ArticleMicroorganisms2022
PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types.
Article in Microorganisms, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Bacterial and Fungal Community Shifts and Environmental Drivers in Talahao Coal Mine Water.Microorganisms · 2026Article
- Structural and evolutionary constraints shape adaptive landscapes of immune-related genes across mammalian phylogeny.PloS one · 2025Article
- Darling (v2.0): Mining disease-related databases for the detection of biomedical entity associations.Computational and structural biotechnology journal · 2025Article
- BioTextQuest v2.0: An evolved tool for biomedical literature mining and concept discovery.Computational and structural biotechnology journal · 2024Article
- Microbial co-occurrence network demonstrates spatial and climatic trends for global soil diversity.Scientific data · 2024Article
- Genomic insights into Yak (Bos grunniens) adaptations for nutrient assimilation in high-altitudes.Scientific reports · 2024Article
- Establishing the ELIXIR Microbiome Community.F1000Research · 2024Article
- Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources.Bioinformatics (Oxford, England) · 2023Article
- Arena3DNAR genomics and bioinformatics · 2023Article
- Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach.PloS one · 2023Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.GigaScience · 2022Article
- A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications.GigaScience · 2022Article
- New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?Journal of fungi (Basel, Switzerland) · 2022Review
- Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining.Biomolecules · 2022Article
- Large scale text mining for deriving useful insights: A case study focused on microbiome.Frontiers in physiology · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.