Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Authors : Julie A. McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K. Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, Jon C. Ison, Rafael C. Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Johanna R. McEntyre, Chris Morris, Juha Muilu, Wolfgang Müller, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky L. Snoep, Stian Soiland-Reyes, Natalie J. Stanford, Neil Swainston, Nicole Washington, Alan R. Williams, Sarala M. Wimalaratne, Lilly M. Winfree, Katherine Wolstencroft, Carole Goble, Christopher J. Mungall, Melissa A. Haendel, Helen Parkinson

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure.

Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers.

We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability.

We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

URL : Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data


Decentralized provenance-aware publishing with nanopublications

Authors : Tobias Kuhn, Christine Chichester, Michael Krauthammer, Núria Queralt-Rosinach, Ruben Verborgh, George Giannakopoulos, Axel-Cyrille Ngonga Ngomo, Raffaele Viglianti, Michel Dumontier

Publication and archival of scientific results is still commonly considered the responsability of classical publishing companies. Classical forms of publishing, however, which center around printed narrative articles, no longer seem well-suited in the digital age.

In particular, there exist currently no efficient, reliable, and agreed-upon methods for publishing scientific datasets, which have become increasingly important for science. In this article, we propose to design scientific data publishing as a web-based bottom-up process, without top-down control of central authorities such as publishing companies.

Based on a novel combination of existing concepts and technologies, we present a server network to decentrally store and archive data in the form of nanopublications, an RDF-based format to represent scientific data.

We show how this approach allows researchers to publish, retrieve, verify, and recombine datasets of nanopublications in a reliable and trustworthy manner, and we argue that this architecture could be used as a low-level data publication layer to serve the Semantic Web in general.

Our evaluation of the current network shows that this system is efficient and reliable.

URL : Decentralized provenance-aware publishing with nanopublications