Toshihisa Takagi

GENAS: a database system for nucleic acid sequence analysis.

A database system, named GENAS (GENe Analyzing System), for computer analysis of sequence was constructed using Adbis which is a relational database management system (1). GENAS enables us to retrieve any sequence data from EMBL nucleotide sequence data library (2) and readily to analyze them (if necessary, together with private data) by various application programs in a interactive manner. Analysis of structure of replication origin of replicons was demonstrated using this system.

Object-Oriented Database with Rule-Based Query Interface for Genomic Computation

A large amount of human genome data has been collected and efficient techniques for handling the data and for building and testing biological hypotheses are needed. We developed an object-oriented database system with rule-based query interface for genomic computation. The database is constructed on a commercially available object-oriented database system Gemstone and contains GenBank entries as complex objects. To handle complex objects in logical queries, concepts of meta variables and meta atoms are adopted in rule-based query interface. This system is powerful to construct database queries from simple keyword search to various biological hypothesis.

A deductive database system for analyzing human nucleotide sequence data

The analysis of the human genome is one of the most significant topics in both biology and medical science. There is a growing need for a well-designed database system for searching and analyzing the human genome data. We developed a deductive database system to search and analyze nucleotide sequence data derived from the GenBank primates data. A deductive database system is a next generation one and it contains an inference mechanism that can handle problems beyond the capabilities of classical database systems. Database queries are described in logical rules. These rules are simple even for molecular biologists who are not experts in computer programs because they are declarative and do not require the procedural commands that are usually used in computer programs. Furthermore, queries based on logical rules are powerful enough to express complicated biological problems. Particularly, recursive rules are suitable for examining secondary structures of nucleotide sequences. In our analysis of TfRs IRE, we noted five stem-and-loop structures.

Evaluation of a deductive database system for CAD applications

In the deductive database, a large number of query processing techniques has been proposed for the efficient processing of a large amount of data. Several deductive databases actually were proposed based on those techniques. There are only few cases among those, however, where such a system is applied to the practical problem. Consequently, it is not clear to what type of actual problems the deductive database can be applied. n n n nIn the CAD system, the “indirect” and “conditional” connection relations among components must be specified to utilize the design diagram more efficiently. It is proposed that the techniques of the deductive database can effectively be applied to such a problem to determine efficiently the connection relations. A prototype system was constructed to demonstrate the idea. The prototype is applied to a practical problem and the performance is evaluated. It is shown that the deductive database can effectively be applied to the forementioned problem. n n n nIn the course of this experiment, several observations are made concerning the realization of the query processing method in the deductive database. This paper outlines the constructed prototype system and discusses the result of evaluation. The range of application for the deductive database as well as the practical usefulness are discussed.

Bidirectional inference of mode information for logic programs

Mode information (directional information concerning the arguments of predicates) is important in improving the speed of the execution of logic programs. This paper proposes a bidirectional inference algorithm for inferring precise mode information. Compared with the conventional inference algorithms, the proposed algorithm has the following two features: (1) the algorithm utilizes not only the modes of the predicates at the top level but also the modes of the built-in predicates used in the program; and (2) by propagating the modes of the top level predicates top-down and that of the built-in predicates bottom-up, more precise mode information can be inferred.

A tool for constructing production systems on the deductive database system adbis

Abstract The authors have designed and implemented a tool for constructing production systems on the deductive database system Adbis that is a relational database management system with inference functions based on Horn set refutation procedures. The production systems developed by using this tool have the following characteristics: (1) users of them can handle large factual data as well as production rules since they are linked with a relational database through the Horn set refuter; (2) the users are able to easily perform a backward reasoning because the left-hand side and right-hand side of production rules are syntactically symmetrical; (3) the inference functions based on Horn set refutation procedures can be used not only for checking the applicability of production rules to data accessed by the production rules, but also for expressing and checking the integrity constraints which the data satisfies. This facility for integrity checking may be useful for debugging; (4) in future, the performance of the production systems are expected to be improved by using the results of much research in Horn set refuters and Prolog.