The Prometheus Database for Plant Taxonomy

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

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

3. Plant Taxonomy Data • The data is hierarchical • Multiple overlapping hierarchies co-exist • distinct hierarchies need identified - manipulation and extraction • aggregation, explicit relationships, attributes on relationships • querying is recursive & dependent on the context of the relationships • Nodes in the hierarchy are aggregate objects • also have association to other objects outside the hierarchy • differentiate between association and composition in relationships • extraction of composite objects required • Levels of the hierarchy bear information • positioning of objects in a hierarchy dependent on domain specific constraints • querying on attributes of relationships required • Domain specific rules are important • data is derived based on domain specific rules • definition of constraints necessary for defining rules

4. Which Database? • Existing Taxonomic Databases are inadequate due to: • simplicity of model of taxonomy • support single classifications only • limitations of underlying database: • Relational model • limited semantics, no explicit relationships, no recursive querying • Graph models • limited semantics, no constraints • Semi-structured data • limited semantics, no a priori schema • Object-Oriented models • limited support for relationships, no recursive querying • Need OODB with relationships + Graph functionality • OODBs with relationships already exist (e.g. OMS, Albano’s, GraphDB) • limited (e.g. no QL, no semantics for relationships, or no constraints) • or based on uncommon models (e.g. collection based model of Albano)

5. Prometheus Approach • Prometheus Model • ODMG model extended with relationships as first class constructs • POOL • OQL + operators for manipulating relationships and graphs • query relationship objects • define query on aggregation relationships only • specify a particular path to be followed through a hierarchy • specify the transitive closure of a relationship • return a hierarchy as a structure • Prometheus database model and QL (POOL) defined • Prometheus prototype implemented using POET (ODMG OODB) and Java

6. Prometheus Taxonomic DB • New model (schema) of plant taxonomy defined • extensive use of relationships • Plant taxonomy DBMS implemented using Prometheus • being tested by taxonomists • stores all examples of data provided • can answer all queries posed • demo via http interface available • Conclusion • Explicit relationships in DB provide ways to improve • modelling power & mapping between model and implementation • support for graph structures • QL support necessary to profit from relationships • increased power of ad hoc querying without being domain specific

7. Acknowledgements • Collaborators • Dr Mark Watson, Dr Martin Pullan, Dr Mark NewmanRoyal Botanic Garden, Edinburgh • Funding • UK 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