Managing complex taxonomic data in an object-oriented database.

This thesis addresses the problem of multiple overlapping classifications in object-oriented databases through the example of plant taxonomy. These multiple overlapping classifications are independent simple classifications that share information (nodes and leaves), therefore overlap. Plant taxonomy was chosen as the motivational application domain because taxonomic classifications are especially complex and have changed over long periods of time, therefore overlap in a significant manner. This work extracts basic requirements for the support of multiple overlapping classifications in general, and in the context of plant taxonomy in particular. These requirements form the basis on which a prototype is defmed and built. The prototype, an extended object-oriented database, is extended from an object-oriented model based on ODMG through the provision of a relationship management mechanism. These relationships form the main feature used to build classifications. This emphasis on relationships allows the description of classifications orthogonal to the classified data (for reuse and integration of the mechanism with existing databases and for classification of non co-operating data), and allows an easier and more powerful management of semantic data (both within and without a classification). Additional mechanisms such as integrity constraints are investigated and implemented. Finally, the implementation of the prototype is presented and is evaluated, from the point of view of both usability and expressiveness (using plant taxonomy as an application), and its performance as a database system. This evaluation shows that the prototype meets the needs of taxonomists

A methodology for composing well-defined character descriptions.

Taxonomy has been described as “the science of documenting biodiversity”, which involves collecting, naming, describing, identifying and classifying specimens of organisms (Keogh, 1995). Descriptions are the fundamental information units used in the process of constructing classifications and communicating taxonomic concepts. The quality of stored description data is limited by the lack of a formal model and methodology for composing specimen descriptions, and by the absence of an agreed defined terminology. This impedes the communication, interpretation and reuse of original descriptions. This paper describes a novel approach to composing and recording taxonomic descriptions of botanical specimens. An underlying model for creating character descriptions is presented together with a process for creating an ontology of defined terms, which will be used to compose these description elements. It is hoped that these developments will facilitate the unambiguous interpretation of descriptions and enhance the taxonomic process

A methodology for composing well-defined character descriptions.

Taxonomy has been described as “the science of documenting biodiversity”, which involves collecting, naming, describing, identifying and classifying specimens of organisms (Keogh, 1995). Descriptions are the fundamental information units used in the process of constructing classifications and communicating taxonomic concepts. The quality of stored description data is limited by the lack of a formal model and methodology for composing specimen descriptions, and by the absence of an agreed defined terminology. This impedes the communication, interpretation and reuse of original descriptions. This paper describes a novel approach to composing and recording taxonomic descriptions of botanical specimens. An underlying model for creating character descriptions is presented together with a process for creating an ontology of defined terms, which will be used to compose these description elements. It is hoped that these developments will facilitate the unambiguous interpretation of descriptions and enhance the taxonomic process

The Prometheus ODMG Database System

Complex applications such as those to support the emerging field of biodiversity informatics, require database systems able to represent and manipulate their data. Object-oriented databases (OODBs), designed to support complex domains such as Computer Aided Engineering, appear to be a solution. A criticism of early OODBs was the lack of an ad hoc query language such as SQL, which led to the development of OQL [CBB+97], a generic ad hoc query language. However OQL does not take full advantage of the semantics captured in the OODB and thereby provides little more power than SQL. This paper presents a database model and query language developed while building a database application for a complex domain, that of botanical taxonomy. Our extensions centre on the provision of relationships as first class constructs in the data model. We describe a prototype database system (Prometheus) in which we have augmented an existing OODB (ODMG compliant) with relationships, and extended OQL with generic operators for manipulating the corresponding structures. By providing richer semantic concepts in the database, the power of the query language is enhanced, thereby providing more powerful ad hoc querying at the application level. The system which has been fully implemented and used to build a taxonomic database, would also benefit other complex domains where semantic-rich relationships are important for capturing the semantics of the domain

The Prometheus ODMG Database System

Complex applications such as those to support the emerging field of biodiversity informatics, require database systems able to represent and manipulate their data. Object-oriented databases (OODBs), designed to support complex domains such as Computer Aided Engineering, appear to be a solution. A criticism of early OODBs was the lack of an ad hoc query language such as SQL, which led to the development of OQL [CBB+97], a generic ad hoc query language. However OQL does not take full advantage of the semantics captured in the OODB and thereby provides little more power than SQL. This paper presents a database model and query language developed while building a database application for a complex domain, that of botanical taxonomy. Our extensions centre on the provision of relationships as first class constructs in the data model. We describe a prototype database system (Prometheus) in which we have augmented an existing OODB (ODMG compliant) with relationships, and extended OQL with generic operators for manipulating the corresponding structures. By providing richer semantic concepts in the database, the power of the query language is enhanced, thereby providing more powerful ad hoc querying at the application level. The system which has been fully implemented and used to build a taxonomic database, would also benefit other complex domains where semantic-rich relationships are important for capturing the semantics of the domain

Implementation of the Prometheus Taxonomic Model: a comparison of database models and query languages and an introduction to the Prometheus Object-Oriented Model.

Types of databases commonly used for handling taxonomic data are compared. It is shown that none of the existing types of databases fully support the requirements of taxonomic data. The results of this comparison provide a rationale for the design and implementation of a new database system based on an Extended Object-Oriented model. The new model, the Prometheus Object-Oriented Model (POOM) and its query language Prometheus Object-Oriented Language (POOL), are discussed in relation to the requirements of taxonomic data and the Prometheus Taxonomic Data Model. POOM provides the ability to represent the semantics of relationships between data. This allows us to build the type of graph structures that are found in taxonomic hierarchies. In addition, the system can query and manipulate these graphs (POOL). These features have been used to improve the original Prometheus Taxonomic Data Model. These improvements and the advantages they offer are described and discussed