PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types – Talk by Savvas Paragkamian and Dr. Evangelos Pafilis

The talk title is: PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types

 

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 knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download.

(PREGO platform: https://prego.hcmr.gr/, Read more: https://doi.org/10.3390/microorganisms10020293)

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