We address the problem of semantic querying of relational databases (RDB) modulo knowledge bases using very expressive knowledge representation formalisms, such as full first-order logic or its various fragments. We propose to use a first-order logic (FOL) reasoner for computing schematic answers to deductive queries, with the subsequent instantiation of these schematic answers using a conventional relational DBMS. In this research note, we outline the main idea of this technique -- using abstractions of databases and constrained clauses for deriving schematic answers. The proposed method can be directly used with regular RDB, including legacy databases. Moreover, we propose it as a potential basis for an efficient Web-scale semantic search technology.
Summary: We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database. Availability: The Pathway Tools software and 20 BioCyc DBs in Tiers 1 and 2 are freely available to academic users; fees apply to some types of commercial use. For download instructions see http: BioCyc.org download.shtml Supplementary information: For more details on programmatic access to BioCyc DBs, see http: bioinformatics.ai.sri.com ptools ptools-resources.html Contact: [email protected]