PREGO article published at MDPI Microorganisms Special Issue of the 9th Conference of Mikrobiokosmos

PREGO is out!

We are on the air :) Very happy to share PREGO’s open access article at the Special Issue of the 9th Mikrobiokosmos Conference.

The full text article is available here in which, we introduce PREGO, a literature and data-mining resource to associate microorganisms, biological processes, and environment types. In addition, we provide a thorough description of the PREGO methodology and its contents. An example of usage is given as well to guide users to the features of the platform.

Last but not least, complementary tools are presented as well. All of them aiming to assist molecular ecologists from a different point of view.

Follow our twitter thread and let us know your impressions!

Some brief details

Which are the associations among microorganisms, environments and processes? PREGO aims to bring together these associations to a one-stop-shop to assist molecular ecologists to discover this hidden knowledge. Looking forward to your feedback!

It is mainly a text mining open source project that relies on the multi year efforts on data MGnifyDB, MG-RAST, IMG of JGI, NCBI BioProject, NCBI PubMed and NCBI Taxonomy and on standards, like Environment Ontology, Gene Ontology, Genome Standards.

Using APIs we regularly retrieve data from Literature (abstracts and full text), Environmental Samples and Genome Annotations and Isolates. From these data we find associations of microorganisms, environments and processes from comentions in text and co-occurrences in environmental samples and Isolates data and metadata. The unification of the identifiers of these entities is facilitated with the EXTRACT tagger.

Special Thanks

PREGO is a collaborative project with our longtime collaborators, Lars Julh Jensen and Georgios Pavlopoulos! Niko Kyrpides and Pier Buttigieg, a big thank you for your input and support.

We would like to thank our colleagues, Lucia Fanini, Christina Pavloudi, Ioulia Santi, George Tsamis, and Miguel Desmarais, for their contribution, great discussions, and their feedback throughout the development of PREGO. We also thank Antonis Potirakis and Dimitris Sidirokastritis for their sysadmin server support. We thank Michail Kouratoras for the design of the PREGO logo. Last but not least, we thank Manolis Badouvas for his administrative feedback and support.

A big thank you to ΕΛΙΔΕΚ - HFRI and ΓΓΕΚ - GSRI for their great support. PREGO would not be possible otherwise!

Follow-up developments and exciting new (applied) projects coming up; stay tuned :)