The health care and life sciences community profile for dataset descriptions

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1 Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, United States
2 Computer Science, Heriot-Watt University, Edinburgh, United Kingdom
3 Department of Radiation Oncology (MAASTRO), GROW - School for Oncology and Developmental Biology, MAASTRO Clinic, Maastricht, The Netherlands
4 Ontotext Corporation, Sofia, Bulgaria
5 CSIRO, Canberra, Australia
6 The Donnelly Centre, University of Toronto, Toronto, Canada
7 Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Geneve, Switzerland
8 Carleton University, Ottawa, Canada
9 SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
10 IO Informatics, Berkeley, CA, United States of America
11 Oxford e-Research Centre, University of Oxford, Oxford, Oxfordshire, United Kingdom
12 Elsevier Labs, Amsterdam, Netherlands
13 Department of Medical Informatics and Epidemiology, Oregon Health Sciences University, Portland, Oregon, United States
14 NIBIO, Osaka, Japan
15 EMBL, European Bioinformatics Institute, Saffron Walden, United Kingdom
16 Database Center for Life Sciences, Sendai, Japan
17 RIKEN, Wako, Japan
18 Cerenode Inc., Troy, United States of America
19 Babraham Institute, Cambridge, United Kingdom
20 Nationwide Children's Hospital, Columbus, Ohio, United States of America
21 Institute for Systems Biology, Seattle, Washington, United States of America
22 Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
23 Department of Exact Sciences, VU University Amsterdam, Amsterdam, Netherlands
24 Research Organization of Information and Systems, Database Center for Life Sciences, Kashiwa, Japan
DOI
10.7287/peerj.preprints.1982v2
Published
Accepted
Subject Areas
Bioinformatics, Taxonomy, Computational Science
Keywords
data profiling, dataset descriptions, metadata, provenance, FAIR data
Copyright
© 2017 Dumontier et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader GD, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall C, Rietveld L, Wimalaratne SM, Yamaguchi A. 2017. The health care and life sciences community profile for dataset descriptions. PeerJ Preprints 5:e1982v2

Abstract

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets.

Author Comment

Revisions to address reviewers comments. Chiefly adding summary of use cases, complete example of summary level description, and more discussion of related work.