Relational Database Schema Research Articles

Modeling fuzzy information in fuzzy extended entity-relationship model and fuzzy relational databases

Computer applications in non-traditional area have put requirement on conceptual data modeling. Some conceptual data models, being the tool of design databases, have been proposed. Information in real world application is often vague or ambiguous. Currently few researches have been done in modeling fuzziness in conceptual data model and design of fuzzy databases. In this paper, based on fuzzy set theory, different levels of fuzziness are introduced into the EER (enhanced/extended entity-relationship) model and the corresponding representations are given. The EER model is then extended to fuzzy EER model. The formal mapping of the fuzzy EER model into the fuzzy relational database schema is proposed in the paper.

An interactive tool for UML class model evolution in database applications

In the context of model-driven development of database applications with UML, the (usually relational) database schema is obtained automatically from the application's structural (class) UML model. Changes in requirements often lead to modifications of the application's structural model. Such changes, in turn, have to be propagated to the underlying database schema. Very often, especially when the system is in production with a large volume of users' live data, the data is considered to be valuable enough to be preserved through these changes. This paper describes an approach to cope with the problem of model evolution with the ultimate requirement to preserve the data stored in the database. The algorithm interactively determines differences between structural UML models before and after the changes and resolves those differences into transformations in the relational database domain.

A On-Demand Mapping Method on Query Request in Relational Database Semantic Query

Relational database semantic query namely RDF access to relational database is an important issue in semantic Web research. To realize the query is to build mapping relation between relational database schema and ontology. However, there is natural isomerism between them. The isomerism can be eliminated by transforming relational database schema into similar ontology and then building mapping between conversion ontology and input ontology. This paper realized an ondemanding mapping method when users request query, avoided building all concepts and attributes mapping between conversion ontology and input ontology and improved mapping efficiency.

A metadata driven approach to performing complex heterogeneous database schema migrations

Enterprise software is evolving at a faster rate than ever before with customer’s expecting upgrades to occur regularly. These upgrades not only have complex consequences for legacy software but the database upgrade also. This paper discusses the challenges associated with relational database schema migrations which commonly occur with major upgrade releases of enterprise software. The most prevalent method of performing a schema migration is to execute SQL script files before or after the software upgrade. This approach performs poorly with large or complex database migrations and also requires separate script files for each supported database vendor. A tool was developed for a complex database upgrade of an enterprise product which uses XML in a metadata-driven approach. The key advantages include the ability to abstract complexity, provide multi-database vendor support and make the database migration more manageable between software releases. This marks an evolutionary step towards autonomic self-migrations.

JBioWH: an open-source Java framework for bioinformatics data integration.

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307.Database URL: http://code.google.com/p/jbiowh

Mapping Process of Relational Schema to OWL Ontologies using XSLT

One of the challenges of the semantic Web is to integrate the information already available on the standard Web, usually stored in relational databases. We propose in this paper a transformation process from existing relational database schema defined by a set of tables into OWL ontologies using XSLT. This process allows us to mapping some constraints on columns such as primary key, foreign key, unique, not null. Our approach start by translate the database schema into a XML document validate by a suitable XML schema. Since our process is based on XSLT stylesheets, its transformation rules can be modified in a very flexible manner in order to consider different mapping strategies and requirements.

A new relational database structure and online interface for the HITRAN database

A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

BackgroundIn recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers.ResultsWe developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases.ConclusionsBioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

An algorithm for synthesizing a relational database scheme into third normal form.

An algorithm for synthesizing a relational database scheme into third normal form.

OpLiDaF - Open Linked Data Framework: una piattaforma per la creazione e la pubblicazione di linked data

ITACH@ Project, Innovative Technologies And Cultural Heritage Aggregation, intends to offer innovative tools for the development of the tourism industry and Italian culture. This paper analyzes the particular technological component defined OpLiDaF, Open Linked Data Framework, a platform aimed the creation, structuring and visualizing data in RDF/XML. The paper discusses also the different formats, with special attention to procedures and techniques of processing data in relational databases, according to the instructions provided by the W3C Working Group RDB2RDF. It is working on the development of standard languages for mapping relational data and relational database schemas into RDF and OWL. The paper aims to show the potential of a language mapping between relational database schemas and ontologies implemented in RDF(S) or OWL, used in the platform OpLiDaF: the R2O (Relational to Ontology), which enables the production of data set extensible semantics explicit and well recognized.

