medical Informatics Association : JAMIA · 2021Article
- Toolkit to Compute Time-Based Elixhauser Comorbidity Indices and Extension to Common Data Models.Healthcare informatics research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.