The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes

Abstract

BackgroundHigh-throughput technologies produce huge amounts of heterogeneous biological data at all cellular levels. Structuring these data together with biological knowledge is a critical issue in biology and requires integrative tools and methods such as bio-ontologies to extract and share valuable information. In parallel, the development of recent whole-cell models using a systemic cell description opened alternatives for data integration. Integrating a systemic cell description within a bio-ontology would help to progress in whole-cell data integration and modeling synergistically.ResultsWe present BiPON, an ontology integrating a multi-scale systemic representation of bacterial cellular processes. BiPON consists in of two sub-ontologies, bioBiPON and modelBiPON. bioBiPON organizes the systemic description of biological information while modelBiPON describes the mathematical models (including parameters) associated with biological processes. bioBiPON and modelBiPON are related using bridge rules on classes during automatic reasoning. Biological processes are thus automatically related to mathematical models. 37% of BiPON classes stem from different well-established bio-ontologies, while the others have been manually defined and curated. Currently, BiPON integrates the main processes involved in bacterial gene expression processes.ConclusionsBiPON is a proof of concept of the way to combine formally systems biology and bio-ontology. The knowledge formalization is highly flexible and generic. Most of the known cellular processes, new participants or new mathematical models could be inserted in BiPON. Altogether, BiPON opens up promising perspectives for knowledge integration and sharing and can be used by biologists, systems and computational biologists, and the emerging community of whole-cell modeling.Electronic supplementary materialThe online version of this article (10.1186/s13326-017-0165-6) contains supplementary material, which is available to authorized users.

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

“…With the advent of the first whole-cell systemic models [32,46], we know that the level of knowledge is now sufficient to tackle the formalization of the cell functioning. A first step was achieved in previous works [34] and now in this paper. BiPOm provides a formal rule-based knowledge representation to relate all cellular components together by considering the cellular system as a whole.…”

“…However, enriching the ontology with precise information of molecule localization may be difficult, because the localization of molecules may not be well characterized experimentally, especially for eukaryotic cells. In addition, our ontology could be extended with other biological processes such as the gene-expression [34] using the same ontological model. Only the class hierarchy has to be extended with new subclasses such as a subclass of the class Participant representing the sequence patterns [14] or a subclass of the class Activity representing the RNA polymerase activity.…”

“…Only the class hierarchy has to be extended with new subclasses such as a subclass of the class Participant representing the sequence patterns [14] or a subclass of the class Activity representing the RNA polymerase activity. Finally, according to our previous works [34], each biological process could be linked by a formal property to a mathematical model that describes the kinetic behavior of the process. This could be achieved using a few additional properties and classes from the Bacterial interlocked Process ONtology (BiPON) [34].…”

“…Finally, according to our previous works [34], each biological process could be linked by a formal property to a mathematical model that describes the kinetic behavior of the process. This could be achieved using a few additional properties and classes from the Bacterial interlocked Process ONtology (BiPON) [34].…”

Automated generation of bacterial resource allocation models

“…Consequently, for encoding resource allocation models in RBApy, we chose not to follow a protein-centered representation as in SBML, but the formal process-centered representation of the bioontology BiPON [14]. The principle behind BiPON is to break down the cell as a system into intertwined biological processes, where each biological process is described as an input/output system itself.…”