OWL Ontology Extraction from Relational Databases via Database Reverse Engineering

The main purpose of the Semantic Web is driving the evolution of the current Web by enabling users to find, share, and combine information more easily. OWL ontologies play a key role in this effort. It is widely believed that the majority of current Web data sources are powered by relational databases (RDB). Thus developing approaches and tools for extracting OWL ontologies from RDB is helpful in bridging the gap between the existing Web data sources and the Semantic Web. This paper proposes a formal approach to automatic extraction of OWL ontologies from RDB using database reverse engineering (DBRE) technologies. The DBRE-based approach first identifies different relational structures to capture the natural domain semantics hidden in the relational schemas and data. Then it performs an automatic RDB-to-OWL schema translation by following a set of predefined translation rules that are based on the conceptual correspondences between RDB schema and OWL DL ontology. Our prototype implementation and case studies show that the proposed approach is feasible and effective.

A modelling framework for social media monitoring

This paper describes a hierarchical, three-level modelling framework for monitoring social media. Immediate social reality is modelled through the first level of the models. They represent various virtual communities at social media sites and adhere to the social world models of the sites, i.e., the site ontologies. The second-level model is a temporal multirelational graph that captures the static and dynamic properties of the first-level models from the perspective of the monitoring site. The third-level model consists of a temporal relational database scheme that models the temporal multirelational graph within the database. The models are specified and instantiated at the monitoring site. An important contribution of the paper is the description of the mappings between the modelling levels and their schematic algorithmic implementation within the monitoring site. The paper also describes theoretical limits for the accuracy and timeliness of monitoring activity, assuming that the monitoring is performed remotely over the internet.

GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database

BackgroundIn the scientific biodiversity community, it is increasingly perceived the need to build a bridge between molecular and traditional biodiversity studies. We believe that the information technology could have a preeminent role in integrating the information generated by these studies with the large amount of molecular data we can find in bioinformatics public databases. This work is primarily aimed at building a bioinformatic infrastructure for the integration of public and private biodiversity data through the development of GIDL, an Intelligent Data Loader coupled with the Molecular Biodiversity Database. The system presented here organizes in an ontological way and locally stores the sequence and annotation data contained in the GenBank primary database.MethodsThe GIDL architecture consists of a relational database and of an intelligent data loader software. The relational database schema is designed to manage biodiversity information (Molecular Biodiversity Database) and it is organized in four areas: MolecularData, Experiment, Collection and Taxonomy. The MolecularData area is inspired to an established standard in Generic Model Organism Databases, the Chado relational schema. The peculiarity of Chado, and also its strength, is the adoption of an ontological schema which makes use of the Sequence Ontology.The Intelligent Data Loader (IDL) component of GIDL is an Extract, Transform and Load software able to parse data, to discover hidden information in the GenBank entries and to populate the Molecular Biodiversity Database. The IDL is composed by three main modules: the Parser, able to parse GenBank flat files; the Reasoner, which automatically builds CLIPS facts mapping the biological knowledge expressed by the Sequence Ontology; the DBFiller, which translates the CLIPS facts into ordered SQL statements used to populate the database. In GIDL Semantic Web technologies have been adopted due to their advantages in data representation, integration and processing.Results and conclusionsEntries coming from Virus (814,122), Plant (1,365,360) and Invertebrate (959,065) divisions of GenBank rel.180 have been loaded in the Molecular Biodiversity Database by GIDL. Our system, combining the Sequence Ontology and the Chado schema, allows a more powerful query expressiveness compared with the most commonly used sequence retrieval systems like Entrez or SRS.

