4,695 research outputs found
A Data Transformation System for Biological Data Sources
Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data
Introducing Dynamic Behavior in Amalgamated Knowledge Bases
The problem of integrating knowledge from multiple and heterogeneous sources
is a fundamental issue in current information systems. In order to cope with
this problem, the concept of mediator has been introduced as a software
component providing intermediate services, linking data resources and
application programs, and making transparent the heterogeneity of the
underlying systems. In designing a mediator architecture, we believe that an
important aspect is the definition of a formal framework by which one is able
to model integration according to a declarative style. To this purpose, the use
of a logical approach seems very promising. Another important aspect is the
ability to model both static integration aspects, concerning query execution,
and dynamic ones, concerning data updates and their propagation among the
various data sources. Unfortunately, as far as we know, no formal proposals for
logically modeling mediator architectures both from a static and dynamic point
of view have already been developed. In this paper, we extend the framework for
amalgamated knowledge bases, presented by Subrahmanian, to deal with dynamic
aspects. The language we propose is based on the Active U-Datalog language, and
extends it with annotated logic and amalgamation concepts. We model the sources
of information and the mediator (also called supervisor) as Active U-Datalog
deductive databases, thus modeling queries, transactions, and active rules,
interpreted according to the PARK semantics. By using active rules, the system
can efficiently perform update propagation among different databases. The
result is a logical environment, integrating active and deductive rules, to
perform queries and update propagation in an heterogeneous mediated framework.Comment: Other Keywords: Deductive databases; Heterogeneous databases; Active
rules; Update
Query Evaluation in Deductive Databases
It is desirable to answer queries posed to deductive databases by computing fixpoints because such computations are directly amenable to set-oriented fact processing. However, the classical fixpoint procedures based on bottom-up processing — the naive and semi-naive methods — are rather primitive and often inefficient. In this article, we rely on bottom-up meta-interpretation for formalizing a new fixpoint procedure that performs a different kind of reasoning: We specify a top-down query answering method, which we call the Backward Fixpoint Procedure. Then, we reconsider query evaluation methods for recursive databases. First, we show that the methods based on rewriting on the one hand, and the methods based on resolution on the other hand, implement the Backward Fixpoint Procedure. Second, we interpret the rewritings of the Alexander and Magic Set methods as specializations of the Backward Fixpoint Procedure. Finally, we argue that such a rewriting is also needed in a database context for implementing efficiently the resolution-based methods. Thus, the methods based on rewriting and the methods based on resolution implement the same top-down evaluation of the original database rules by means of auxiliary rules processed bottom-up
Aggregated fuzzy answer set programming
Fuzzy Answer Set programming (FASP) is an extension of answer set programming (ASP), based on fuzzy logic. It allows to encode continuous optimization problems in the same concise manner as ASP allows to model combinatorial problems. As a result of its inherent continuity, rules in FASP may be satisfied or violated to certain degrees. Rather than insisting that all rules are fully satisfied, we may only require that they are satisfied partially, to the best extent possible. However, most approaches that feature partial rule satisfaction limit themselves to attaching predefined weights to rules, which is not sufficiently flexible for most real-life applications. In this paper, we develop an alternative, based on aggregator functions that specify which (combination of) rules are most important to satisfy. We extend upon previous work by allowing aggregator expressions to define partially ordered preferences, and by the use of a fixpoint semantics
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