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A design and implementation of a declarative object-oriented language is presented. The language is strongly and mostly statically typed and supports software reuse techniques such as inheritance, subtype and parametric polymorphism. It differs significantly from the existing strongly typed object-oriented languages in its declarative constraint language which is based on a suitably extended logic...
A large portion of the Semantic Web is expected to be generated from the hidden Web of relational databases. The methods to translate relational content to OWL/RDF are reasonably straightforward, however these methods tend to lose most, if not all, important integrity constraints that are present in the relational data. In this paper, we present a para-consistent logic based method to maintain several...
The problem of extracting consistent query answers from an inconsistent database has been mainly approached from two directions: ldquorepairingrdquo the database or rewriting queries so that only consistent answers are returned. Logic programming with explicit negation has been widely used in order to specify repairs such that each answer set of the repair program corresponds to a repair. In this...
This paper proposes a graph data model that can represent the Biochemical Network. In the data model, the Node class and extended Node subclasses are used to represent the Biochemical Entities and Interactions, and the Edge class is used to describe the relationships between nodes. Furthermore, the Path and Hyper-Path classes are proposed to represent various processes and pathways. The study presented...
Incomplete information is usually present in a database in the form of null values. Several other forms of incompleteness such as fuzzy information, partial values and disjunctive information have been studied extensively. Most of the research on indefinite information has been carried out under the Closed World Assumption(CWA). In this paper, we present a data structure that supports the opposite...
Knowledge of neuronal circuitry is foundational to the neurosciences, but no tools have been developed for cataloguing this knowledge. Part of the problem is that the concepts used to describe neural circuits are rapidly evolving and vary substantially across different species. The NeuronBank project (http://neuronbank.org) is developing an informatics infrastructure for managing the dynamic, domain-specific...
In this paper, we propose two architectures for curating PDB data to improve its quality. The first one, PDB Data Curation System, is developed by adding two parts, Checking Filter and Curation Engine, between User Interface and Database. This architecture supports the basic PDB data curation. The other one, PDB Data Curation System with XCML, is designed for further curation which adds four more...
In this paper, we propose an architecture that extends the Object-Oriented Database (OODB) system architecture by adding domain specific additional layers to manage protein structure data. The two layers introduced above OODB are Protein-QL, domain-specific query language and Protein-OODB, a domain-specific data layer. This architecture is designed specifically for the protein domain, but it is the...
A novel neuron data model with a neuron domain specific query language is proposed in this paper. It is inspired by the project NeuronBank. This data model is composed of five components: neuron data structure, constraints, operations, domain-specific query language (NeuroQL), and controlled vocabulary. It can capture and enforce more domain semantics than traditional data models, such as attributes...
In this paper, we present the design and implementation of a protein structure data and analysis system that is only used in the lab for analyzing the proprietary data. It is capable of storing public protein data, such as the data in Protein Data Bank (PDB) Berman et al., (2000), and life scientists' proprietary data. This toolkit is targeted at life scientists who want to maintain proprietary protein...
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