A new way to publish metagenomics studies

The explosion of metagenomics studies in recent years calls for a new publication format. Professor Folker Meyer introduces the Metagenome report, published in Standards in Genomic Sciences.

Metagenomics or environmental DNA sequencing is becoming more and more popular, with tens of thousands of groups using it for a wide variety of scientific problems. The resulting data sets are large and difficult to analyze often requiring years for the final analysis of data sets to be completed. Publishing the data prior to finishing the entire study provides a good way to both comply with the funding associated requirements of data release and also lets other researchers use the data in their studies.

With individual metagenomic projects ranging from a few gigabases to hundreds of gigabases, individual metagenome frequently having 500 million sequences, the primary data analysis is a considerable effort, making that data available to other researchers is a significant contribution in its own right, if the data is made “accessible” via the addition of appropriate descriptions aka metadata.

Standards in Genomic Sciences (SIGS) is now accepting Metagenome reports, a new article type designed to allow publication of your shotgun metagenomics data sets with metadata. It is similar to the various forms of genome publications, but for one or more shotgun metagenomes and the accompanying metadata. It creates a peer-reviewed, citable reference for the metagenomic data in your study and supports rapid publication of the data.

While the metagenome reports allow adding a limited set of conclusions and insights drawn from the data, their primary purpose is to get the word out about the data sets. The expectation is that you will report on your detailed analysis independently, citing your data as will others that use your data in their work.

SIGS has in the past used the standards maintained by the Genomics Standard Consortium (GSC), and similarly to the established SIGS genome reports, Metagenome reports come with a template, a number of required tables with GSC compliant metadata. Staying with a well-defined format ensures that the results are machine readable, making discovery of your data sets much easier for others. In addition to enabling discovery, GSC-compliant metadata are supported by the majority of the widely used tools and platforms e.g. MG-RAST or EBI’s MG-Portal or JGI’s IMG/M.

The Metagenome report requires addition of the metadata that you already had to provide to either MG-RAST or MG-Portal for releasing your data to the public, so they are easy to create from the data in either resource.

Folker Meyer

Folker Meyer is a computational biologist at Argonne National Laboratory and a Professor at the Department of Medicine, University of Chicago. He is the driving force behind the MG-RAST system for the analysis of environmental DNA.

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