Standard reporting requirements for biological sam

Authors: Norman Morrison Dan Bearden Jacob G Bundy Tim Collette Felicity Currie Matthew P Davey Nathan S Haigh David Hancock Oliver A H Jones Simone Rochfort SusannaAssunta Sansone Dalibor Štys Quincy Teng Dawn Field Mark R Viant

Publish Date: 2007/08/24

Volume: 3, Issue: 3, Pages: 203-210

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Abstract

Metabolomic technologies are increasingly being applied to study biological questions in a range of different settings from clinical through to environmental As with other highthroughput technologies such as those used in transcriptomics and proteomics metabolomics continues to generate large volumes of complex data that necessitates computational management Making sense of this wealth of information also requires access to sufficiently detailed and well annotated metadata Here we provide standard reporting requirements for describing biological samples taken from an environmental context and involved in metabolomic experiments It is our intention that these reporting requirements should guide and support the standardised annotation dissemination and interpretation of environmental metabolomics metadataHighthroughput omic technologies metabolomics proteomics transcriptomics etc continue to generate a wealth of data that when analysed in unison potentially offer the key to our most comprehensive understanding of the fundamental complexities of life to date Climate change developing cleaner energy sources combating environmental pollution halting loss of biodiversity improving nutrition and formulating directed heath care are some of the major challenges facing society today In order to address these challenges using omic technologies it is important to be able to place the data they produce in context Questions one might want to ask include What was the original purpose of the experiment What was the biological sample used Where was it located When was it obtained What were the environmental conditions This type of ‘data about data’ or metadata is most often stored in laboratory note books occasionally summarised for human consumption in scientific journals but all too frequently some information remains only in the mind of the investigator Concomitant with an increasing number of omic experiments now being carried out the quantity of associated experimental metadata has reached unprecedented levels and traditional approaches to biological metadata management are no longer adequate In order to make use of this knowledge there is a pressing need for formal approaches to experimental metadata annotation storage and retrieval Here we the Metabolomics Standards InitiativeEnvironmental Context Working SubGroup MSIECWSG present a first step towards addressing this need in the context of environmental metabolomicsThis effort should be considered within the wider context of the reporting requirements for all types of biological samples in metabolomics experiments currently being developed by the Metabolomics Society http//wwwmetabolomicssocietyorg/—Metabolomics Standards Initiative MSI of which it is part See Preface this issue Additionally the requirements we have identified should be thought of as minimal and should not be considered as an exhaustive setIt is our intention that these reporting requirements should guide standardised annotation and support the development of a data exchange format and ontology for the dissemination and meaningful interpretation of environmentally derived metabolomic data Furthermore they should aim to do so in a range of identifiable contexts such as academic journals software tools and public databasesConsistent with a general description of sample for omics technology Morrison et al 2006a we define here a ‘biological sample’ as a discrete entity comprised of one or more organisms or parts thereof Examples include a species of plant or animal a community of bacteria a tissue biopsy or a biofluid eg urine Furthermore a biological sample may also include a physical substrate as a component part Examples include soil sediment seawater or icecore samplesA search of the literature provides many and varied definitions of the term ‘environment’ indicating the context dependency and semantic heterogeneity in which it is used Famously when asked for his definition Albert Einstein replied “The environment is everything that is not me” This erudite response captures the fact that the environment is defined as the totality of circumstances external to a definable entity In the context of these reporting requirements we define the environment as everything external to the ‘biological sample’ under investigation The challenge therefore is not to provide reporting requirements for everything but to provide a framework where the environmental features considered relevant to a particular sample which will be highly context dependent can be captured in a structured form We have also tried to arrange our requirements in a manner which makes them flexible and extensible so that they can adapt to the needs of the community in the futureThis working group considers ‘environmental metabolomics’ to be the application of metabolomics to the investigation of both freeliving organisms obtained directly from the natural environment whether studied in that environment or transferred to a laboratory for further experimentation and of organisms reared under laboratory conditions whether studied in the laboratory or transferred to the environment for further experimentation where any laboratory experiments specifically serve to mimic scenarios encountered in the natural environment

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