Paper Info
Title
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes.
Abstract
High-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.We 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.BiPON 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.
Year
DOI
Venue
2017
10.1186/s13326-017-0165-6
J. Biomedical Semantics
Keywords
Field
DocType
Biological ontology,Mathematical models,Multi-scale systemic description,Prokaryotic biological processes,Systems biology
Data science,Data integration,Data mining,Biological data,Process ontology,Biological Ontologies,Computer science,Prokaryotic cells,Systems biology,Structuring,Semantics
Journal
Volume
Issue
ISSN
8
1
2041-1480
Citations 
PageRank 
References 
0
0.34
16
Authors
8
Name
Order
Citations
PageRank
Vincent J Henry100.34
Anne Goelzer2253.17
Arnaud Ferré300.34
Stephan Fischer400.34
Marc Dinh510.72
Valentin Loux6162.09
Christine Froidevaux747971.56
Fromion, Vincent863.20