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Updates from Europe PMC, a global database of life sciences literature

Europe PMC team

 | 11 November 2020


 | Editor's pick

Enriching Europe PMC publications with Metagenomics annotations

We are excited to announce the recent release of metagenomics annotations for Europe PMC publications. Thanks to the machine learning framework of Dr. Maaly Nassar for the joint EMERALD project between Europe PMC and MGnify teams, recognising metagenomics key terms in literature can now provide detailed biome descriptions for unravelling microbial implications in a variety of environmental-, engineered- and host-associated phenomena. Using a mixture of a literature-based machine learning (ML) and natural language processing (NLP) approaches, terms pertinent to 16 novel metagenomics concepts were identified in Europe PMC literature. Those concepts cover entities related to biome sample and origin as well as metagenomics experimental methods, and are all available in the Europe PMC annotations platform. Check the table below to learn about these concepts (annotation types) and their descriptions.

Annotation type



The organism where the microbiome is found


Microbiome’s man-made environment


Micrbiome’s natural environment


Sampling date


Microbiome’s place or geocoordinates


Microbiome’s site within place


Host body region/structure where microbiome is found


Host/Environment state


Sample from which the microbiome is extracted


Host/Environment treatments


Nucleic acid extraction-kit


Target gene(s) (e.g. hypervariable regions of 16s/18s rRNA gene)


PCR primers


Library strategy (e.g amplicon, whole metagenome)


Library construction method (e.g. paired-end, single-end)


Sequencing platform

Publications with the new annotations are searchable on Europe PMC using the search syntax (ANNOTATION_PROVIDER:”Metagenomics”). Entity types can be highlighted in the text of open access articles using the SciLite annotations tool.

Additionally, these annotations are available for programmatic access via Europe PMC search and annotation APIs. 

Explore metagenomics annotation types in Europe PMC and give us your feedback. Want to know more about Europe PMC annotation platform? Get in touch with

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Europe PMC is a service of the Europe PMC Funders' Group, in partnership with EMBL’s European Bioinformatics Institute (EMBL-EBI); and in cooperation with the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NCBI/NLM) . It includes content provided to the PubMed Central (NLM/PMC) archive by participating publishers.