PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types.

ABSTRACT: To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO kno

SUBMITTER: Zafeiropoulos H 

PROVIDER: S-EPMC8879827 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature