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SATORI: A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories

Abstract

The number of data sets in biomedical repositories has grown rapidly over the past decade, providing scientists in fields like genomics and other areas of high-throughput biology with tremendous opportunities to re-use data. Scientists are able to test hypotheses computationally instead of generating their own data, to complement their own data sets with data generated by others, and to conduct meta analyses across many data sets. In order to effectively exploit existing data, it is crucial to understand the content of repositories and to discover data relevant to a question of interest. These are challenging tasks, as most repositories currently only support finding data sets through text-based search of metadata and in some cases also through metadata-based browsing. In order to address these challenges, we have developed SATORI - an ontology-guided visual exploration system - that combines a powerful metadata search with a tree map and a node-link diagram that visualize the repository structure, provide context to retrieved data sets, and serve as an interface to drive semantic querying and browsing of the repository. The requirements for SATORI were derived in semi-structured interviews with biomedical data scientists. We demonstrate its utility by describing several usage scenarios using a stem cell data repository, discoveries we made in the process of developing them, and an evaluation of SATORI with domain experts. We have integrated an open-source, web-based implementation of SATORI in the data repository of the Refinery Platform for biomedical data analysis and visualization (http://refinery-platform.org).

Citation

F Lekschas, N Gehlenborg. “SATORI: A System for Ontology-Guided Visual Exploration of Biomedical Data Repositories” bioRxiv 046755; doi: https://doi.org/10.1101/046755 (2017).

Publisher URL

http://biorxiv.org/content/early/2016/04/05/046755