BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint.

ABSTRACT:

Background

Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole-cell scale. In such representations, the cell is considered as a system composed of interlocked subsystems. The need is now to define a relevant formalization of the systemic description of cellular processes.

Results

We introduce BiPOm (Biological interlocked Process Ontology for metabolism) an ontology to represent metabolic processes as interlocked subsystems using a limited number of classes and properties. We explicitly formalized the relations between the enzyme, its activity, the substrates and the products of the reaction, as well as the active state

SUBMITTER: Henry V 

PROVIDER: S-EPMC7376860 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature