Bio-Curation for Cellular Signalling: The KAMI Project

  • Russ Harmer
  • Yves-Stan Le Cornec
  • Sébastien Légaré
  • Ievgeniia Oshurko
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10545)


The general question of what constitutes bio-curation for rule-based modelling of cellular signalling is posed. A general approach to the problem is presented, based on rewriting in hierarchies of graphs, together with a specific instantiation of the methodology that addresses our particular bio-curation problem. The current state of the ongoing development of the KAMI (Knowledge Aggregator & Model Instantiator) bio-curation tool, based on this approach, is detailed along with our plans for future development.



This work was sponsored by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under grant numbers W911NF-14-1-0367 and W911NF-15-1-0544. The views, opinions, and/or findings contained in this report are those of the authors and should not be interpreted as representing the official views or policies, either expressed or implied, of the Defense Advanced Research Projects Agency or the Department of Defense.

The first author thanks specially Walter Fontana for many discussions over the years related to this work. Thanks also to Pierre Boutillier, John Bachman and Ben Gyori; and to Adrien Basso-Blandin and Ismaïl Lahkim Bennani who worked on prototypes of KAMI and ReGraph respectively.


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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Russ Harmer
    • 1
  • Yves-Stan Le Cornec
    • 1
  • Sébastien Légaré
    • 1
  • Ievgeniia Oshurko
    • 1
  1. 1.Université de Lyon, CNRS – ENS Lyon – Université Claude Bernard Lyon 1, LIPLyonFrance

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