Pathway Synthesis Using the Act Ontology

Saurabh Srivastava, Jonathan Kotker, Stephi Hamilton, Paul Ruan, Jeff Tsui, J. Christopher Anderson, Rastislav Bodik, and Sanjit A. Seshia. Pathway Synthesis Using the Act Ontology. In Proceedings of the 4th International Workshop on Bio-Design Automation (IWBDA), June 2012.

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Abstract

We describe here the Act Ontology, a formalism for uniformly describing biochemical function, and its use in building an enzymatic pathway synthesizer. A formal description of biochemical function allows us to reason about it, and, for the particular case of enzymes, this function allows us to build a synthesizer tool that given a target chemical can automatically infer the most likely pathway that leads to it. The pathway can include known as well as hypothetical enzymes with predicted function.

BibTeX

@InProceedings{srivastava-iwbda12,
  author = 	 {Saurabh Srivastava and Jonathan Kotker and Stephi Hamilton and Paul Ruan and Jeff Tsui and J. Christopher Anderson and Rastislav Bodik and Sanjit A. Seshia},
  title = 	 {Pathway Synthesis Using the Act Ontology},
  booktitle = 	 {Proceedings of the 4th International Workshop on Bio-Design Automation (IWBDA)},
  month = {June},
  year = 	 {2012},
  abstract = {We describe here the Act Ontology, a formalism for uniformly 
describing biochemical function, and its use in building an enzymatic pathway synthesizer. 
A formal description of biochemical function allows us to reason about it, and, 
for the particular case of enzymes, this function allows us 
to build a synthesizer tool that given a target chemical can 
automatically infer the most likely pathway that leads to 
it. The pathway can include known as well as hypothetical 
enzymes with predicted function.},
}