Heterogeneous biological data integration with declarative query language

Abstract

The requirements for scalable integration systems for modern biology are indisputable, due to the very large, heterogeneous, and complex datasets available in public databases. The management and fusion of this big data with local databases represents a major challenge, since it underlies the computational inferences and models that will be subsequently generated and validated experimentally. In this paper, we present an alternative conception for local integration, called BIRD (Biological Integration and Retrieval Data), based on four concepts: (i) a hybrid flat file and relational database architecture permits the rapid management of large volumes of heterogeneous datasets; (ii) a generic model allows the simultaneous organization and classification of local databases according to real-world requirements; (iii) configuration rules are used to divide and map each resource into several model entities; and (iv) a simple, declarative query language (BIRD-QL) facilitates information extraction from heterogeneous datasets. This flexible, generic design allows the integration of diverse formats in a searchable database with high-level functionalities depending on the specific scientific context. It has been validated in the context of real world projects, notably the SM2PH (Structural Mutation to the Phenotypes of Human Pathologies) project.