EMERALD METAGENOMICS ANNOTATIONS PIPELINE

Metagenomics is a culture-independent method for studying the microbes inhabiting a particular environment. Comparing the composition of samples (functionally/taxonomically), either from a longitudinal study or cross-sectional studies can provide clues into how the microbiota has adapted to the environment. However, a recurring challenge is that key metadata about the sample and molecular methods used to extract and sequence the genetic material are often missing from sequence records, making it difficult to account for confounding factors. Nevertheless, this missing metadata may be found in the narrative of publications describing the research. This respository offers a new metagenomics annotations pipeline that regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles in EuropePMC. These metadata are now available for researchers to explore and retrieve in the MGnify and Europe PMC websites, and Europe PMC annotations API.