Publications

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30 Publications visible to you, out of a total of 30

Abstract (Expand)

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools.

Authors: Dagmar Waltemath, Richard Adams, Frank T Bergmann, Michael Hucka, Fedor Kolpakov, Andrew K Miller, Ion I Moraru, David Nickerson, Sven Sahle, , Nicolas Le Novère

Date Published: 15th Dec 2011

Publication Type: Not specified

Abstract (Expand)

MOTIVATION: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, may have little experience in the use of such standards and require tools to support this form of data annotation. RESULTS: RightField is an open source application that provides a mechanism for embedding ontology annotation support for Life Science data in Excel spreadsheets. Individual cells, columns or rows can be restricted to particular ranges of allowed classes or instances from chosen ontologies. The RightField-enabled spreadsheet presents selected ontology terms to the users as a simple drop-down list, enabling scientists to consistently annotate their data. The result is 'semantic annotation by stealth', with an annotation process that is less error-prone, more efficient, and more consistent with community standards. AVAILABILITY AND IMPLEMENTATION: RightField is open source under a BSD license and freely available from http://www.rightfield.org.uk

Authors: , , Matthew Horridge, , , , ,

Date Published: 15th Jul 2011

Publication Type: Journal

Abstract (Expand)

RightField is a Java application that provides a mechanism for embedding ontology annotation support for scientific data in Microsoft Excel or Open Office spreadsheets. The result is semantic annotation by stealth, with an annotation process that is less error-prone, more efficient, and more consistent with community standards. By automatically generating RDF statements for each cell a rich, Linked Data querying environment allows scientists to search their data and other Linked Data resources interchangeably, and caters for queries across heterogeneous spreadsheets. RightField has been developed for Systems Biologists but has since adopted more widely. It is open source (BSD license) and freely available from http://www.rightfield.org.uk

Authors: Katy Wolstencroft, Stuart Owen, Matthew Horridge, Wolfgang Mueller, Finn Bacall, Jacky Snoep, Franco du Preez, Quyen Nguyen, Olga Krebs, Carole Goble

Date Published: 2012

Publication Type: Journal

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