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<html lang="en">
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<title>ISA commons | Welcome</title>
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<span style="font-weight: lighter; color: #666; font-size:1.5em; line-height: 30px; text-rendering: optimizelegibility;">The ISA Commons is a growing community that uses the <strong>ISA
metadata tracking framework</strong> to facilitate standards-compliant <strong>collection, curation,
management</strong> and <strong>reuse</strong> of datasets in an increasingly diverse set of life science domains.</span>
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The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework
</h4>
<p>AMIA Joint Summits on Translational Science, 2013</p>
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<span style="border-bottom: #1C75BC 2px solid; font-size: 1.2em">How to cite us!</span>
<br>
Towards interoperable bioscience data
</h4>
<p>Nature Genetics, 2012</p>
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<strong>The ISA commons and FAIRSharing initiatives feature strongly in this article "My data are your data"</strong>
</h4>
<p>Nature Biotechnology, 2012</p>
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<a href="http://www.nature.com/nbt/journal/v30/n6/full/nbt.2243.html" target="_blank" class="button round small snow shady">Read the paper!</a>
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<strong>OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets</strong>
</h4>
<p>Bioinformatics, 2012</p>
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<a href="http://bioinformatics.oxfordjournals.org/content/29/4/525" target="_blank" class="button round small snow shady">Read the paper!</a>
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<strong>MetaboLights: an open-access repository for metabolomics at EBI powered by ISA</strong>
</h4>
<p>Nucleic Acids Research, 2012</p>
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<a href="http://nar.oxfordjournals.org/content/early/2012/10/28/nar.gks1004" class="button round small snow shady" target="_blank">Read the paper!</a>
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<strong>Open source software in life science research</strong>
</h4>
<p>Woodhead Publishing, 2012</p>
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<a href="http://www.amazon.com/Open-source-software-science-research/dp/1907568972" target="_blank" class="button round small snow shady">Buy the book!</a>
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The ISA metadata tracking framework <i>in action </i>in the <strong>Harvard's Stem Cell Discovery Engine</strong>
</h4>
<p>Nucleic Acids Research, 2011</p>
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<br>
The ISA software suite
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<p>Bioinformatics, 2010</p>
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<div class="information grid_16" style="font-size: 1.1em; line-height: 23px; color: #666">
<strong>What is the ISA framework?</strong><br/>
At the heart of this open source framework is the general-purpose
<a href="http://isa-tools.org/format/specification.html" target="_blank"><strong>ISA data model</strong></a>, 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 <a href="http://isa-tools.org/software-suite/" target="_blank"><strong>ISA software suite</strong></a> - 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.
<br/><br/>
<strong>Who is part of the ISA Commons?</strong><br/>
A growing <strong><i>ecosystem of public and internal resources</i></strong> that use the ISA formats,
and/or are powered by one or more component of the ISA software suite. But also <strong><i>grass-root standards
groups</i></strong> 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 <strong>ISA Working Group</strong>.
<br/><br/>
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:
<div class="information grid_8 tableItem" style="font-size: 1.1em; line-height: 23px; color: #666">
<li>Rob Davey (The Genome Analysis Centre)</li>
<li>Reza Salek (European Bioinformatics Institute)</li>
<li>Norman Morrison (University of Manchester, FAIRdom)</li>
<li>Sharon Gaheen (US NIH caNanoLab project)</li>
<li>Nina Jeliazkova (H2020 eNanoMapper project)</li>
<li>Nikolay Kochev (H2020 eNanoMapper project)</li>
<li>Richard Marchese Robinson (Liverpool John-Moores University)</li>
<li>Susanna-Assunta Sansone (Oxford e-Research Centre)</li>
<li>Philippe Rocca-Sera (Oxford e-Research Centre)</li>
</div>
<div class="information grid_8 tableItem" style="font-size: 1.1em; line-height: 23px; color: #666">
<li>Steffen Neumann (Leibniz Institute of Plant Biochemistry)</li>
<li>Peter Li (GigaScience/Beijing Genomics Institute)</li>
<li>Rob Davidson (GigaScience/Beijing Genomics Institute)</li>
<li>Ralf Weber (University of Birmingham)</li>
<li>Cyril Pommier (Unité de Recherche Génomique Info)</li>
<li>Yvan Le Bras (IRISA-INRIA)</li>
<li>Alejandra Gonzalez Beltran (Oxford e-Research Centre)</li>
<li>David Johnson (Oxford e-Research Centre)</li>
</div>
<div class="clear"></div>
<br/>
<div class="clear"></div>
<strong>Do you want to join in?</strong><br/>
The open ISA framework belongs to its community of users and contributors, who are assisted by a
<a href="http://isa-tools.org/team/" target="_blank"><strong>dedicated team</strong></a> 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
<a href="http://isa-tools.org/blog/" target="_blank"><strong>ISA-tools blog</strong></a>.
