biodiversity informatics ()

Areas of Expertise

Projects

Visual Exploration of Species-referenced Repositories (VESpeR)

Summary: Visualisation techniques have been recognised as one of the major directions in future research when handling and querying biological data, offering the ability to find patterns and outliers in data which traditional query interfaces cannot match.

TaxVis: Visualisation Tools for Integrating Large Alternative Linnaean Taxonomies

The TaxViz project is developing visualisation techniques for comparing multiple taxonomic hierarchies. Biological taxonomy involves the classification and naming of plants, animals and all the other living organisms on earth, however taxonomists often disagree over how the organisms should be...

TDWG Taxon Concept Transfer Schema

The Taxon Concept Modelling project is associated developing standard data models for representing taxonomic names and concepts for use in the biodiversity community. The work is associated with the Taxon Names and Cocnepts interest group of the International Taxonomic Database Working Group.

Prometheus

The aim of the project is to construct a database system that will meet the requirements of current taxonomy practices. In particular, it will allow taxonomists to view and explore alternative classifications. The system will support provision of single authoritative classifications for use by...

SEEK: Science Environment for Ecological Knowledge

The goals of the project are to make fundamental improvements in how researchers can 1) gain global access to ecological data and information, 2) rapidly locate and utilize distributed computational services, and 3) exercise powerful new methods for capturing, reproducing, and extending the...

TDWG Core Ontology

This project aims to progress the development of Taxonomic Concept schema (TCS) in line with Taxonomic Database Working gorup (TDWG) architecture and documentation. This work is to ensure that: Best current practice is followed in developing TDWG standardsTCS is documented according to 2006 TDWG...

Prometheus II: Capturing and Relating Character Concept Definitions in Plant Taxonomy

Taxonomy has been described as “the science of documenting biodiversity”, which involves collecting, naming, describing, identifying and classifying specimens of organisms. Descriptions are the fundamental information units used in the process of constructing classifications and communicating...

Members

Dr Alan Cannon

Research Fellow

a.cannon@napier.ac.uk

+44 131 455 2437

Professor Jessie Kennedy

Director of IIDI

j.kennedy@napier.ac.uk

+44 131 455 2772

Dr Martin Graham

Research Fellow

m.graham@napier.ac.uk

+44 131 455 2749

Publications

Craig, P., Kennedy, J. (2008). Concept Relationship Editor: A visual interface to support the assertion of synonymy relationships between taxonomic classifications. In: Börner, K., Gröhn, M., Park, J., Roberts, J. (Eds.) Visualization and Data Analysis 2008, Proceedings of the SPIE, 6809, () ( ed.). (pp. 680906-680912). San Jose, CA: . Society of Photo-Optical Instrumentation Engineers, Bellingham, WA, ETATS-UNIS .

Graham, M., Craig, P., Kennedy, J. (2008). Visualisation to Aid Biodiversity Studies through Accurate Taxonomic Reconciliation. In: Gray, A., Jeffery, K., Shao, J. (Eds.) Proceedings of British National Conference on Database Systems: Sharing Data, Information and Knowledge, 5071/2008, () (LNCS 5071 ed.). (pp. 280-291). Cardiff, UK: . Springer-Verlag.

Graham, M., Kennedy, J. (2007). Visual Exploration of Alternative Taxonomies through Concepts. Ecological Informatics, 2, (3), 248-261.

Graham, M., Kennedy, J., Downey, L. (2006). Visual Comparison and Exploration of Natural History Collections. In: Celentano, A., Mussio, P. (Eds.) Advanced Visual Interfaces (AVI) 2006, , () ( ed.). (pp. 310-313). Venice, Italy: . ACM Press.

Kennedy, J., Hyam, R., Kukla, R., Paterson, T. (2006). A Standard Data Model Representation for Taxonomic Information. OMICS: A Journal of Integrative Biology, 10, (2), 220-230.

Kennedy, J., Gales, R., Kukla, R. (2006). Converting an Existing Taxonomic Data Resource to Employ an Ontology and LSIDs. In: Belbin, L., Rissoné, A., Weitzman, A. (Eds.) Proceedings of TDWG (2006), St Louis, MI., , () ( ed.). (pp. ). : . .

Kennedy, J., Gales, R., Kukla, R., Hyam, R., Wieczorek, J., Hagedorn, G., Döring, M., Vieglais, D. (2006). Developing a Core Ontology for Taxonomic Data. In: Belbin, L., Rissoné, A., Weitzman, A. (Eds.) Proceedings of TDWG (2006), St Louis, MI, , () ( ed.). (pp. ). USA: . .

