Title: Naturally Speaking: A Systems Biology Tool with Natural Language Interfaces


Author: Marco Antoniotti, Ian T. Lau, and Bud Mishra 


This short paper describes a systems biology software tool that can engage in 
a dialogue with a biologist by responding to questions posed to it in English 
(or another natural language) regarding the behavior of a complex biological 
system, and by suggesting a set of  facts  about the biological system based 
on a timetested  generate and test  approach. Thus, this bioinformatics system
improves the quality of the interaction that a biologist can have with a system
built on rigorous mathematical modeling, but without being aware of the 
underlying mathematically sophisticated concepts or notations. Given the nature 
of the mathematical semantics of our Simpathica/XSSYS tool, it was possible to
construct a well-founded natural language interface on top of the computational
kernel. We discuss our tool and illustrate its use with a few examples. The
natural language subsystem is available as an integrated subsystem of the
Simpathica/XSSYS tool and through a simple Web-based interface; we describe 
both systems in the paper. More details about the system can be found at: 
http://bioinformatics.nyu.edu, and its sub-pages.