NLIMED: Natural Language Interface for ModelEntity Discovery in Biosimulation ModelRepositories

Abstract

Semantic annotation is a crucial step to assure reusability and reproducibility of biosimulation models in biology and physiology. For this purpose, the COmputational Modeling in BIology NEtwork (COMBINE) community recommends the use of the Resource Description Framework (RDF). This grounding in RDF provides the flexibility to enable searching for entities within models (e.g. variables, equations, or entire models) by utilising the RDF query language SPARQL. However, the rigidity and complexity of the SPARQL syntax and the nature of the tree-like structure of semantic annotations, are challenging for users. Therefore, we propose NLIMED, an interface that converts natural language queries into SPARQL. We use this interface to query and discover model entities from repositories of biosimulation models. NLIMED works with the Physiome Model Repository (PMR) and the BioModels database and potentially other repositories annotated using RDF. Natural language queries are first chunked into phrases and annotated against ontology classes and predicates utilising different natural language processing tools. Then, the ontology classes and predicates are composed as SPARQL and finally ranked using our SPARQL Composer and our indexing system. We demonstrate that NLIMEDs approach for chunking and annotating queries is more effective than the NCBO Annotator for identifying relevant ontology classes in natural language queries. Comparison of NLIMEDs behaviour against historical query records in the PMR shows that it can adapt appropriately to queries associated with well-annotated models.