ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories. Availability and Implementation: Software, documentation, case studies and implementations at http://www.isa-tools.org Contact: isatools@googlegroups.com

[1]  Andrew M. Waterhouse,et al.  The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation , 2009, Genome Biology.

[2]  J. M. Hancock,et al.  Post-publication sharing of data and tools , 2009, Nature.

[3]  Lennart Martens,et al.  The Proteomics Identifications database: 2010 update , 2009, Nucleic Acids Res..

[4]  Christopher G. Chute,et al.  BioPortal: ontologies and integrated data resources at the click of a mouse , 2009, Nucleic Acids Res..

[5]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[6]  Karlis Podnieks,et al.  A System for Information Management in BioMedical Studies—SIMBioMS , 2009, Bioinform..

[7]  Nigel W. Hardy,et al.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project , 2008, Nature Biotechnology.

[8]  Winston A Hide,et al.  Big data: The future of biocuration , 2008, Nature.

[9]  Raffaella Corvi,et al.  The carcinoGENOMICS project: critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays. , 2008, Mutation research.

[10]  Dennis B. Troup,et al.  NCBI GEO: archive for high-throughput functional genomic data , 2008, Nucleic Acids Res..

[11]  Paul T. Spellman,et al.  A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB , 2006, BMC Bioinformatics.

[12]  Nigel W. Hardy,et al.  The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". , 2008, Omics : a journal of integrative biology.

[13]  Hideaki Sugawara,et al.  Archiving next generation sequencing data , 2009, Nucleic Acids Res..

[14]  Nigel W. Hardy,et al.  The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics , 2007, Nature Biotechnology.

[15]  John Wilbanks,et al.  'Omics Data Sharing , 2009, Science.

[16]  Ibrahim Emam,et al.  ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression , 2008, Nucleic Acids Res..

[17]  Rolf Apweiler,et al.  The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries , 2006, BMC Bioinformatics.