<br/><br/>
<div class="container_15">
<div class="grid_5" align="center">
<p><span class="blueButton"><a href="https://groups.google.com/forum/#!forum/isaforum"
class="caseStudyLink"><strong>Join the ISA forum for open
discussions</strong></a></span></p>
</div>
<div class="grid_5" align="center">
<p><span class="blueButton"><a href="mailto:[email protected]?subject=ISAcommons"
class="caseStudyLink"><strong>Contact us for general
inquiries</strong></a></span></p>
</div>
<div class="grid_5" align="center">
<p><span class="blueButton"><a href="mailto:[email protected]?subject=ISAcommons"
class="caseStudyLink"><strong>Using ISA? Get your paper or
project added</strong></a></span></p>
</div>
</div>
</div>
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<br/><br/>
<div align="center">
<img src="assets/img/front-page/public-resource.png" alt="Public Resources"
style="margin-bottom: 10px"/>
</div>
<div class="grid_16">
<div class="tableHeadItem">
<div class=" grid_5">
<strong>System or project</strong>
</div>
<div class=" grid_5">
Organization & location
</div>
<div class=" grid_5">
Dataset type
</div>
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</div>
<div class="caseStudy">
<div class="information grid_5 tableItem caseStudyTitle">
<a href="http://www.nature.com/scientificdata" target="_blank">Scientific Data</a>
</div>
<div class="information grid_5 tableItem">
<a href="https://www.nature.com/sdata/" target="_blank">Nature Publishing Group</a>
</div>
<div class="information grid_5 tableItem">data descriptor metadata<br/>
</div>
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</div>
<div class="caseStudy">
<div class="information grid_5 tableItem caseStudyTitle">
<a href="http://gigadb.org/site/about" target="_blank">GigaDB</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.gigasciencejournal.com/" target="_blank">GigaScience journal</a> at <a
href="http://www.genomics.cn/en/index" target="_blank">BGI</a>, China
</div>
<div class="information grid_5 tableItem">
life science and biomedical <br/>
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information grid_5 tableItem caseStudyTitle">
<a href="https://www.ebi.ac.uk/metabolights/" target="_blank">Metabolights</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.ebi.ac.uk" target="_blank">European Bioinformatics Institute (EBI)</a>, UK
</div>
<div class="information grid_5 tableItem">
metabolomics
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="https://genelab-data.ndc.nasa.gov/genelab/">NASA GeneLab Data Repository</a>
</div>
<div class="information grid_5 tableItem">
<a href="https://www.nasa.gov/" target="_blank">National Aeronautics and Space Administration (NASA)</a>, USA
</div>
<div class="information grid_5 tableItem">
space biology
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="https://cssi-dcc.nci.nih.gov/cssiportal/">CSSI Data Coordinating Center (DCC)</a>
</div>
<div class="information grid_5 tableItem">
<a href="https://frederick.cancer.gov/" target="_blank">Frederick National Laboratory for Cancer Research</a>, USA
</div>
<div class="information grid_5 tableItem">
cancer and biomedical
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="https://cesgo.genouest.org">CeSGO</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.inria.fr/en/" target="_blank">INRIA</a> and Brittany region, France
</div>
<div class="information grid_5 tableItem">
all types
</div>
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</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="https://dataverse.harvard.edu/">Harvard DataVerse</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.harvard.edu" target="_blank">Harvard University</a>, USA
</div>
<div class="information grid_5 tableItem">
all types
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="https://documentation.tgac.ac.uk/display/COPO/Overview">Collaborative Open Plant Omics
(COPO)</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.bbsrc.ac.uk" target="_blank">BBSRC</a>, UK
</div>
<div class="information grid_5 tableItem">
plant sciences
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="http://www.transplantdb.eu">transPLANT</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.transplantdb.eu/partners" target="_blank">transPLANT Consortium</a>,
European Union
</div>
<div class="information grid_5 tableItem">
plant genomic variation
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="https://urgi.versailles.inra.fr/ephesis/ephesis/viewer.do#dataResults/trialSetIds=5,6,7">INRA
Plant Phenotying</a>
</div>
<div class="information grid_5 tableItem">
<a href="https://urgi.versailles.inra.fr/" target="_blank">Unité de Recherche Génomique Info,
INRA Versailles</a>, France
</div>
<div class="information grid_5 tableItem">
high-throughput plant phenotyping
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="http://cosmos-fp7.eu/index.html">COSMOS - COordination Of Standards In MetabOlomicS</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://cosmos-fp7.eu/partner.html" target="_blank">COSMOS Consortium</a>, European Union
</div>
<div class="information grid_5 tableItem">
metabolomics
