Transforming Controlled Natural Language Biomedical Queries into Answer Set Programs

We introduce a controlled natural language for biomedical queries, called BIOQUERYCNL, and present an algorithm to convert a biomedical query in this language into a program in answer set programming (ASP)—a formal framework to automate reasoning about knowledge. BIOQUERYCNL allows users to express complex queries (possibly containing nested relative clauses and cardinality constraints) over biomedical ontologies; and such a transformation of BIOQUERYCNL queries into ASP programs is useful for automating reasoning about biomedical ontologies by means of ASP solvers. We precisely describe the grammar of BIOQUERYCNL, implement our transformation algorithm, and illustrate its applicability to biomedical queries by some examples.