Data standardization, sharing and publication
Edited by:
Dr Craig Hooker, Dr Heather Piwowar, Dr David Shotton
Collection published: 26 January 2011
Last updated: 22 October 2012
This series aims to promote best practice in data sharing and publication through data standardization. This ongoing collection brings together articles describing domain-specific data standards and how to implement them, providing or linking to a reference data set prepared and formatted to serve as an example.
BMC Research Notes is collaborating with BioSharing to develop a comprehensive catalogue of domain-specific data standards across biology and medicine, which will include a number of the exemplary data notes in this article collection.
The series also encompasses articles on broader aspects of scientific data sharing, archiving, and open data. This series aims to encourage sharing and publication of data in re-usable and harvestable formats by increasing awareness of existing and emerging data standards and best practices. Contributions to the series are welcome from all fields of biology and medicine and you can contact BMC Research Notes' editorial team and read our call for contributions for more information.
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Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis
Arlin Stoltzfus, Brian O'Meara, Jamie Whitacre, Ross Mounce, Emily L Gillespie, Sudhir Kumar, Dan F Rosauer, Rutger A Vos BMC Research Notes 2012, 5:574 (22 October 2012)
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Editor’s summary
As part of our series on data sharing Arlin Stoltzfus and colleagues call for a standardized system for handling information from phylogenetic trees, including centralized data deposition, and user friendly means of data retrieval and integration.
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Open by default: a proposed copyright license and waiver agreement for open access research and data in peer-reviewed journals
Iain Hrynaszkiewicz, Matthew J Cockerill BMC Research Notes 2012, 5:494 (7 September 2012)
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Adventures in data citation: sorghum genome data exemplifies the new gold standard
Scott C Edmunds, Tom J Pollard, Brian Hole, Alexandra T Basford BMC Research Notes 2012, 5:223 (9 May 2012)
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Editor’s summary
Editor of Giga Science, Scott Edmunds et al. discuss using Digital Object Identifiers (DOI) to make published datasets citable, encouraging authors to make their work publically available to the scientific community.
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Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy
Alejandra N González-Beltrán, May Y Yong, Gairin Dancey, Richard Begent BMC Research Notes 2012, 5:10 (6 January 2012)
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Editor’s summary
As part of our thematic series, Richard Begent and colleagues present recommendations for creating an information checklist to provide a consistent framework for transparently reporting the results of therapeutic experiments.
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The BrainMap strategy for standardization, sharing, and meta-analysis of neuroimaging data
Angela R Laird, Simon B Eickhoff, P Mickle Fox, Angela M Uecker, Kimberly L Ray, Juan J Saenz, D Reese McKay, Danilo Bzdok, Robert W Laird, Jennifer L Robinson, Jessica A Turner, Peter E Turkeltaub, Jack L Lancaster, Peter T Fox BMC Research Notes 2011, 4:349 (9 September 2011)
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Editor’s summary
Neuroimaging data standards are being utilised by the BrainMap project, which provides the human brain mapping community with data sets and computational tools to establish a basis for neuroimaging-based models of healthy brain function.
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The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions
Bernard de Bono, Robert Hoehndorf, Sarala Wimalaratne, George Gkoutos, Pierre Grenon BMC Research Notes 2011, 4:313 (30 August 2011)
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A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human."
Julian L Griffin, Helen J Atherton, Christoph Steinbeck, Reza M Salek BMC Research Notes 2011, 4:272 (29 July 2011)
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Editor’s summary
This Metabolomics Standard Initiative (MSI) metadata description and associated dataset from a metabolomic comparison study highlights the importance of a standardised description of datasets to further cross-discipline understanding.
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A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics
Jenna Kenyani, J Alberto Medina-Aunon, Salvador Martinez-Bartolomé, Juan-Pablo Albar, Jonathan M Wastling, Andrew R Jones BMC Research Notes 2011, 4:86 (28 March 2011)
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Editor’s summary
A new software tool, which allows the simple deposition of proteomics data in the PRoteomics IDEntifications (PRIDE) database, could pave the way for increased public access to proteomics data and fuel innovation through knowledge sharing.
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Flow cytometry data standards
Josef Spidlen, Parisa Shooshtari, Tobias R Kollmann, Ryan R Brinkman BMC Research Notes 2011, 4:50 (7 March 2011)
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Editor’s summary
Novel open file formats can be used to describe flow cytometry data analysis in a standardized and computationally exchangeable format allowing for enhanced scientific collaboration and highlights the need for a public data repository.
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Geospatial resources for supporting data standards, guidance and best practice in health informatics
Tony Mathys, Maged N Kamel Boulos BMC Research Notes 2011, 4:19 (26 January 2011)
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A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication
Iain Hrynaszkiewicz BMC Research Notes 2010, 3:235 (2 September 2010)
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Data and programming code from the studies on the learning curve for radical prostatectomy
Andrew J Vickers, Angel M Cronin BMC Research Notes 2010, 3:234 (2 September 2010)
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