Approach

Which is our aim?

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.

What is the scientific background?

On 2008 in an innovative study, Jeroen Raes and Peer Bork first argued that is “time to consider molecular systems biology at the ecosystem level”. The era of eco-systems biology had already started.

African dust “veil” as captured in South Heraklion, Crete March 2018

The information hidden in the vast body of biology literature is of great importance. Processes - organisms - environments associations already recorded in literature as well as associations not yet recorded but can be extracted from the literature thanks to text-mining techniques can be further exploited.

At the same time, ‘omics technologies, such as metagenomics, metatranscriptomics and metaproteomics have ensured an overall characterization of microbial ecosystems.

The data produced along with the information gathered are valuable. In the case of microbial ecology, their integration shall contribute in elucidating crucial parts of the ecological functioning.

As also Raes and Bork pointed out in their study, the integration of such networks and merging with the macroecological theory may help us in our attempt to understand the wiring of the main biological systems.

Where do we draw inspiration from?

Pioneers in such integrative approaches are the STRING and STITCH data-(knowledge)-bases (and family of tools). Both systematically collect pieces of information from a number of interaction databases, literature mining analyses, experimental datasets and more. Among others, key features they build upon: a consistent association scoring scheme, interaction source tracking provenance, user friendly interface with ready-to-print visual components.

What is coming up?

Large - scale text-mining, data-mining, and network analysis will all be combined in the PREGO project in an attempt to understand further ecosystem functioning. Three different modules for extracting association will be implemented and a knowledge base will be produced with the results of all those modules.

Finally, a web-platform will render the computed Process - Environment - Organism associations searchable by text, ontology terms, organism names, and sequences.