Anguix: Cell Signaling Modeling Improvement through Sabio-RK association to Reactome

Author(s)

Montoni, Fabio ; De Sousa, Ronaldo N. ; De Lima Junior, Marcelo B. ; Campos, Cristiano G. S. ; Wang, Willian ; Constantino, Vivian M. ; Sanctos, Cassia S. ; Armelin, Hugo A. ; Reis, Marcelo S. ; IEEE

• Document type: Journal article
• Source: 2022 IEEE 18TH INTERNATIONAL CONFERENCE ON E-SCIENCE (ESCIENCE 2022); v. N/A, p. 2-pg., 2022-01-01.

Abstract

Kinetics of biochemical reactions are widely spread in scientific papers and repositories such as Sabio-RK. This information is extremely important for the study of cell signaling pathways; however, to the best of our knowledge, there is no method available to integrate pathways reactions topology data with kinetic data. Therefore, we propose here an integration of kinetic data stored in Sabio-RK to the Reactome graph database. That integration, called Anguix, can be deployed using a Python program and also can be easily accessed using Neo4J. We believe the Anguix graph database might contribute to the modeling of cell signaling pathways, by combining the completeness of Reactome with kinetic and quantitative data stored in Sabio-RK. (AU)

• FAPESP's process: 20/08555-5 - Designing of a biochemical reaction database for model selection of cell signaling pathways
• Grantee: Fabio Montoni
• Support Opportunities: Scholarships in Brazil - Technical Training Program - Technical Training
• FAPESP's process: 13/07467-1 - CeTICS - Center of Toxins, Immune-Response and Cell Signaling
• Grantee: Hugo Aguirre Armelin
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 21/04355-4 - Efficient implementations of Bayesian methods for cell signaling pathway model selection
• Grantee: Willian Wang
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• FAPESP's process: 20/10329-3 - Bayesian model selection of cell signaling pathways and designing of cell growth classifiers
• Grantee: Cássia Sampaio Sanctos
• Support Opportunities: Scholarships in Brazil - Technical Training Program - Technical Training
• FAPESP's process: 19/24580-2 - Bayesian dynamic model selection of non-isolated cell signaling pathways
• Grantee: Ronaldo Nogueira de Sousa
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 19/21619-5 - Finding the Goldilocks zones of cell signaling pathways in cancer therapy
• Grantee: Marcelo da Silva Reis
• Support Opportunities: Regular Research Grants