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Nassar2022 - Microbiome body-site NER model

ABSTRACT: body-site model is a Named Entity Recognition (NER) model that identifies and annotates the body-site of microbiome samples in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with body-site metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications

SUBMITTER: Maaly Nassar  

PROVIDER: MODEL2202160002 | BioModels | 2023-09-13

REPOSITORIES: BioModels

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A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications.

Nassar Maaly M   Rogers Alexander B AB   Talo' Francesco F   Sanchez Santiago S   Shafique Zunaira Z   Finn Robert D RD   McEntyre Johanna J  

GigaScience 20220801

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, especially when comparing results between independent studies, is that key metadata about the sample and molecular methods used to extract and sequence the ge  ...[more]

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