Prioritized fuzzy logic based information processing in relational databases

Many years of research related to fuzzy logic and fuzzy set theory extensions to relational databases have not lead to stable implementations, standardized languages or fuzzy relational database application development tools and methods. The main goal of this paper is the modelling and the implementation of a set of tools that allow usage of fuzzy logic enriched with priorities in relational database applications. In order to achieve that goal, at first, the relational data model is extended with the elements of fuzzy set theory. After that, a fuzzy extension of the SQL query language, called the PFSQL, is defined. An interpreter for that language is integrated inside an implementation of the fuzzy JDBC driver. An implementation of the CASE tool for modelling of fuzzy relational database schemas rounds up a set of tools for the implementation of Java fuzzy database applications. In this sense, this paper presents a step towards a methodology for the fuzzy relational database application development.

Ologs: A Categorical Framework for Knowledge Representation

In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as semantic networks) cannot. An olog is similar to a relational database schema; in fact an olog can serve as a data repository if desired. Unlike database schemas, which are generally difficult to create or modify, ologs are designed to be user-friendly enough that authoring or reconfiguring an olog is a matter of course rather than a difficult chore. It is hoped that learning to author ologs is much simpler than learning a database definition language, despite their similarity. We describe ologs carefully and illustrate with many examples. As an application we show that any primitive recursive function can be described by an olog. We also show that ologs can be aligned or connected together into a larger network using functors. The various methods of information flow and institutions can then be used to integrate local and global world-views. We finish by providing several different avenues for future research.

A Relational Model for the Possibilistic Valid-time Approach

In real world, it is very common that some objects or concepts have properties with a time-variant or time-related nature. Modelling this kind of objects or concepts in a (relational) database schema is possible, but time-variant and time-related attributes have an impact on the consistency of the entire database and must be appropriately managed. Therefore, temporal database models have been proposed to deal with this problem in the literature. Time can be affected by imprecision, vagueness and / or uncertainty, since existing time measuring devices are inherently imperfect. Additionally, human beings manage time using temporal indications and temporal notions, which may also be imprecise. However, the imperfection in human-used temporal indications is supported by human interpretation, whereas information systems need appropriate support in order to accomplish this task. Several proposals for dealing with such imperfections when modelling temporal data exist. Some of these proposals transform the temporal data into a compact representation but there is not a formal model for managing and handling uncertainty regarding temporal information. In this work we present a novel model to deal with imprecision in valid-time databases together with the definition and implementation of the data manipulation language, DML.

Form-Driven Application Development

In the paper a form-driven approach to the application development is presented. Our development environment IIS*Studio suports presented form-driven approach. It is aimed to provide the information system design and generating executable application prototypes. A form type is central IIS*Studio concept, used to model the structure and constraints of various business documents. On the one hand, a set of specified form types represents a platform independent model (PIM) of a real system. On the other hand, it is a PIM of the future software application. Starting from such a platform independent specification, through the chain of transformations, IIS*Studio generates a set of relational database subschemas in the 3 rd normal form and also a global relational database schema by integration of the subschemas. It enables a full implementation of database schemas under different target database management systems. IIS*Studio comprises a tool for the formal specification of business applications, and a generator of the executable application prototypes. The case study presented in the paper illustrates main features of IIS*Studio application generator tool and the methodological aspects of its usage. We consider the chain of transformations from a PIM, through the series of platform specific models with different degree of platform specificity, towards executable program code, as a crucial in our approach.

