Annotation of environmental OMICS data: application to the transcriptomics domain

OMICS. Summer 2006;10(2):172-8. doi: 10.1089/omi.2006.10.172.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Ecology / standards*
  • Environment*
  • Gene Expression Profiling*
  • Genomics / standards*
  • Meta-Analysis as Topic
  • Oligonucleotide Array Sequence Analysis*