european crop wild relative database progress report pgr forum workshop 4. jay moore

European crop wild relative database

Progress report PGR Forum Workshop 4.

Jay Moore



Introduction to the databaseDevelopment plan Project methodologyDatabase architectureData sources and ontology/descriptorsDiscussion of requirements

Introduction to the database

Information about c.w.r. biology, distribution and status Data sources - diverse

depth, coverage, accuracy, descriptors, language

Webs of evidence

Aims To capture the relevant data To link with pre-existing databases To respond to queries



Development plan



Activity Q4 2003 Q1 2004 Q2 2004 Q3 2004 Q4 2004 Q1 2005 Q2 2005 Q3 2005 Total Days Advise on User Requirement Survey and Analysis 1 1 2 Devise/Adopt XML Schema 1 2 3 Agree Architecture (Hardware/Software/Database) 1 1 Analyse Euro+Med Synchronisation 2 2 Build Case Study Collation Database 2 2 4 Build Interface to Euro+Med 4 4 Formulate Use Cases 2 2 Build Version 2.0 Taxon and Case Study Databases 4 4 Build Generalised Interface to Other Sources 4 4 Build Web Interface 3 3 6 Meetings and Administration 1 1 1 1 1 1 1 1 8

Progress to date is on schedule Development is iterative Changes to the database go through a ‘Change Control’

process

Database platform

mySQL database management systemLeading open-source high-spec database

Active Server Pages web applicationPragmatic decision - leading commercial application

builder

Open source packaged applications

hosted by University of Birmingham



Database architecture

Snowflake schema Data loading (Extract/Translate/Load) tool Browser to navigate snowflake structure Query tool to ask questions about the data Modelling tool to generate hypotheses



taxonomy

fact

ontology

location

language

provenance

Data model



Database architectureData warehouse snowflake schema:

Single ‘fact’ table stores each datum Each datum has many ‘dimensions’Tree structure for each dimension of the data

Discussion of requirements

Estimate of number of pieces of data Decide on dimensions of the data



Data sources and ontology/descriptors

Published taxonomic literaturePublished ecological informationPublished and unpublished data acquired

from media searchesOpen source ontologies and descriptor lists???



Questions



european crop wild relative database progress report pgr forum workshop 4. jay moore

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