1. The Prometheus Database for Plant Taxonomy Cédric Raguenaud, Jessie Kennedy, Peter Barclay Napier University, Edinburgh http://www.dcs.napier.ac.uk/~prometheus

2. What is plant taxonomy? (vi) (i) family genus (iii) family genus tribe (iv) species genus tribe (v) genus variety species (ii) family genus

3. Plant Taxonomy Data äThe data is hierarchical äMultiple overlapping hierarchies co-exist ädistinct hierarchies need identified - manipulation and extraction äaggregation, explicit relationships, attributes on relationships äquerying is recursive & dependent on the context of the relationships äNodes in the hierarchy are aggregate objects äalso have association to other objects outside the hierarchy ädifferentiate between association and composition in relationships äextraction of composite objects required äLevels of the hierarchy bear information äpositioning of objects in a hierarchy dependent on domain specific constraints äquerying on attributes of relationships required äDomain specific rules are important ädata is derived based on domain specific rules ädefinition of constraints necessary for defining rules

4. Which Database? äExisting Taxonomic Databases are inadequate due to: äsimplicity of model of taxonomy äsupport single classifications only älimitations of underlying database: äRelational model älimited semantics, no explicit relationships, no recursive querying äGraph models älimited semantics, no constraints äSemi-structured data älimited semantics, no a priori schema äObject-Oriented models älimited support for relationships, no recursive querying äNeed OODB with relationships + Graph functionality äOODBs with relationships already exist (e.g. OMS, Albano’s, GraphDB) älimited (e.g. no QL, no semantics for relationships, or no constraints) äor based on uncommon models (e.g. collection based model of Albano)

5. Prometheus Approach äPrometheus Model äODMG model extended with relationships as first class constructs äPOOL äOQL + operators for manipulating relationships and graphs äquery relationship objects ädefine query on aggregation relationships only äspecify a particular path to be followed through a hierarchy äspecify the transitive closure of a relationship äreturn a hierarchy as a structure äPrometheus database model and QL (POOL) defined äPrometheus prototype implemented using POET (ODMG OODB) and Java

6. Prometheus Taxonomic DB äNew model (schema) of plant taxonomy defined äextensive use of relationships äPlant taxonomy DBMS implemented using Prometheus äbeing tested by taxonomists ästores all examples of data provided äcan answer all queries posed ädemo via http interface available äConclusion äExplicit relationships in DB provide ways to improve ämodelling power & mapping between model and implementation äsupport for graph structures äQL support necessary to profit from relationships äincreased power of ad hoc querying without being domain specific

7. Acknowledgements äCollaborators äDr Mark Watson, Dr Martin Pullan, Dr Mark Newman Royal Botanic Garden, Edinburgh äFunding äUK Engineering and Physical Sciences Research Council and Biological and Biotechnology Research Council - Bioinformatics Initiative WE HAVE A DEMO WITH US please ask to see it off-line http://www.dcs.napier.ac.uk/~prometheus