The value of broadening searches for data across multiple repositories has been identified by the biomedical research community. As part of the US National Institutes of Health (NIH) Big Data to Knowledge initiative, we work with an international community of researchers, service providers and knowledge experts to develop and test a data index and search engine, which are based on metadata extracted from various data sets in a range of repositories. DataMed is designed to be, for data, what PubMed has been for the scientific literature. DataMed supports the findability and accessibility of data sets. These characteristics—along with interoperability and reusability—compose the four FAIR principles to facilitate knowledge discovery in today's big data–intensive science landscape.
Subscribe to Journal
Get full journal access for 1 year
only $17.42 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Wilkinson, M.D. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data 3, 160018 (2016).
Collins, F.S. & Tabak, L.A. Policy: NIH plans to enhance reproducibility. Nature 505, 612–613 (2014).
Bourne, P.E. et al. The NIH Big Data to Knowledge (BD2K) initiative. J. Am. Med. Inform. Assoc. 22, 1114 (2015).
Lu, Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database (Oxford) 2011, baq036 (2011).
Sansone, S.-A. et al. DATS: the data tag suite to enable discoverability of datasets. Sci. Data 4, 170059 (2017).
Noruzi, A. Google Scholar: the new generation of citation indexes. Libri 55, 170–180 (2005).
Hands, A. Microsoft Academic Search—http://academic.research.microsoft.com. Tech. Serv. Q. 29, 251–252 (2012).
Kejariwal, D. & Mahawar, K.K. Is your journal indexed in PubMed? Relevance of PubMed in biomedical scientific literature today. WebmedCentral MISCELLANEOUS 3, WMC003159 (2012).
Huh, S. Journal Article Tag Suite 1.0: National Information Standards Organization standard of journal extensible markup language. Sci. Ed. 1, 99–104 (2014).
Perez-Riverol, Y. et al. Nat. Biotechnol. 35, 406–409 (2017)
Brase, J. in 2009 Fourth International Conference on Cooperation and Promotion of Information Resources in Science and Technology (COINFO 2009) 257–261 (IEEE, 2009).
Chodorow, K. MongoDB: The Definitive Guide (O'Reilly Media, 2013).
Kuć, R. & Rogozinski, M. ElasticSearch Server (Packt Publishing, 2016).
Coll, I.S. & Cruz, J.M.B. Open archives initiative. Protocol for metadata harvesting (OAI-PMH): descripción, funciones y aplicaciones de un protocolo. Prof. Inf. 12, 99–106 (2003).
Richardson, L. & Ruby, S. RESTful Web Services (O'Reilly Media, 2008).
Westbrook, J., Ito, N., Nakamura, H., Henrick, K. & Berman, H.M. PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21, 988–992 (2005).
Kiryakov, A., Popov, B., Terziev, I. Manov, D. & Ognyanoff, D. Semantic annotation, indexing, and retrieval. Web Semantics 2, 49–79 (2004).
Haustein, S., Peters, I., Sugimoto, C.R., Thelwall, M. & Larivière, V. Tweeting biomedicine: an analysis of tweets and citations in the biomedical literature. J. Assoc. Inf. Sci. Technol. 65, 656–669 (2014).
This project is funded by grant U24AI117966 from NIAID, NIH, as part of the BD2K program. The co-authors, who are the lead investigators and chairs/co-chairs of the core activities, thank all contributors to the bioCADDIE consortium and list them in the Supplementary Note in alphabetical order within each activity group (each name appears only once even though many people participated in different activities).
The authors declare no competing financial interests.
About this article
Cite this article
Ohno-Machado, L., Sansone, SA., Alter, G. et al. Finding useful data across multiple biomedical data repositories using DataMed. Nat Genet 49, 816–819 (2017). https://doi.org/10.1038/ng.3864
A knowledge management system framework for an open biomedical repository: communities, collaboration and corroboration
Journal of Knowledge Management (2020)
Nucleic Acids Research (2020)
Proceedings of the Association for Information Science and Technology (2020)
Journal of Information Science (2020)