Expanding BioPAX format by integrating Gene Regulation

Authors

  • Irma Martínez-Flores Centro de Ciencias Genómicas, UNAM
  • Verónica Jiménez-Jacinto Centro de Ciencias Genómicas, UNAM
  • Alejandra C. López-Fuentes Centro de Ciencias Genómicas, UNAM
  • Julio Collado-Vides Centro de Ciencias Genómicas, UNAM

DOI:

https://doi.org/10.14806/ej.16.1.186

Keywords:

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

Abstract

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.

Author Biographies

  • Irma Martínez-Flores, Centro de Ciencias Genómicas, UNAM
    Programa de Genómica Computacional, Dr.
  • Verónica Jiménez-Jacinto, Centro de Ciencias Genómicas, UNAM
    Programa de Genómica Computacional, M.C.
  • Alejandra C. López-Fuentes, Centro de Ciencias Genómicas, UNAM
    Programa de Genómica Computacional, I.IF.
  • Julio Collado-Vides, Centro de Ciencias Genómicas, UNAM
    Programa de Genómica Computacional, Dr.
Embnet.journal 16.1

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Published

2010-08-04

Issue

Vol. 16 No. 1

Section

Research Papers

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