The Prometheus Database for Plant

Taxonomy

Cédric Raguenaud, Jessie Kennedy, Peter BarclayNapier University, Edinburgh

http://www.dcs.napier.ac.uk/~prometheus

What is plant taxonomy?

(vi)

(i)

family

genus

(iii) family

genus

tribe

(iv)

species

genus

tribe

(v)genus

variety

species

(ii)family

genus

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

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)

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

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

Acknowledgements

Collaborators Dr Mark Watson, Dr Martin Pullan, Dr Mark Newman

Royal Botanic Garden, Edinburgh

Funding UK Engineering and Physical Sciences Research Council and

Biological and Biotechnology Research Council - Bioinformatics Initiative

WE HAVE A DEMO WITH USplease ask to see it off-line

http://www.dcs.napier.ac.uk/~prometheus