GORP: An object-oriented design for genomic objects, relationships and processes

Journal ArticleThe Eccles Institute for Human Genetics (EIHG) has developed a genomic database based on a novel level of abstraction. Objects, relationships, and processes are explicitly represented in an object model. This model has been implemented in a traditional relational database management system. Translating this database model into an object-oriented programming language has proven to be a challenging exercise. This paper describes a C++ object-oriented design which faithfully implements a persistent object model of the original abstractions. In addition, a new level of meta-information is provided which enhances an application's ability to adapt to changes in the database schema. This is a description of work in progress and includes a survey of relationships and processes in the current EIHG databases

Object-oriented views: a novel approach for tool integration in design environments (dissertation)

Object-oriented databases have been proposed to serve as the data management component of integrated design environments. One central database represents a bottleneck, however, requiring all design tools to work on the same information model and preventing the extensibility of the system over time. In this dissertation, I propose a view-based object server that successfully addresses these problems by supporting design views tailored to the needs of individual design tools.A view on an object-oriented schema corresponds to a virtual subschema graph with restructured generalization and property decomposition hierarchies. I present a methodology for supporting multiple view schemata, called MutliView. MultiView is anchored on the following four ideas: (1) the customization of individual classes using object algebra, (2) the integration of these derived classes into one global schema graoh, (3) the extraction of virtual and base classes from the global schema as required by the view, and (4) the generation of a class hierarchy for these selected view classes. MutliView's division of view specification into these well-defined tasks, some of which have been successfully automated, makes it a powerful tool for supporting the specification of views by non-database experts while enforcing view consistency.In this dissertation, I describe solutions for all four tasks underlying MultiView. For the first task, I have formulated class derivatin operators modeled after the well-known relational algebra operators. For the second task, I have developed a classification algorithm that automatically integrates derived classes into one global schema. For the third task, I have designed a view definition language that can be used to declaratively specify the view classes required for a particular view. For the last task, I have developed an algorithm that generates a complete, minimal and consistent view schema. I present proofs of correctness, complexity analysis, and numerous illustrative examples for all algorithms.MultiView is applied to address the tool integration problem in a behavioral synthesis system. For this purpose, I first develop a unified design object model for behavioral synthesis. I then formulate customized design views of this model tailored to the needs of particular design tools. The resulting system allows the design tools to work on their view of the information model, while MultiView assures the consistent integration of the diverse design data into one object model

Developing a hyper media interface as a navigational tool for an object oriented database management system, 1995

A common difficulty associated with any large scale information base is traversing the repository in a coherent and purposeful manner. The scope and diversity of the media therein tends to be more of a distraction rather than a source of information. This phenomena is particularly relevant in current hypertext or hypermedia systems and is often referred to as becoming "lost in hyperspace". A solution to this hyperspace problem involves modeling the hyper system after the structured links associated with a database schema. The database schema inherently defines the formations necessary for the two basic forms of navigation in a hyper base - structural and associative. In order to depict the semantic relationships between nodes and links in a hyper system a model that is both readable and logic-oriented is necessary. Such a model can be expressed through conceptual graph notation. This paper documents the design of a hyper-media interface as a navigational tool for an object oriented database management system called 02. The navigational paths through the database are represented as a conceptual graph model

Object-Oriented Software Representation of Polymer Materials Information in Engineering Design

The software application POISE, Polymer Objects in a Smalltalk™ Environment, integrates knowledge representation, user interfaces, and data management; a system of tools for the materials domain expert involved in design. Engineering design solutions initially build from generalisations. POISE represents multiple levels of generalisations from classifications of polymer information. The class-instance paradigm classifies software objects. An object’s behaviour is an exclusive function of its class. Polymer’s behaviours are a function of multiple orthogonal factors, like chemistry and processing, therefore multiple orthogonal classes must represent polymers. Taxonomy only represents one of these factors. The Enhancer mechanism resolves this conflict between classification and representation. Polymer classification is not well established, with new materials evolving. The software compensates by evolving the classification schema. Guided with a specialised interface tool, the domain expert updates the schema by adding new polymer families and re-classifying existing classes. Through analysing the generalisations in the classification, the domain expert can develop an appropriate classification. This analysis relies on the engineering properties differentiating the principal material qualities. Standard properties do not distinguish specific structural differences in polymer materials, necessitating new properties. Material properties distinguish materials in the domain whereas the classes describe the properties of polymer objects. Domain experts add new properties to the polymer classes to distinguish polymer objects. Properties are independent objects that partially describe the class template; Partial Template Objects. Persistence of personal design information and management of shared data requires dichotomous database management. Shared data requires multi-user access, and consequently transaction management. Transaction management in object-oriented systems often holds resources for a long duration. Transaction declaration hinders transparent access to storage, and corrupts the representation. For single-user design information, transactions are implicit with access. Database proxies provide transparent per-object transaction management to persistent design information. The WorkBase is an object-storage utility that utilises Enhancers as proxies

Exploring object-oriented GIS for watershed resource management

The adoption of object-oriented programming for spatial technological advancement is an emerging trend in GIS. This research seeks to explore Object-Oriented GIS (OOGIS) and its potential application in watershed resource management. OOGIS provides a more intuitive and realistic abstraction of real world features as intelligent objects. The ability to embed behavior, geometry, and attribution with the objects provides considerable advantages in the processing and analysis of geospatial data. The main objective of this research was to design a prototype OOGIS for watershed resource management using the object relational Arclnfo 8.1 Geodatabase. The study builds on the OOGIS concepts of inheritance, polymorphism, and encapsulation and defines a schema for the project. Behavior is embedded in the watershed features through the use of methods and reflex methods that automatically perform functions such as data validation and text placement. Message propagation is tested using related objects, and a smart object-based topologically integrated geometric network is established for streams and roads. Because of the embedded topological relationships and methods this network is self-adapting. The resulting system indicates that OOGIS has many advantages over the more traditional entity-relationship model. The system provides a more intuitive representation of a watershed through the integration of intelligent behaviors and is particularly effective in addressing GIS maintenance issues at a database level through the use of reflex validation methods

Object-oriented querying of existing relational databases

In this paper, we present algorithms which allow an object-oriented querying of existing relational databases. Our goal is to provide an improved query interface for relational systems with better query facilities than SQL. This seems to be very important since, in real world applications, relational systems are most commonly used and their dominance will remain in the near future. To overcome the drawbacks of relational systems, especially the poor query facilities of SQL, we propose a schema transformation and a query translation algorithm. The schema transformation algorithm uses additional semantic information to enhance the relational schema and transform it into a corresponding object-oriented schema. If the additional semantic information can be deducted from an underlying entity-relationship design schema, the schema transformation may be done fully automatically. To query the created object-oriented schema, we use the Structured Object Query Language (SOQL) which provides declarative query facilities on objects. SOQL queries using the created object-oriented schema are much shorter, easier to write and understand and more intuitive than corresponding S Q L queries leading to an enhanced usability and an improved querying of the database. The query translation algorithm automatically translates SOQL queries into equivalent SQL queries for the original relational schema

Compensation methods to support cooperative applications: A case study in automated verification of schema requirements for an advanced transaction model

Compensation plays an important role in advanced transaction models, cooperative work and workflow systems. A schema designer is typically required to supply for each transaction another transaction to semantically undo the effects of . Little attention has been paid to the verification of the desirable properties of such operations, however. This paper demonstrates the use of a higher-order logic theorem prover for verifying that compensating transactions return a database to its original state. It is shown how an OODB schema is translated to the language of the theorem prover so that proofs can be performed on the compensating transactions