All Outputs (129)

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.

Refactoring data transforms in MaTSE for flexibility. (2009)
Presentation / Conference Contribution
Craig, P., & Kennedy, J. (2009, October). Refactoring data transforms in MaTSE for flexibility

In early prototypes of the Microarray Time-series Explorer
(MaTSE) data transforms were tightly coupled with visualisation components. While this allowed us to achieve our initial objective of developing the application to the level where we were ab... Read More about Refactoring data transforms in MaTSE for flexibility..

Re-architecting Visualizations to Java Swing. (2009)
Presentation / Conference Contribution
Graham, M., & Kennedy, J. (2009, October). Re-architecting Visualizations to Java Swing. Paper presented at REVISE: Refactoring Visualization from Experience, VizWeek Workshop

The minimum information about a genome sequence (MIGS) specification (2008)
Journal Article
Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, M. J., Angiuoli, S. V., Ashburner, M., Axelrod, N., Baldauf, S., Ballard, S., Boore, J., Cochrane, G., Cole, J., Dawyndt, P., De Vos, P., dePamphilis, C., …Wipat, A. (2008). The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26, 541-547. https://doi.org/10.1038/nbt1360

With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international worki... Read More about The minimum information about a genome sequence (MIGS) specification.

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..

Multiform Views of Multiple Trees (2008)
Presentation / Conference Contribution
Graham, M., & Kennedy, J. (2008, July). Multiform Views of Multiple Trees. Presented at 2008 12th International Conference Information Visualisation, London, UK

We describe a case study of TaxVis, a multiple view system for examining relationships between sets of multiple classification trees. The system displays multiform views of the dataset, which in turn can either be a singular view of the larger forest... Read More about Multiform Views of Multiple Trees.

Visualisation to Aid Biodiversity Studies through Accurate Taxonomic Reconciliation. (2008)
Presentation / Conference Contribution
Graham, M., Craig, P., & Kennedy, J. (2008, July). Visualisation to Aid Biodiversity Studies through Accurate Taxonomic Reconciliation. Presented at BNCOD 2008

All aspects of organismal biology rely on the accurate identification
of specimens described and observed. This is particularly important for
ecological surveys of biodiversity, where organisms must be identified and
labelled, both for the purpose... Read More about Visualisation to Aid Biodiversity Studies through Accurate Taxonomic Reconciliation..

Concept relationship editor: a visual interface to support the assertion of synonymy relationships between taxonomic classifications (2008)
Presentation / Conference Contribution
Craig, P., & Kennedy, J. (2008, January). Concept relationship editor: a visual interface to support the assertion of synonymy relationships between taxonomic classifications. Presented at Visualization and Data Analysis 2008

An increasingly common approach being taken by taxonomists to define the relationships between taxa in alternative hierarchical classifications is to use a set-based notation which states relationship between two taxa from alternative classifications... Read More about Concept relationship editor: a visual interface to support the assertion of synonymy relationships between taxonomic classifications.

Exploring multiple trees through DAG representations (2007)
Journal Article
Graham, M., & Kennedy, J. (2007). Exploring multiple trees through DAG representations. IEEE Transactions on Visualization and Computer Graphics, 13, 1294-1301. https://doi.org/10.1109/TVCG.2007.70556

We present a Directed Acyclic Graph visualisation designed to allow interaction with a set of multiple classification trees, specifically to find overlaps and differences between groups of trees and individual trees. The work is motivated by the need... Read More about Exploring multiple trees through DAG representations.

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.

Developing a core ontology for taxonomic data. (2006)
Presentation / Conference Contribution
Kennedy, J., Gales, R., Hyam, R., Kukla, R., Wieczorek, J., Hagedorn, G., Döring, M., & Vieglais, D. (2006, October). Developing a core ontology for taxonomic data. Presented at Taxonomy Data Working Group (TDWG) 2006

Over recent years several sub-groups within the Taxonomic Databases Working Group (TDWG) have developed models and exchange standards to facilitate data sharing within the taxonomic community. These include ABCD, SDD, DwC, TCS and Spatial Data Standa... Read More about Developing a core ontology for taxonomic data..

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.

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..

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.

Time-series Explorer: An Animated Information Visualisation for Microarray Time-course Data (2005)
Journal Article
Craig, P., Kennedy, J., & Cumming, A. (2005). Time-series Explorer: An Animated Information Visualisation for Microarray Time-course Data. BMC Bioinformatics, 6(Suppl 3), P8. https://doi.org/10.1186/1471-2105-6-S3-P8

Microarray technologies are a relatively new development that allow biologists to monitor the activity of thousands of genes (normally around 8,000) in parallel across multiple stages of a biological process. While this new perspective on biological... Read More about Time-series Explorer: An Animated Information Visualisation for Microarray Time-course Data.

Extending Taxonomic Visualisation to Incorporate Synonymy and Structural Markers (2005)
Journal Article
Graham, M., & Kennedy, J. (2005). Extending Taxonomic Visualisation to Incorporate Synonymy and Structural Markers. Information Visualization, 4(3), 206-223. https://doi.org/10.1057/palgrave.ivs.9500096

The visualisation of taxonomic hierarchies has evolved from indented lists of names to techniques that can display thousands of nodes and onto hundreds of thousands of nodes over multiple taxonomies. However, challenges remain within multiple hierarc... Read More about Extending Taxonomic Visualisation to Incorporate Synonymy and Structural Markers.

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.

Animated interval scatter-plot views for the exploratory analysis of large scale microarray time-course data. (2005)
Journal Article
Craig, P., Kennedy, J., & Cumming, A. (2005). Animated interval scatter-plot views for the exploratory analysis of large scale microarray time-course data. Information Visualization, 4(3), 149-163. https://doi.org/10.1057/palgrave.ivs.9500101

Microarray technologies are a relatively new development that allow biologists to monitor the activity of thousands of genes (normally around 8,000) in parallel across multiple stages of a biological process. While this new perspective on biological... Read More about Animated interval scatter-plot views for the exploratory analysis of large scale microarray time-course data..

Coordinated parallel views for the exploratory analysis of microarray time-course data. (2005)
Presentation / Conference Contribution
Craig, P., Kennedy, J., & Cumming, A. (2005, July). Coordinated parallel views for the exploratory analysis of microarray time-course data. Presented at Third International Conference on Coordinated & Multiple Views in Exploratory Visualization

Microarray time-course data relate to the recorded activity of thousands of genes, in parallel, over multiple discrete points in time during a biological process. Existing techniques that attempt to support the exploratory analysis of this data rely... Read More about Coordinated parallel views for the exploratory analysis of microarray time-course data..