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

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

Microorganisms

Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, P.O. Box 2214, 71003 Heraklion, Crete, Greece.

Published: January 2022

AI Article Synopsis

  • - PREGO is a comprehensive knowledge base that reveals the relationships between microorganisms, biological processes, and environmental conditions by utilizing text mining and data integration techniques to gather information from scientific literature and public databases.
  • - It contains an extensive collection of associations, including over 364,000 microbial taxa, 1,090 environmental types, and nearly 58 million total associations, accessible through a web portal, API, and bulk download options.
  • - The knowledge base aims to help researchers analyze and interpret experimental data, illustrated through a detailed presentation of its web interface and a case study of sulfur-cycle microbes in lagoon sediment.

Article 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 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. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO's capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8879827PMC
http://dx.doi.org/10.3390/microorganisms10020293DOI Listing

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