Dataset Information

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 of all involved molecules. We further showed that the information of molecules such as molecular types or molecular properties can be deduced by automatic reasoning using logical rules. The information necessary to populate BiPOm can be extracted from existing databases or existing bio-ontologies.

Conclusion

BiPOm provides a formal rule-based knowledge representation to relate all cellular components together by considering the cellular system as a whole. It relies on a paradigm shift where the anchorage of knowledge is rerouted from the molecule to the biological process.

Availability

BiPOm can be downloaded at https://github.com/SysBioInra/SysOnto.

SUBMITTER: Henry V

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

REPOSITORIES: biostudies-literature

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Publications

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

Henry Vincent V Saïs Fatiha F Inizan Olivier O Marchadier Elodie E Dibie Juliette J Goelzer Anne A Fromion Vincent V

BMC bioinformatics 20200723 1

<h4>Background</h4>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.<h4>Results</h4>We introduce BiPOm (Biological interlocked Pro ...[more]

PMID: 32703160

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Dataset Information

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

Background

Results

Conclusion

Availability

Publications

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

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