Annotation of environmental OMICS data: Application to the transcriptomics domain

Norman Morrison, A. Joseph Wood, David Hancock, Sonia Shah, Luke Hakes, Tanya Gray, Bela Tiwari, Peter Kille, Andrew Cossins, Matthew Hegarty, Michael J. Allen, William H. Wilson, Peter Olive, Kim Last, Cas Kramer, Thierry Bailhache, Jonathan Reeves, Denise Pallett, Justin Warne, Karim NasharHelen Parkinson, Susanna Assunta Sansone, Philippe Rocca-Serra, Robert Stevens, Jason Snape, Andy Brass, Dawn Field

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Researchers working on environmentally relevant organisms, populations, and communities are increasingly turning to the application of OMICS technologies to answer fundamental questions about the natural world, how it changes over time, and how it is influenced by anthropogenic factors. In doing so, the need to capture meta-data that accurately describes the biological "source" material used in such experiments is growing in importance. Here, we provide an overview of the formation of the "Env" community of environmental OMICS researchers and its efforts at considering the meta-data capture needs of those working in environmental OMICS. Specifically, we discuss the development to date of the Env specification, an informal specification including descriptors related to geographic location, environment, organism relationship, and phenotype. We then describe its application to the description of environmental transcriptomic experiments and how we have used it to extend the Minimum Information About a Microarray Experiment (MIAME) data standard to create a domain-specific extension that we have termed MIAME/Env. Finally, we make an open call to the community for participation in the Env Community and its future activities. © Mary Ann Liebert, Inc.
    Original languageEnglish
    Pages (from-to)172-178
    Number of pages6
    JournalOmics : a journal of integrative biology
    Volume10
    Issue number2
    DOIs
    Publication statusPublished - 2006

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