Standard Annotation of Environmental OMICS Data: Application to the Transcriptomics Domain

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.

The Positive Role of the Ecological Community in the Genomic Revolution

“…With exact information on location -namely latitude/longitude/altitude(depth) -we can place biological samples and their molecules in a global reference. We can also combine this information with a vast array of geo-spatial information from a variety of sources (Lombardot et al, 2006;Morrison et al, 2006).…”

“…For example, the environmental genomics community in the UK has recently proposed an extension of MIAME ("Minimum Information about a Microarray Experiment") (Brazma et al, 2001), the accepted standard for the description of transcriptomic experiments. This extension, termed MIAME/Env, captures information on location, environmental conditions, biological treatments and phenotype of the samples under study (Morrison et al, 2006). The GSC has drawn on the Env specification to develop the MIGS specification and the Metabolomics Standards Initiative (MSI) is evaluating Env for the sake of describing metabolomic datasets (http://msiworkgroups.sourceforge.net/).…”

“…To do this, NEBC provides bioinformatics support, in particular through a freely available computing platform called Bio-Linux which contains a large number of bioinformatics tools that can evolve according to the needs of the community (Field et al). NEBC also works in the area of standards development and compliance (Morrison et al, 2006), and participates in community-building activities, such as the organization of workshops that bring researchers and data management experts together (Field et al, 2006b). …”

Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata

“…There is a strong need for developing methods to facilitate the capture of metadata describing the growing number of genomic and metagenomic projects, including information about isolation source and habitat (Morrison et al 2006;Field et al 2008). …”

“…For our purposes here, we define habitat as "the place or environment where an organism naturally or normally lives and grows." It is distinguished from "sample source", which is the environmental context in which a sample is collected, as defined in Morrison et al 2006. Multiple habitat terms can be associated with a species; by contrast, a sample is associated with a description of its (unique) source.…”