Back to Search
Start Over
Leaf—An open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research
- Source :
- Journal of the American Medical Informatics Association : JAMIA
- Publication Year :
- 2019
- Publisher :
- Cold Spring Harbor Laboratory, 2019.
-
Abstract
- ObjectiveAcademic medical centers and health systems are increasingly challenged with supporting appropriate secondary use of data that originate from multiple sources. Enterprise Data Warehouses (EDWs) have emerged as central resources for these data, but they often require an informatician to extract meaningful information, thereby limiting direct access by end users. To overcome this challenge, we have developed Leaf, a lightweight self-service web application for querying and extracting clinical data from heterogeneous data sources.Materials and MethodsLeaf utilizes a flexible biomedical concept system to define hierarchical items and ontologies. Each Leaf concept contains both textual representations and associated SQL query building blocks, exposed by a simple drag-and-drop user interface. Leaf generates abstract syntax trees which are compiled into dynamic SQL queries.ResultsLeaf is a successful production-supported tool at the University of Washington, which hosts a central Leaf instance querying an EDW with over 300 active users. Through the support of UW Medicine (https://uwmedicine.org), the Institute of Translational Health Sciences (https://www.iths.org) and the National Center for Data to Health (https://ctsa.ncats.nih.gov/cd2h/), Leaf source code has been released into the public domain athttps://github.com/uwrit/leaf.DiscussionLeaf allows the querying of single or multiple clinical databases simultaneously, even those of different data models. This enables fast installation without costly extraction or duplication from existing databases.ConclusionLeaf differs from existing cohort discovery tools because it does not specify a required data model and is designed to seamlessly integrate with existing enterprise user authentication systems and clinical databases in situ. We demonstrate its unique technical strengths and success alongside its friendly user interface. We believe Leaf to be useful for health system analytics, clinical research data warehouses, precision medicine biobanks and clinical studies involving large patient cohorts.
- Subjects :
- 0301 basic medicine
SQL
biomedical informatics
Computer science
Information Storage and Retrieval
Health Informatics
030204 cardiovascular system & hematology
Ontology (information science)
computer.software_genre
Research and Applications
Data modeling
World Wide Web
Translational Research, Biomedical
03 medical and health sciences
User-Computer Interface
0302 clinical medicine
Data Warehousing
Web application
Humans
030212 general & internal medicine
data integration
030304 developmental biology
computer.programming_language
0303 health sciences
Internet
leaf
business.industry
cloud computing
Enterprise data management
Unified Medical Language System
Data warehouse
observational health data sciences and informatics
3. Good health
030104 developmental biology
Data model
Databases as Topic
Vocabulary, Controlled
cohort discovery
13. Climate action
Analytics
User interface
business
computer
Data integration
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Journal of the American Medical Informatics Association : JAMIA
- Accession number :
- edsair.doi.dedup.....90717479b9284c299d1797e6b7b58331
- Full Text :
- https://doi.org/10.1101/632471