Transcript Ecogeography of Wild Relatives of Rice

European crop wild relative database
Progress report
Jay Moore
PGR Forum Workshop 4.
European crop wild relative database
Progress report
PGR Forum Workshop 4.
Introduction to the database
Development plan
Project methodology
Database architecture
Data sources and ontology/descriptors
Discussion of requirements
European crop wild relative database
Progress report
PGR Forum Workshop 4.
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
European crop wild relative database
Progress report
PGR Forum Workshop 4.
Development plan
Activity
Advise on User Requirement Survey and Analysis
Devise/Adopt XML Schema
Agree Architecture (Hardware/Software/Database)
Analyse Euro+Med Synchronisation
Build Case Study Collation Database
Build Interface to Euro+Med
Formulate Use Cases
Build Version 2.0 Taxon and Case Study Databases
Build Generalised Interface to Other Sources
Build Web Interface
Meetings and Administration
Q4 2003
1
1
Q1 2004
1
2
1
2
2
Q2 2004
Q3 2004
Q4 2004
Q1 2005
Q2 2005
Q3 2005
3
1
3
1
1
2
4
2
4
4
1
1
1
1
1
Progress to date is on schedule
Development is iterative
Changes to the database go through a ‘Change Control’ process
Total Days
2
3
1
2
4
4
2
4
4
6
8
European crop wild relative database
Progress report
PGR Forum Workshop 4.
Database platform
mySQL database management system
Leading open-source high-spec database
Active Server Pages web application
Pragmatic decision - leading commercial application builder
Open source packaged applications
hosted by University of Birmingham
European crop wild relative database
Progress report
PGR Forum Workshop 4.
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
European crop wild relative database
Progress report
PGR Forum Workshop 4.
Database architecture
Data warehouse snowflake schema:
Data
model
location
provenanc
e
fact
taxonom
y
ontology
language
Single ‘fact’ table stores each datum
Each datum has many ‘dimensions’
Tree structure for each dimension of the data
European crop wild relative database
Progress report
PGR Forum Workshop 4.
European crop wild relative database
Progress report
PGR Forum Workshop 4.
European crop wild relative database
Progress report
Discussion of requirements
 Estimate of number of pieces of data
 Decide on dimensions of the data
PGR Forum Workshop 4.
European crop wild relative database
Progress report
PGR Forum Workshop 4.
Data sources and ontology/descriptors
Published taxonomic literature
Published ecological information
Published and unpublished data acquired from
media searches
Open source ontologies and descriptor lists
???
European crop wild relative database
Progress report
Questions
PGR Forum Workshop 4.