The ISA Commons is a growing community that uses the ISA metadata tracking framework to facilitate standards-compliant collection, curation, management and reuse of datasets in an increasingly diverse set of life science domains.

  • Metabolomics, 2016

  • BMC Bioinformatics, 2014

  • PLOS ONE, 2015

  • BMC Bioinformatics, 2014

  • Frontiers in Bioengineering and Biotechnology, 2014

  • Bioinformatics, 2010

  • Nature Nanotechnology, 2013

  • Beilstein Journal of Nanotechnology, 2015

  • PLOS ONE, 2015

  • Bioinformatics, 2012

  • Nucleic Acids Research, 2012

  • Woodhead Publishing, 2012

  • Nucleic Acids Research, 2011

  • Nature Biotechnology, 2012

  • Molecular Informatics, 2013

  • AMIA Joint Summits on Translational Science, 2013

What is the ISA framework?
At the heart of this open source framework is the general-purpose ISA data model, built on the ‘Investigation’ (the project context), ‘Study’ (a unit of research) and ‘Assay’ (analytical measurement) metadata categories. The extensible, hierarchical structure of this model enables the representation of studies employing one or a combination of technologies, focusing on the description of its experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships). The ISA software suite - the second element of this framework – acts to create and edit ISA format files (ISA-Tab and JSON), store, serve and covert them to a growing number of other related data formats.

Who is part of the ISA Commons?
A growing ecosystem of public and internal resources that use the ISA formats, and/or are powered by one or more component of the ISA software suite. But also grass-root standards groups that leverage on the ISA data model and formats. All groups are listed in the table below, illustrating the flexibility of the format and the versatility of the software components. The sustainability and maintenance of the ISA data model, formats, and tools, is guided by the ISA Working Group.

To coordinate the development the ISA standards and tools, the community contributes via the ISA Working Group that consists of an invited set of international researchers and developers. The ISA Working Group consists of the following people:
  • Rob Davey (The Genome Analysis Centre)
  • Reza Salek (European Bioinformatics Institute)
  • Norman Morrison (University of Manchester, FAIRdom)
  • Sharon Gaheen (US NIH caNanoLab project)
  • Nina Jeliazkova (H2020 eNanoMapper project)
  • Nikolay Kochev (H2020 eNanoMapper project)
  • Richard Marchese Robinson (Liverpool John-Moores University)
  • Susanna-Assunta Sansone (Oxford e-Research Centre)
  • Philippe Rocca-Sera (Oxford e-Research Centre)
  • Steffen Neumann (Leibniz Institute of Plant Biochemistry)
  • Peter Li (GigaScience/Beijing Genomics Institute)
  • Rob Davidson (GigaScience/Beijing Genomics Institute)
  • Ralf Weber (University of Birmingham)
  • Cyril Pommier (Unité de Recherche Génomique Info)
  • Yvan Le Bras (IRISA-INRIA)
  • Alejandra Gonzalez Beltran (Oxford e-Research Centre)
  • David Johnson (Oxford e-Research Centre)

  • Do you want to join in?
    The open ISA framework belongs to its community of users and contributors, who are assisted by a dedicated team based at the University of Oxford, UK, who have supported its open development since 2007. You can keep up to date with the latest ISA-related developments by checking out the ISA-tools blog.

    Public Resources
    System or project
    Organization & location
    Dataset type
    data descriptor metadata
    life science and biomedical
    INRIA and Brittany region, France
    all types
    transPLANT Consortium, European Union
    plant genomic variation
    PhenoMeNal Consortium, European Union
    eNanoMapper Consortium, European Union
    proteomics, nanomaterial, toxicology
    metabolomics, mass spectrometry, LC-MS, GC-MS
    diXa Consortium, European Union
    toxicology, toxicogenomics
    Bioplatforms Australia framework data initiative
    wheat genotyping and pathogen; pest; soil biodiversity, metagenomics
    Nutrigenomics, pan European consortium
    nutritional clinical interventions and observations
    ERA-Net ERASysAPP and European Research Infrastructure ISBE joint action, European Union
    systems biology
    in vitro systemic toxicity; toxicogenomics

    Other groups
    System or project
    Organization & location
    Investigation types
    The pKa Cooperative for Protein Electrostatics
    protein electrostatics

    Internal Resources
    System or project
    Organization & location
    Investigation types
    neuroscience; vaccine-protection; mouse phenotype; drug infusion
    Biomedical Information Research Network's (BIRN) Knowledge Engineering Working Group, USA
    gene expression
    Environmental Microbiology activities
    microbial interactions; metagenomics
    NIEHS’ Center for Environmental Health resource locator
    environmental research, population, patient and laboratory-based studies
    Janssen internal system

    Public Resources

    These international public repositories endorse the ISA software suite (and the ISA converter) for the preparation of submissions in Pride-xml, SRA-xml and MAGE-Tab formats, respectively.

  • ArrayExpress - functional genomics data
  • PRIDE - proteomics data repository
  • ENA - European Nucleotide Archive