Annotation of environmental OMICS data: application to the transcriptomics domain.
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.
Morrison
Norman
N
School of Computer Science, University of Manchester, Manchester, United Kingdom. Norman.Morrison@manchester.ac.uk
Wood
A Joseph
AJ
Hancock
David
D
Shah
Sonia
S
Hakes
Luke
L
Gray
Tanya
T
Tiwari
Bela
B
Kille
Peter
P
Cossins
Andrew
A
Hegarty
Matthew
M
Allen
Michael J
MJ
Wilson
William H
WH
Olive
Peter
P
Last
Kim
K
Kramer
Cas
C
Bailhache
Thierry
T
Reeves
Jonathan
J
Pallett
Denise
D
Warne
Justin
J
Nashar
Karim
K
Parkinson
Helen
H
Sansone
Susanna-Assunta
SA
Rocca-Serra
Philippe
P
Stevens
Robert
R
Snape
Jason
J
Brass
Andy
A
Field
Dawn
D
D004463:Ecology / Q000592:standards*; D004777:Environment; D020869:Gene Expression Profiling; D023281:Genomics / Q000592:standards*; D015201:Meta-Analysis as Topic; D020411:Oligonucleotide Array Sequence Analysis