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PHI-base 4
1. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
PHI-base 4
A New Approach For Capturing Host-Pathogen Interactions
Jacek Grzebyta
Biomathematics and Bioinformatics Department
Rothamsted Research
Molecular Biology of Plant Pathogens, September 2010
Jacek Grzebyta PHI-base 4
2. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
What is PHI-base?
http://www.phibase.org
Pathogen Host Interaction database (PHI-base) contains curated
molecular and biological information of genes affecting the
outcome of the pathogen – host interaction
Jacek Grzebyta PHI-base 4
3. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
How big is PHI-base?
PHI-base contains:
1023 genes (216 non-EMBL genes)
171 reference organism species:
– 75 hosts
– 96 pathogens
64 diseases
Jacek Grzebyta PHI-base 4
4. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
Who is using PHI-base?
Jacek Grzebyta PHI-base 4
5. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
What we are missing in the current version
Community curation tools
To protect the data integrity we have to build non-wiki web based curation
tools.
Jacek Grzebyta PHI-base 4
6. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
What we are missing in the current version
Community curation tools
To protect the data integrity we have to build non-wiki web based curation
tools.
Linkage to external databases
Automatic validation tools able to work on EBI/NCBI sequences and non-EBI
as well (species specific databases).
Jacek Grzebyta PHI-base 4
7. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
What we are missing in the current version
Community curation tools
To protect the data integrity we have to build non-wiki web based curation
tools.
Linkage to external databases
Automatic validation tools able to work on EBI/NCBI sequences and non-EBI
as well (species specific databases).
More complex cases
Current database schema is not able to manage multiple gene knockout/in
cases. Also it does not capture host’s gene modification
Jacek Grzebyta PHI-base 4
8. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
The software architecture
Display OpenCms
Spring MVC
Processing
Hibernate with Spring support Parsers
Storage
Database External Databases
Jacek Grzebyta PHI-base 4
9. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
New PHI-base advantages
Simple web – content construction
Modularisation
Uniprot & EMBL linkage
Open source software
Jacek Grzebyta PHI-base 4
10. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
To do
More databases linkage (species specific databases)
Advanced searching
Data export (FASTA, RDF)
Jacek Grzebyta PHI-base 4
11. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
Schema overview
Wild Type
Reference Information
From external databases
Perturbed Type
Mainly by genetic changes
Jacek Grzebyta PHI-base 4
12. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
PHI-base future
This year in cooperation with EMBL-EBI we gained new BBSRC
grant no. BB/i000488/1 – Phytopath
Jacek Grzebyta PHI-base 4
13. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4
PHI-base future
Others
Thank you
Jacek Grzebyta PHI-base 4
14. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4 Abstract
PHI-base future
Others
Abstract
The PHI-base database contains molecular and biological information on genes for which there is
experimental information on their effect on host-pathogen interactions. This information is
retrieved from the peer reviewed scientific literature and the curation process is assisted by
volunteer species experts. Due to limitations of the current database we decided to create new
version of PHI-base. The aims were to provide a more useful schema, together with curation tools,
and to facilitate database administration. The main feature of the new database schema is the
differentiation between the model (reference) host-pathogen and the experiment specific
interaction using a more complex data model. The development of web curation tools facilities
community curation by allowing species experts to add new data and also to upgrade existing data.
Quality control will be provided by the use of editorial control tools to permit a main curator to
approve the entries of community curators before they appear in the database.
Jacek Grzebyta PHI-base 4
15. Basic information about PHI-base
What is missing in PHI-base?
PHI-base 4 Abstract
PHI-base future
Others
Tools
Java Language
OpenCms
Spring Framework
Hibernate
XML – Java Object Mapping
Jacek Grzebyta PHI-base 4