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.
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How to cite us!
Towards interoperable bioscience dataNature Genetics, 2012
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Data standards can boost metabolomics research, and if there is a will, there is a way
Metabolomics, 2016
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linkedISA: semantic representation of ISA-Tab experimental metadata
BMC Bioinformatics, 2014
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From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: Roles of Data Models and Workflows in Bioinformatics
PLOS ONE, 2015
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The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again
BMC Bioinformatics, 2014
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MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments
Frontiers in Bioengineering and Biotechnology, 2014
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The ISA software suiteBioinformatics, 2010
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Standardizing data, introducing ISA-Tab-Nano
Nature Nanotechnology, 2013
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An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology
Beilstein Journal of Nanotechnology, 2015
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Ten Simple Rules for Creating a Good Data Management Plan
PLOS ONE, 2015
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OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets
Bioinformatics, 2012
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MetaboLights: an open-access repository for metabolomics at EBI powered by ISA
Nucleic Acids Research, 2012
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Open source software in life science research
Woodhead Publishing, 2012
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The ISA metadata tracking framework in action in the Harvard's Stem Cell Discovery Engine
Nucleic Acids Research, 2011
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The ISA commons and FAIRSharing initiatives feature strongly in this article "My data are your data"
Nature Biotechnology, 2012
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The ToxBank Data Warehouse: a research cluster of 7 EU FP7 Health systems toxicology and toxicogenomics projects
Molecular Informatics, 2013
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The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework
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.
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:
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.
System or project
Organization & location
Dataset type
space biology
cancer and biomedical
high-throughput plant phenotyping
diXa Consortium, European Union
toxicology, toxicogenomics
Bioplatforms Australia framework data initiative
Bioplatforms Australia, Australia
wheat genotyping and pathogen; pest; soil biodiversity, metagenomics
insect toxicity; bacterial genomics
cellular signatures
tissue and cancer stem cell
microarray, NGS, metabolomics, metagenomics, proteomics
UMR1332 INRA
and CBiB University of Bordeaux,
France
plant metabolomics
Nutrigenomics, pan European consortium
nutritional clinical interventions and observations
systems biology
System or project
Organization & location
Investigation types
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
toxicogenomics; functional genomics
IPB’s Metabolomics portal
The Leibniz Institute of Plant Biochemistry (IPB)’s Bioinformatics & Mass Spectrometry (MS),
Germany
plant metabolomics
NIEHS’ Center for Environmental Health resource locator
environmental research, population, patient and laboratory-based studies
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.