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Research article - Peer-reviewed, 2010

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

Smedley, Damian; Schofield, Paul; Chen, Chao-Kung; Aidinis, Vassilis; Ainali, Chrysanthi; Bard, Jonathan; Balling, Rudi; Birney, Ewan; Blake, Andrew; Bongcam-Rudloff, Erik; Brookes, Anthony J.; Cesareni, Gianni; Chandras, Christina; Eppig, Janan; Flicek, Paul; Gkoutos, Georgios; Greenaway, Simon; Gruenberger, Michael; Heriche, Jean-Karim; Lyall, Andrew;
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Abstract

The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them. Despite a rapid acceleration in uptake of syntactic and semantic standards for interoperability, it is still difficult for users to find which databases support the standards and interfaces that they need. To solve these problems, several groups are developing registries of databases that capture key metadata describing the biological scope, utility, accessibility, ease-of-use and existence of web services allowing interoperability between resources. Here, we describe some of these initiatives including a novel formalism, the Database Description Framework, for describing database operations and functionality and encouraging good database practise. We expect such approaches will result in improved discovery, uptake and utilization of data resources.Database URL: http://www.casimir.org.uk/casimir_ddf

Published in

Database
2010, volume: 2010, article number: baq014

Authors' information

Smedley, Damian
European Bioinformatics Institute (EMBL-EBI)
Schofield, Paul
Chen, Chao-Kung
European Bioinformatics Institute (EMBL-EBI)
Aidinis, Vassilis
Biomedical Sciences Research Center Alexander Fleming
Ainali, Chrysanthi
King's College London (KCL)
Bard, Jonathan
University of Oxford
Balling, Rudi
University of Luxembourg
Birney, Ewan
European Bioinformatics Institute (EMBL-EBI)
Blake, Andrew
Medical Research Council (MRC)
Bongcam-Rudloff, Erik (Bongcam Rudloff, Erik)
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Brookes, Anthony J.
University of Leicester
Cesareni, Gianni
University of Rome Tor Vergata
Chandras, Christina
Biomedical Sciences Research Center Alexander Fleming
Eppig, Janan
The Jackson Laboratory
Flicek, Paul
European Bioinformatics Institute (EMBL-EBI)
Gkoutos, Georgios
University of Cambridge
Greenaway, Simon
Medical Research Council (MRC)
Gruenberger, Michael
University of Cambridge
Hériché, Jean-Karim
European Molecular Biology Laboratory (EMBL)
Lyall, Andrew
European Bioinformatics Institute (EMBL-EBI)
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UKÄ Subject classification

Information Science

Publication Identifiers

DOI: https://doi.org/10.1093/database/baq014

URI (permanent link to this page)

https://res.slu.se/id/publ/31121