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Data standardization, sharing and publication

This series aimed to promote best practice in data sharing and publication through data standardization. This collection brought 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 encompassed articles on broader aspects of scientific data sharing, archiving, and open data. This series aimed 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 were welcomed from all fields of biology and medicine, and you can contact the BMC Research Notes editorial team and read our call for contributions for more information.

Dr Craig Hooker, Dr Heather Piwowar, Dr David Shotton

  1. In many research articles, where protein purification is required for various assays, (protein-protein interactions, activity assays, etc.), we always have access to the final results, but seldom have access t...

    Authors: Mario Lebendiker, Tsafi Danieli and Ario de Marco
    Citation: BMC Research Notes 2014 7:585
    Content type: Correspondence Published on:

  2. We report the outcomes of BioMed Central’s public consultation on implementing open data-compliant licensing in peer-reviewed open access journals. Respondents (42) to the 2012 consultation were six to one in ...

    Authors: Iain Hrynaszkiewicz, Stefan Busch and Matthew J Cockerill
    Citation: BMC Research Notes 2013 6:318
    Content type: Editorial Published on:

  3. Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapi...

    Authors: Arlin Stoltzfus, Brian O'Meara, Jamie Whitacre, Ross Mounce, Emily L Gillespie, Sudhir Kumar, Dan F Rosauer and Rutger A Vos
    Citation: BMC Research Notes 2012 5:574
    Content type: Data Note Published on:

  4. Copyright and licensing of scientific data, internationally, are complex and present legal barriers to data sharing, integration and reuse, and therefore restrict the most efficient transfer and discovery of s...

    Authors: Iain Hrynaszkiewicz and Matthew J Cockerill
    Citation: BMC Research Notes 2012 5:494
    Content type: Editorial Published on:

  6. Biology, biomedicine and healthcare have become data-driven enterprises, where scientists and clinicians need to generate, access, validate, interpret and integrate different kinds of experimental and patient-...

    Authors: Alejandra N González-Beltrán, May Y Yong, Gairin Dancey and Richard Begent
    Citation: BMC Research Notes 2012 5:10
    Content type: Data Note Published on:

  7. Neuroimaging researchers have developed rigorous community data and metadata standards that encourage meta-analysis as a method for establishing robust and meaningful convergence of knowledge of human brain st...

    Authors: Angela R Laird, Simon B Eickhoff, P Mickle Fox, Angela M Uecker, Kimberly L Ray, Juan J Saenz Jr, D Reese McKay, Danilo Bzdok, Robert W Laird, Jennifer L Robinson, Jessica A Turner, Peter E Turkeltaub, Jack L Lancaster and Peter T Fox
    Citation: BMC Research Notes 2011 4:349
    Content type: Technical Note Published on:

  8. The practice and research of medicine generates considerable quantities of data and model resources (DMRs). Although in principle biomedical resources are re-usable, in practice few can currently be shared. In...

    Authors: Bernard de Bono, Robert Hoehndorf, Sarala Wimalaratne, George Gkoutos and Pierre Grenon
    Citation: BMC Research Notes 2011 4:313
    Content type: Short Report Published on:

  9. Metabolomics is a rapidly developing functional genomic tool that has a wide range of applications in diverse fields in biology and medicine. However, unlike transcriptomics and proteomics there is currently n...

    Authors: Julian L Griffin, Helen J Atherton, Christoph Steinbeck and Reza M Salek
    Citation: BMC Research Notes 2011 4:272
    Content type: Data Note Published on:

  10. Proteomic techniques allow researchers to perform detailed analyses of cellular states and many studies are published each year, which highlight large numbers of proteins quantified in different samples. Howev...

    Authors: Jenna Kenyani, J Alberto Medina-Aunon, Salvador Martinez-Bartolomé, Juan-Pablo Albar, Jonathan M Wastling and Andrew R Jones
    Citation: BMC Research Notes 2011 4:86
    Content type: Data Note Published on:

  11. Flow cytometry is a widely used analytical technique for examining microscopic particles, such as cells. The Flow Cytometry Standard (FCS) was developed in 1984 for storing flow data and it is supported by all...

    Authors: Josef Spidlen, Parisa Shooshtari, Tobias R Kollmann and Ryan R Brinkman
    Citation: BMC Research Notes 2011 4:50
    Content type: Data Note Published on: