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Outputs (45)

VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees (2012)
Journal Article
Paterson, T., Graham, M., Kennedy, J., & Law, A. (2012). VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees. BMC Bioinformatics, 13(Suppl 8), S5. https://doi.org/10.1186/1471-2105-13-S8-S5

Pedigree genotype datasets are used for analysing genetic inheritance and to map genetic markers and traits. Such datasets consist of hundreds of related animals genotyped for thousands of genetic markers and invariably contain multiple errors in bot... Read More about VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees.

BioVis 2011 Conference Proceedings. (2011)
Presentation / Conference Contribution
(2011, October). BioVis 2011 Conference Proceedings

The rapidly expanding field of biology creates enormous challenges for computational visualization techniques for enabling researchers to gain insight from their large and highly complex data sets. The goal of the BioVis 2011 symposium is to create t... Read More about BioVis 2011 Conference Proceedings..

A rule based taxonomy of dirty data. (2011)
Presentation / Conference Contribution
Li, L., Peng, T., & Kennedy, J. A rule based taxonomy of dirty data. Presented at Annual International Academic Conference on Data Analysis, Data Quality and Metadata Management

There is a growing awareness that high quality of data is a key to today’s business success and that dirty data existing within data sources is one of the causes of poor data quality. To ensure high quality data, enterprises need to have a process, m... Read More about A rule based taxonomy of dirty data..

Research directions in data wrangling: Visualizations and transformations for usable and credible data (2011)
Journal Article
Kandel, S., Heer, J., Plaisant, C., Kennedy, J., van Ham, F., Riche, N. H., Weaver, C., Lee, B., Brodbeck, D., & Buono, P. (2011). Research directions in data wrangling: Visualizations and transformations for usable and credible data. Information Visualization, 10(4), 271-288. https://doi.org/10.1177/1473871611415994

In spite of advances in technologies for working with data, analysts still spend an inordinate amount of time diagnosing data quality issues and manipulating data into a usable form. This process of ‘data wrangling’ often constitutes the most tedious... Read More about Research directions in data wrangling: Visualizations and transformations for usable and credible data.

Improving data quality in data warehousing applications (2010)
Presentation / Conference Contribution
Li, L., Peng, T., & Kennedy, J. (2010, June). Improving data quality in data warehousing applications. Presented at Proceedings of the 12th International Conference on Enterprise Information Systems

There is a growing awareness that high quality of data is a key to today’s business success and dirty data that exits within data sources is one of the reasons that cause poor data quality. To ensure high quality, enterprises need to have a process,... Read More about Improving data quality in data warehousing applications.

A Multiple Viewed Interrelated Ontology Model for Holistic Component Specification and Retrieval (2009)
Presentation / Conference Contribution
Li, C., Liu, X., & Kennedy, J. (2009, December). A Multiple Viewed Interrelated Ontology Model for Holistic Component Specification and Retrieval. Presented at International Conference on Advanced Software Engineering and Its Applications: ASEA 2009, Jeju Island, Korea

Despite the success that Component-Based Development has achieved so far, component mismatch remains as a major hurdle for wider and smoother component reuse due to the lack of effective and automated approaches to component specification and retriev... Read More about A Multiple Viewed Interrelated Ontology Model for Holistic Component Specification and Retrieval.

Form (2009)
Book Chapter
Kennedy, J., & Cannon, A. (2009). Form. In L. Liu, & M. T. Özsu (Eds.), Encyclopedia of Database Systems. Springer-Verlag

Semantics-Based Component Repository: State of Arts and a Calculation Rating Factor-based Framework. (2008)
Presentation / Conference Contribution
Li, C., Liu, X., & Kennedy, J. (2008, July). Semantics-Based Component Repository: State of Arts and a Calculation Rating Factor-based Framework. Presented at COMPSAC '08. 32nd Annual IEEE International Computer Software and Applications, 2008

Nowadays, Component-Based Development (CBD) has been widely used in software engineering. As a core activity in the CBD process, component retrieval has attracted extensive research attention. Despite the research efforts so far, one major problem st... Read More about Semantics-Based Component Repository: State of Arts and a Calculation Rating Factor-based Framework..

Visual Exploration of Alternative Taxonomies through Concepts (2007)
Journal Article
Graham, M., & Kennedy, J. (2007). Visual Exploration of Alternative Taxonomies through Concepts. Ecological Informatics, 2(3), 248-261. https://doi.org/10.1016/j.ecoinf.2007.07.004

A graphical user interface is presented that allows users of taxonomic data to explore concept relationships between conflicting but related taxonomic classifications.
Ecological analyses that use taxonomic metadata depend on accurate naming of spe... Read More about Visual Exploration of Alternative Taxonomies through Concepts.

Converting an existing taxonomic data resource to employ an ontology and LSIDs. (2006)
Presentation / Conference Contribution
Kennedy, J., Gales, R., & Kukla, R. (2006, October). Converting an existing taxonomic data resource to employ an ontology and LSIDs. Presented at Taxonomic Data Working Group (TDWG) 2006

Data sharing is fundamental to biodiversity and taxonomic data applications, however previous attempts at developing mechanisms to facilitate sharing within the community have had limited effect. Reasons for this include the lack of take up of data e... Read More about Converting an existing taxonomic data resource to employ an ontology and LSIDs..

Visual comparison and exploration of natural history collections (2006)
Presentation / Conference Contribution
Graham, M., Kennedy, J., & Downey, L. (2006, May). Visual comparison and exploration of natural history collections. Presented at Proceedings of the working conference on Advanced visual interfaces - AVI '06, Venice, Italy

Natural history museum collections contain a wealth of specimen level data that is now opening up for digital access. However, current interfaces to access and manipulate this data are standard text-based query mechanisms, giving no leeway for explor... Read More about Visual comparison and exploration of natural history collections.

Standard Data Model Representation for Taxonomic Information (2006)
Journal Article
Kennedy, J., Hyam, R., Kukla, R., & Paterson, T. (2006). Standard Data Model Representation for Taxonomic Information. OMICS, 10(2), 220-230. https://doi.org/10.1089/omi.2006.10.220

The names used by biologists to label the observations they make are imprecise. This is an issue as workers increasingly seek to exploit data gathered from multiple, unrelated sources on line. Even when the international codes of nomenclature are fol... Read More about Standard Data Model Representation for Taxonomic Information.

Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration (2005)
Presentation / Conference Contribution
Kennedy, J., Kukla, R., & Paterson, T. (2005, July). Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration. Presented at Second International Workshop, DILS 2005, San Diego, CA, USA

Biologists use scientific names to label the organisms described in
their data; however, these names are not unique identifiers for taxonomic entities.
Alternative taxonomic classifications may apply the same name, associated
with alternative defi... Read More about Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration.

The Prometheus Description Model: an examination of the taxonomic description-building process and its representation (2005)
Journal Article
Pullan, M. R., Armstrong, K. E., Paterson, T., Cannon, A., Kennedy, J. B., Watson, M. F., McDonald, S. M., & Raguenaud, C. (2005). The Prometheus Description Model: an examination of the taxonomic description-building process and its representation. Taxon, 54(3), 751-765. https://doi.org/10.2307/25065431

A model for representing taxonomic descriptive data is presented. The model has been developed in response to the growing requirement for the global exchange of descriptive data. Meaningful exchange of data requires that data be represented in a form... Read More about The Prometheus Description Model: an examination of the taxonomic description-building process and its representation.

Ontology-Driven Automated Generation of Data Entry Interfaces to Databases (2004)
Presentation / Conference Contribution
Cannon, A., Kennedy, J. B., Paterson, T., & Watson, M. F. (2004, July). Ontology-Driven Automated Generation of Data Entry Interfaces to Databases. Presented at Key Technologies for Data Management (Proc. BNCOD21): Lecture Notes in Computer Science 3112, Edinburgh, Scotland

This paper discusses an ontology based approach for the automatic generation of data entry interfaces to databases. An existing domain ontology is mapped to a system domain model, which a domain expert can then specialise using their domain expertise... Read More about Ontology-Driven Automated Generation of Data Entry Interfaces to Databases.

Approaches to Storing and Querying Structural Information in Botanical Specimen Descriptions. (2004)
Presentation / Conference Contribution
Paterson, T., & Kennedy, J. (2004, July). Approaches to Storing and Querying Structural Information in Botanical Specimen Descriptions. Presented at 21st Annual British National Conference on Databases (BNCOD21)

We are developing an ontology as a defined terminology for the taxonomic description of botanical specimens. To allow these descriptions to unambiguously refer to a given plant structure, the ontology specifies compositional relationships between ana... Read More about Approaches to Storing and Querying Structural Information in Botanical Specimen Descriptions..

A universal character model and ontology of defined terms for taxonomic description. (2004)
Presentation / Conference Contribution
Paterson, T., Kennedy, J., Pullan, M. R., Cannon, A., Armstrong, K. E., Watson, M. F., Raguenaud, C., McDonald, S. M., & Russell, G. (2004, March). A universal character model and ontology of defined terms for taxonomic description. Presented at Data Integration in the Life Sciences. First International Workshop, DILS 2004

Taxonomists classify biological specimens into groups (taxa) on the basis of similarities between their observed features (characters). The description of these characters is therefore central to taxonomy, but there is currently no agreed model, defi... Read More about A universal character model and ontology of defined terms for taxonomic description..

A methodology for composing well-defined character descriptions. (2003)
Report
Paterson, T., Cannon, A., Raguenaud, C., Russell, G., Armstrong, K. E., MacDonald, S. M., Pullan, M. R., Watson, M. F., & Kennedy, J. (2003). 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... Read More about A methodology for composing well-defined character descriptions..

Supporting taxonomic names in cell and molecular biology databases (2003)
Journal Article
Kennedy, J. (2003). Supporting taxonomic names in cell and molecular biology databases. OMICS, 7(1), 13-16. https://doi.org/10.1089/153623103322006508

Groups of organisms require labels or names to refer to them; however, the idea of a single static name index, although tempting for its simplicity, is both impractical and unadvisable as a basis for referring to organisms for which data has been col... Read More about Supporting taxonomic names in cell and molecular biology databases.