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Process, environment, organism (PREGO) is a systems-biology approach to elucidate ecosystem function at the microbial dimension. To understand how ecosystems function it is fundamental to understand what processes occur in which environments (where), and which organisms carry them out (who). Its main motivation is to provide a one-stop-shop for researchers interested in searching and visually exploring such what - where - who associations.
Correspondence: pafilis[at]hcmr.gr; prego[at]hcmr.gr; Tel: +30 2810 337748
Institute of Marine Biology, Biotechnology & Aquaculture HCMR Thalassocosmos 71500 Gournes, Crete, Greece P.O.Box 2214, 71003 Heraklion, Crete, Greece
If you use PREGO in your research or analysis please cite:
Zafeiropoulos, H.; Paragkamian, S.; Ninidakis, S.; Pavlopoulos, GA.; Jensen, LJ.; Pafilis, E. PREGO: a literature and data-mining resource to associate microorganisms, biological processes, and environment types. Microorganisms 10.2 (2022). Full text{:target="_blank" rel="noopener"}
PREGO team is happy to receive feedback from its' users! If you have any ideas, requests or bugs please submit an issue at our repository{:target="_blank" rel="noopener"} and/or send an email (see above Contact).
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The PREGO software along with the mined associations is under CC BY 4.0 license (raw data from the resources are have their own licenses). Scripts where additional libraries have been used are subject to their individual licenses.
prego_gathering_data{:target="_blank" rel="noopener"}, here are the scripts that gather data from resources and extract associations.
prego_daemons{:target="_blank" rel="noopener"}, here are the scripts that periodically update the PREGO knowledge base.
prego_mappings{:target="_blank" rel="noopener"}, here are the scripts that transform all identifiers to the ones that PREGO has adopted.
prego_statistics{:target="_blank" rel="noopener"}, here are the scripts which count all contents of PREGO and summarize them in the different taxonomic ranks.
Additional software and curated lists are under their individual licenses:
text mining tagger{:target="_blank" rel="noopener"}, BSD 2-Clause "Simplified" License
mamba{:target="_blank" rel="noopener"}, the web server, Copyright, Sune Pletscher-Frankild and Lars Juhl Jensen, University of Copenhagen. All rights reserved.
tagger dictionary{:target="_blank" rel="noopener"} is the basis of knowledge of taxa, environments, processes and molecular functions that the tagger extracts. Available at: https://download.jensenlab.org/prego_dictionary.tar.gz, CC-BY license
This project has received funding from the Hellenic Foundation for Research and Innovation (HFRI) and the General Secretariat for Research and Innovation (GSRI) (grant No 241).