phi-base 4

Basic information about PHI-baseWhat is missing in PHI-base?

PHI-base 4PHI-base future

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PHI-base 4A New Approach For Capturing Host-Pathogen Interactions

Jacek Grzebyta

Biomathematics and Bioinformatics DepartmentRothamsted Research

Molecular Biology of Plant Pathogens, September 2010

Jacek Grzebyta PHI-base 4



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What is PHI-base?http://www.phibase.org

Pathogen Host Interaction database (PHI-base) contains curatedmolecular and biological information of genes affecting theoutcome of the pathogen – host interaction


http://www.phibase.org



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How big is PHI-base?

PHI-base contains:

I 1023 genes (216 non-EMBL genes)I 171 reference organism species:

– 75 hosts– 96 pathogens

I 64 diseases




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Who is using PHI-base?




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What we are missing in the current version

Community curation toolsTo protect the data integrity we have to build non-wiki web based curationtools.

Linkage to external databasesAutomatic validation tools able to work on EBI/NCBI sequences and non-EBIas well (species specific databases).

More complex casesCurrent database schema is not able to manage multiple gene knockout/incases. Also it does not capture host’s gene modification




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The software architecture

OpenCms

Spring MVC

Hibernate with Spring support

Database

Parsers

External Databases

Display

Processing

Storage




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New PHI-base advantages

I Simple web – content construction

I Modularisation

I Uniprot & EMBL linkage

I Open source software




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To do

I More databases linkage (species specific databases)

I Advanced searching

I Data export (FASTA, RDF)




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Schema overview

Reference InformationFrom external databases

Perturbed TypeMainly by genetic changes

Wild Type




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PHI-base future

This year in cooperation with EMBL-EBI we gained new BBSRCgrant no. BB/i000488/1 – Phytopath




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Thank you




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Abstract

Abstract

The PHI-base database contains molecular and biological information on genes for which there isexperimental information on their effect on host-pathogen interactions. This information isretrieved from the peer reviewed scientific literature and the curation process is assisted byvolunteer species experts. Due to limitations of the current database we decided to create newversion 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 thedifferentiation between the model (reference) host-pathogen and the experiment specificinteraction using a more complex data model. The development of web curation tools facilitiescommunity 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 toapprove the entries of community curators before they appear in the database.




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Abstract

Tools

I Java Language

I OpenCms

I Spring Framework

I Hibernate

I XML – Java Object Mapping


phi-base 4

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