Expanding BioPAX format by integrating Gene Regulation

Irma Martínez-Flores, Verónica Jiménez-Jacinto, Alejandra C. López-Fuentes, Julio Collado-Vides


We are currently working in collaboration with BioPAX, specifically in the expansion of the ontology related to transcriptional regulation of bacteria. RegulonDB has been the main source of data, since the information curated in this database is high quality, as well as very complete and updated.

This work describes in general terms the process that was followed to get a suitable mapping template document, which shows RegulonDB data with their corresponding BioPAX classes. The process of how the implementation has been done is also described. The way this process helped to develop a more complete and robust format is also explained.


ontologies; BioPAX; RegulonDB; standard exchange formats; biological databases; transcriptional regulation


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