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DataMed - an open source discovery index for finding biomedical datasets.

Xiaoling Chen1, Anupama E Gururaj1, Burak Ozyurt2

  • 1School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

Journal of the American Medical Informatics Association : JAMIA
|January 19, 2018
PubMed
Summary
This summary is machine-generated.

DataMed is an open-source system that enhances biomedical data discovery and reuse. It efficiently indexes and searches diverse datasets, improving access to valuable research information.

Keywords:
data discovery indexdatasetinformation disseminationinformation storage and retrievalmetadata

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Area of Science:

  • Biomedical Informatics
  • Data Science
  • Information Retrieval

Background:

  • Biomedical data reuse is crucial but hindered by data volume and complexity.
  • Efficient discovery of relevant datasets is a significant challenge in the biomedical domain.

Purpose of the Study:

  • To develop and introduce DataMed, an open-source biomedical data discovery system.
  • To promote the creation of additional data indexes within the biomedical field.

Main Methods:

  • Developed DataMed, comprising a data ingestion pipeline and a search engine.
  • Utilized the DatA Tag Suite (DATS) metadata model for data standardization.
  • Evaluated the ingestion pipeline accuracy, DATS model prevalence, and search engine performance.

Main Results:

  • The ingestion pipeline achieved 90% accuracy.
  • The DataMed search engine demonstrated an average precision of 0.2033 and P@10 of 0.6022.
  • Core DATS elements showed varied frequency across repositories.

Conclusions:

  • DataMed is a publicly available, open-source package for the biomedical community.
  • The system effectively indexes and searches diverse biomedical datasets.
  • Advanced NLP and terminology services enhance search relevance.