Wednesday, 11 November 2020

Enriching Europe PMC publications with Metagenomics annotations

We are excited to announce the recent release of metagenomics annotations for Europe PMC publications. Thanks to our joint work with MGnify on the EMERALD project, 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

Description

Host

The organism where the microbiome is found

Engineered

Microbiome's man-made environment

Ecoregion

Micrbiome's natural environment

Date

Sampling date

Place

Microbiome's place or geocoordinates

Site

Microbiome's site within place

Body-site

Host body region/structure where microbiome is found

State

Host/Environment state

Sample-material

Sample from which the microbiome is extracted

Treatment

Host/Environment treatments

Kit

Nucleic acid extraction-kit

Gene

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

Primer

PCR primers

LS

Library strategy (e.g amplicon, whole metagenome)

LCM

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

Sequencing

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 annotations@europepmc.org


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