Querying new information from knowledge sources, in general, and published literature, in particular, aims to provide precise and quick answers to questions raised about a system under study. In this paper, we present ACCORDION (Automated Clustering Conditional On Relating Data of Interactions tO a Network), a novel tool and a methodology to enable efficient answering of biological questions by automatically assembling new  or expanding existing models using published literature. Our approach integrates information extraction and clustering with simulation and formal analysis to allow for  automated iterative process that includes assembling, testing and selecting  most relevant models, given a set of desired system properties. We demonstrate our methodology on a model of the circuitry that controls T cell differentiation. To evaluate our approach, we compare the model that we obtained, using our automated model extension approach, with the previously published manually extended T cell  model. Besides being able to automatically and rapidly reconstruct the manually extended model , ACCORDION can provide multiple viable extended model versions . As such, it replaces large number of tedious or even impractical manual experiments and guides alternative interventions in real biological systems.
Querying new information from knowledge sources, in general, and published literature, in particular, aims to provide precise and quick answers to questions raised about a system under study. In this paper, we present ACCORDION (Automated Clustering Conditional On Relating Data of Interactions tO a Network), a novel tool and a methodology to enable efficient answering of biological questions by automatically assembling new , or expanding existing models using published literature. Our approach integrates information extraction and clustering with simulation and formal analysis to allow for an automated iterative process that includes assembling, testing and selecting the most relevant models, given a set of desired system properties. We applied our methodology to a model of the circuitry that con-trols T cell differentiation. To evaluate our approach, we compare the model that we obtained, using our automated model extension approach, with the previously published manually extended T cell differentiation model. Besides demonstrating automated and rapid reconstruction of a model that was previously built manually , ACCORDION can assemble multiple models that satisfy desired properties . As such, it replaces large number of tedious or even imprac-tical manual experiments and guides alternative hypotheses and interventions in biological systems.
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