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="http://phenomenal-h2020.eu/">PhenoMeNal</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://phenomenal-h2020.eu/home/members/" target="_blank">PhenoMeNal Consortium</a>,
European Union
</div>
<div class="information grid_5 tableItem">
metabolomics
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="https://mastr-ms.readthedocs.org/en/master/">Mastr-MS</a>
</div>
<div class="information grid_5 tableItem">
<a href="https://ccg.murdoch.edu.au" target="_blank">Centre for Comparative Genomics</a> and
<a href="http://www.metabolomics.net.au" target="_blank">Metabolomics Australia</a>, Australia
</div>
<div class="information grid_5 tableItem">
metabolomics
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="http://enanomapper.net">eNannoMapper</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://enanomapper.net/partners" target="_blank">eNanoMapper Consortium</a>, European
Union
</div>
<div class="information grid_5 tableItem">
proteomics, nanomaterial, toxicology
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information grid_5 tableItem caseStudyTitle">
<a href="http://library.stanford.edu/research/data-management-services/data-best-practices/creating-metadata/metadata-tools" target="_blank">Stanford University Libraries</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.stanford.edu" target="_blank">Stanford University</a>, USA
</div>
<div class="information grid_5 tableItem">research data<br/>
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information grid_5 tableItem caseStudyTitle">
<a href="http://researchdata.ox.ac.uk/home/tools-services-and-training/browse-subject/science-resources/" target="_blank">Research Data Oxford</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.ox.ac.uk" target="_blank">University of Oxford</a>, UK
</div>
<div class="information grid_5 tableItem">research data<br/>
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="https://stemcellcommons.github.io/cscb-website/stem-cell-commons">Stem Cell Commons</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.hsph.harvard.edu" target="_blank">Harvard School of Public Health</a>, USA
</div>
<div class="information grid_5 tableItem">
microarray, NGS
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="https://github.com/rmylonas/MetaDB">MetaDB</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.fmach.it" target="_blank">Edmund Mach Foundation</a>, Italy
</div>
<div class="information grid_5 tableItem">
metabolomics, mass spectrometry, LC-MS, GC-MS
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
<a href="http://www.dixa-fp7.eu">Data infrastructure for chemical safety (diXa)</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.dixa-fp7.eu/consortium" target="_blank">diXa Consortium</a>, European Union
</div>
<div class="information grid_5 tableItem">
toxicology, toxicogenomics
</div>
<div class="clear"></div>
</div>
<!--BioPlatforms Australia-->
<div class="caseStudy">
<div class="information in grid_5 tableItem caseStudyTitle">
Bioplatforms Australia framework data initiative
</div>
<div class="information grid_5 tableItem">
<a href="http://bioplatforms.com.au" target="_blank">Bioplatforms Australia</a>, Australia
</div>
<div class="information grid_5 tableItem">
wheat genotyping and pathogen; pest; soil biodiversity, metagenomics<br/>
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information grid_5 tableItem caseStudyTitle">
<a href="https://data.csiro.au">CSIRO dataset portal</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.csiro.au/" target="_blank">Commonwealth Scientific and industrial Research
Organisation (CSIRO)</a>, Australia
</div>
<div class="information grid_5 tableItem">
insect toxicity; bacterial genomics<br/>
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information grid_5 tableItem caseStudyTitle">
<a href="http://lincs.hms.harvard.edu/data/metadata-standards/" target="_blank">HMS Library of
Integrated
Network-based Cellular Signatures (LINCS) project</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://lincs.hms.harvard.edu">Harvard Medical School (HMS) LINCS Center</a>, USA
</div>
<div class="information grid_5 tableItem">
cellular signatures
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information grid_5 tableItem caseStudyTitle">
<a href="http://discovery.hsci.harvard.edu/" target="_blank">HSCI Stem cell Discovery engine</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://hsci.harvard.edu/" target="_blank">Harvard Stem Cell
Institute (HSCI)</a>
and <a href="http://hms.harvard.edu/" target="_blank">Harvard Medical School</a>, USA
</div>
<div class="information grid_5 tableItem">
tissue and cancer stem cell
</div>
<div class="clear"></div>
</div>
<div class="caseStudy">
<div class="information grid_5 tableItem caseStudyTitle">
<a href="http://pentaconhq.princeton.edu" target="_blank">Personalized NSAID Therapeutics
Consortium (PENTACON)</a>
</div>
<div class="information grid_5 tableItem">
<a href="http://www.nhlbi.nih.gov" target="_blank">National Heart, Lung, and Blood Institute
(NIH-NHLBI)</a>, USA
</div>
<div class="information grid_5 tableItem">
microarray, NGS, metabolomics, metagenomics, proteomics
</div>
<div class="clear"></div>