Kennedy, J., Kukla, R., Paterson, T. (2005). Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration. In: Ludaescher, B., Raschid, L. (Eds.) Data Integration in the Life Sciences, 3615, () ( ed.). (pp. 80-95). Berlin Heidelberg: . Springer-Verlag.

Pullan, M.R., Armstrong, K., Paterson, T., Cannon, A., Kennedy, J. (2005). The Prometheus Description Model: An examination of the taxonomic description building process and its representation. Taxon, 54, (3), 751-765.

Cannon, A., Kennedy, J., Paterson, T., Watson, M. (2004). Ontology-Driven Automated Generation Of Data Entry Interfaces. In: Williams, H., Mackinnon, L. (Eds.) Key Technologies for Data Management (Proc. BNCOD21): Lecture Notes in Computer Science 3112, , () ( ed.). (pp. 150-164). : . Springer-Verlag.

Paterson, T., Kennedy, J., Pullan, M.R., Cannon, A., Armstrong, K., Watson, M., Raguenaud, C., McDonald, S., Russell, G. (2004). A Universal Character Model and Ontology of Defined Terms for Taxonomic Description. In: Rahm, E. (Ed.) Lecture Notes in Bioinformatics: Proceedings of Data Integration in the Life Sciences (DILS) Leipzig 2004, LNBI 2994, () (LNBI 2994 ed.). (pp. 63-78). : . Springer-Verlag.

Paterson, T., Kennedy, J. (2004). Approaches to Storing and Querying Structural Information in Botanical Specimen Descriptions. In: MacKinnon, L., Burger, A., Trinder, P. (Eds.) Proceedings of the 21st Annual British National Conference on Databases (BNCOD21), , () ( ed.). (pp. 80-91). Edinburgh: . Heriot-Watt University.

Kennedy, J. (2003). Supporting Taxonomic Names in Cell and Molecular Biology Databases. Omics A Journal of Integrative Biology, 7, (1), 13-16.

Paterson, T., Cannon, A., Raguenaud, C., Russell, G., Armstrong, K., MacDonald, S., Pullan, M.R., Watson, M., Kennedy, J. (2003). A Methodology for Composing Well-Defined Character Descriptions. Unpublished, (), ..

Graham, M., Watson, M., Kennedy, J. (2002). Novel visualisation techniques for working with multiple, overlapping classification hierarchies. Taxon, 51, (2), 351-358.

Raguenaud, C., Kennedy, J. (2002). Multiple Overlapping Classifications: Issues and Solutions. In: Kennedy, J. (Ed.) 14th International conference on Scientific and Statistical Database Management - SSDBM 2002, , () ( ed.). (pp. 77-86). : . IEEE Computer Society Press.

Cooper, R., McKirdy, J., Griffiths, T., Barclay, P., Paton, N.W., Gray, P., Kennedy, J., Goble, C. (2000). Conceptual Modelling for Database User Interfaces. In: Arisawa, H., Catarci, T. (Eds.) Visual Database Systems - VDB5, 2000, , () ( ed.). (pp. 129-138). : . Kluwer.

Pullan, M.R., Watson, M., Kennedy, J., Raguenaud, C., Hyam, R. (2000). The Prometheus Taxonomic Model: a practical approach to representing multiple classification. Taxon, 49, (), 55-75.

Raguenaud, C., Kennedy, J., Barclay, P. (2000). The Prometheus Database for Taxonomy. In: Gunther, O., Lenz-H, J. (Eds.) 12th International Conference on Scientific and Statistical Database Management, SSDBM 2000, , () ( ed.). (pp. 250-252). : . IEEE Computer Society Press.

Raguenaud, C., Kennedy, J., Barclay, P. (2000). The Prometheus Taxonomic Database. In: (Ed.) Bio-Informatics and Biomedical Engineering, 2000, , () ( ed.). (pp. 63-70). : . IEEE Computer Society Press.

Graham, M., Kennedy, J., Hand, C. (1999). The Challenge of Visualising Multiple Overlapping Classification. In: Paton, N., Griffiths, T. (Eds.) IEEE User Interfaces to Data Intensive Systems (UIDIS) 1999, , () ( ed.). (pp. 42-51). Scotland: . IEEE Computer Society Press.