CLAug 12, 2016Code
Extracting Biological Pathway Models From NLP Event RepresentationsMichael Spranger, Sucheendra K. Palaniappan, Samik Ghosh
This paper describes an an open-source software system for the automatic conversion of NLP event representations to system biology structured data interchange formats such as SBML and BioPAX. It is part of a larger effort to make results of the NLP community available for system biology pathway modelers.
CLAug 12, 2016
Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR PathwayMichael Spranger, Sucheendra K. Palaniappan, Samik Ghosh
This paper evaluates the difference between human pathway curation and current NLP systems. We propose graph analysis methods for quantifying the gap between human curated pathway maps and the output of state-of-the-art automatic NLP systems. Evaluation is performed on the popular mTOR pathway. Based on analyzing where current systems perform well and where they fail, we identify possible avenues for progress.