Data Integration in Logic-based Models of Biological Mechanisms

Abstract

Discrete, logic-based models are increasingly used to describe biological mechanisms. Initially introduced to study gene regulation, these models evolved to cover various molecular mechanisms, such as signalling, transcription factor cooperativity, and even metabolic processes. The abstract nature and amenability of discrete models to robust mathematical analyses make them appropriate for addressing a wide range of complex biological problems. Recent technological breakthroughs have generated a wealth of high throughput data. Novel, literature-based representations of biological processes and emerging algorithms offer new opportunities for model construction. Here, we review up-to-date efforts to address challenging biological questions by incorporating omic data into logic-based models, and discuss critical difficulties in constructing and analysing integrative, large-scale, logic-based models of biological mechanisms.

A large-scale Boolean model of the Rheumatoid Arthritis Fibroblast-Like Synoviocytes predicts drug synergies in the arthritic joint

“…Besides building and analysing large-scale biological models, one of the main challenges in systems modelling is the use of standards and proper annotation of such models to enhance a model’s reusability (Niarakis et al , 2022, 2021). The models obtained in our pipeline are in a standard format (SBML-Qual) and thoroughly annotated using the MIRIAM scheme (Le Novère et al , 2005), including PubMed IDs and pathway identifiers to annotate components and reactions.…”

“…Discrete logic-based qualitative modelling has been increasingly used to model largescale networks for which kinetic data is scarce (Hemedan et al, 2022;Hall & Niarakis, 2021).…”

“…Discrete logic-based qualitative modelling has been increasingly used to model large-scale networks for which kinetic data is scarce (Hemedan et al , 2022; Hall & Niarakis, 2021). For example, in a Boolean model, each node can take only two values, 0 (FALSE) and 1 (TRUE).…”