관계형 데이터베이스 응용시스템을 위한 통합 설계방법론 개발 -객체지향 분석.설계 방법론을 중심으로-

본 논문에서는 UML(Unified Modeling Language)을 토대로 유스케이스(use case) 중심의 객체지향 분석 설계 방법론을 기반으로 한, 관계형 데이터베이스 통합 설계방법론에 대하여 다룬다. 본 통합 설계방법론에서 사용하는 개념모델은 비즈니스 프로화일(business profile)에 기반을 두고 있으며, 6단계로 구성되어 있다. 첫 번째 단계에서는 비즈니스 유스케이스(business use case)가 식별되어 마크로액티비티 다이어그램(macroactivity diagram)으로 표현되고, 두 번째 단계에서 마크로액티비티 다이어그램은 비즈니스 객체(business object)와 비즈니스 객체흐름(business object flow) 그리고 비즈니스 사용자책임(business worker's responsibilities)을 이용하여 상세 비즈니스 활동다이어그램(detailed business activity diagram)으로 변환된다. 세 번째 단계에서는 상세 비즈니스 활동다이어그램을 기반으로 시스템 전체의 정적 구조를 설명하는 비즈니스 클래스다이어그램(business class diagram)으로 변환된다. 네 번째 단계에서 비즈니스 클래스다이어그램은 대응하는 관계형 데이터베이스 초기 개념모델을 대표하는 클래스다이어그램으로 변환된다. 다섯 번째 단계에서 클래스다이어그램에 일반화와 특수화, 역할과 활동, 클래스 추가 그리고 중복 연관에 따른 추가적인 변환이 이루어지고, 마지막으로 관계형 데이터베이스 스키마로 변환이 이루어지게 된다. 본 논문에서 제시하는 방법론을 적용함으로써, 객체지향 분석 설계 방법론과 관계형 데이터베이스 설계방법론 사이에 유기적 연결이 이루어지게 되어, 객체지향 분석 설계 방법론 관계형 데이터베이스설계 방법론을 통합적으로 다룰 수 있게 된다. 이에따라 관계형 데이터베이스 기반의소프트웨어 시스템에 대한 객체지향 방식의 일관된 그리고 통합된 구축방안이 제공된다. 사례 연구로 제안한 통합 설계 방법론을 비자발급시스템에 대하여 적용한다. In this paper we present an integrated design methodology for relational database based on object-oriented analysis and design. The integrated design methodology is based on business profile and has six phases. In the first phase, business use cases are identified and described by macroactivity diagrams and then the macroactivity diagrams are transformed to detailed business activity diagrams by using objects, object flows and business worker's responsibilities. In the third phase, the detailed business activity diagrams are transformed to business class diagrams that describe the static structure of the entire business system based on detailed business activity diagrams. In the four phase, the business class diagrams are transformed to class diagrams that represent the initial conceptual model of the target relational database. In the five phase, we add additional transformations on the class diagrams with generalization and specialization of associations, roles, activities, additional classes and redundant associations. Eventually, the final class diagrams are transformed to relational database schema. The methodology presented in this paper by applying that proposal for organic connection between object-oriented analysis and design methodology and relational database design methodology. And it will be able to deal with integration management. By the integrated design methodology, we can make more easily software systems based on relational database. In the case study, proposal integrated design methodology applied for a visa issuing system.

MOLECULAR EVENT EXTRACTION FROM LINK GRAMMAR PARSE TREES IN THE BIONLP’09 SHARED TASK

The BioNLP’09 Shared Task deals with extracting information on molecular events, such as gene expression and protein localization, from natural language text. Information in this benchmark are given as tuples including protein names, trigger terms for each event, and possible other participants such as bindings sites. We address all three tasks of BioNLP’09: event detection, event enrichment, and recognition of negation and speculation. Our method for the first two tasks is based on a deep parser; we store the parse tree of each sentence in a relational database scheme. From the training data, we collect the dependencies connecting any two relevant terms of a known tuple, that is, the shortest paths linking these two constituents. We encode all such linkages in a query language to retrieve similar linkages from unseen text. For the third task, we rely on a hierarchy of hand-crafted regular expressions to recognize speculation and negated events. In this paper, we added extensions regarding a post-processing step that handles ambiguous event trigger terms, as well as an extension of the query language to relax linkage constraints. On the BioNLP Shared Task test data, we achieve an overall F1-measure of 32%, 29%, and 30% for the successive Tasks 1, 2, and 3, respectively.

A virtual tutor for relational schema normalization

The idea of virtualization has been successfully practiced in many fi elds of information technology such as the virtualizations of operating systems, memories, networks, and even human tutors. This research is a virtualization of human tutoring in the domain of relational database schema normalization implemented as an intelligent tutoring system usable as a virtual tutor to facilitate the knowledge acquisition of relational database schema normalization.