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1.  ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level 
Bioinformatics  2010;26(18):2354-2356.
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
doi:10.1093/bioinformatics/btq415
PMCID: PMC2935443  PMID: 20679334
2.  Towards Interoperable Reporting Standards for Omics Data: Hopes and Hurdles 
Background
As the size and complexity of scientific datasets and the corresponding information stores grow, standards for collecting, describing, formatting, submitting and exchanging information are playing an increasingly active role. Several initiatives occupy strategic positions in the international scenario, both within and across domains. However, the job of harmonising reporting standards is still very much a work in progress; both software interoperability and the data integration remain challenging as things stand.
Results
The status quo with respect to standardization initiatives is summarized here, with particular emphasis on the motivation for, and the challenges of, ongoing synergistic activities amongst the academic community focused on the creation of truly interoperable standards.
Conclusions
Groups generating standards should engage with ongoing cross-domain activities to simplify the integration of heterogeneous data sets to the greatest possible extent.
PMCID: PMC3041584  PMID: 21347181
3.  ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression 
Nucleic Acids Research  2008;37(Database issue):D868-D872.
ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse—a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas—a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200 000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently—ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.
doi:10.1093/nar/gkn889
PMCID: PMC2686529  PMID: 19015125

Results 1-3 (3)