DataMed - an open source discovery index for finding biomedical datasets


Journal Article

© The Author 2018. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. Objective: Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain. Materials and Methods: DataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health-funded biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium. It consists of 2 main components: (1) a data ingestion pipeline that collects and transforms original metadata information to a unified metadata model, called DatA Tag Suite (DATS), and (2) a search engine that finds relevant datasets based on user-entered queries. In addition to describing its architecture and techniques, we evaluated individual components within DataMed, including the accuracy of the ingestion pipeline, the prevalence of the DATS model across repositories, and the overall performance of the dataset retrieval engine. Results and Conclusion: Our manual review shows that the ingestion pipeline could achieve an accuracy of 90% and core elements of DATS had varied frequency across repositories. On a manually curated benchmark dataset, the DataMed search engine achieved an inferred average precision of 0.2033 and a precision at 10 (P@10, the number of relevant results in the top 10 search results) of 0.6022, by implementing advanced natural language processing and terminology services. Currently, we have made the DataMed system publically available as an open source package for the biomedical community.

Full Text

Duke Authors

Cited Authors

  • Chen, X; Gururaj, AE; Ozyurt, B; Liu, R; Soysal, E; Cohen, T; Tiryaki, F; Li, Y; Zong, N; Jiang, M; Rogith, D; Salimi, M; Kim, HE; Rocca-Serra, P; Gonzalez-Beltran, A; Farcas, C; Johnson, T; Margolis, R; Alter, G; Sansone, SA; Fore, IM; Ohno-Machado, L; Grethe, JS; Xu, H

Published Date

  • March 1, 2018

Published In

Volume / Issue

  • 25 / 3

Start / End Page

  • 300 - 308

Electronic International Standard Serial Number (EISSN)

  • 1527-974X

International Standard Serial Number (ISSN)

  • 1067-5027

Digital Object Identifier (DOI)

  • 10.1093/jamia/ocx121

Citation Source

  • Scopus