phi-base 4
TRANSCRIPT
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
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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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
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
Jacek Grzebyta PHI-base 4
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
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
Jacek Grzebyta PHI-base 4
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
Who is using PHI-base?
Jacek Grzebyta PHI-base 4
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
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
Jacek Grzebyta PHI-base 4
![Page 6: PHI-base 4](https://reader034.vdocument.in/reader034/viewer/2022042614/559751ef1a28abf15b8b45a4/html5/thumbnails/6.jpg)
Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
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
Jacek Grzebyta PHI-base 4
![Page 7: PHI-base 4](https://reader034.vdocument.in/reader034/viewer/2022042614/559751ef1a28abf15b8b45a4/html5/thumbnails/7.jpg)
Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
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
Jacek Grzebyta PHI-base 4
![Page 8: PHI-base 4](https://reader034.vdocument.in/reader034/viewer/2022042614/559751ef1a28abf15b8b45a4/html5/thumbnails/8.jpg)
Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
The software architecture
OpenCms
Spring MVC
Hibernate with Spring support
Database
Parsers
External Databases
Display
Processing
Storage
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
New PHI-base advantages
I Simple web – content construction
I Modularisation
I Uniprot & EMBL linkage
I Open source software
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
To do
I More databases linkage (species specific databases)
I Advanced searching
I Data export (FASTA, RDF)
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
Schema overview
Reference InformationFrom external databases
Perturbed TypeMainly by genetic changes
Wild Type
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
PHI-base future
This year in cooperation with EMBL-EBI we gained new BBSRCgrant no. BB/i000488/1 – Phytopath
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
Thank you
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
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.
Jacek Grzebyta PHI-base 4
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Basic information about PHI-baseWhat is missing in PHI-base?
PHI-base 4PHI-base future
Others
Abstract
Tools
I Java Language
I OpenCms
I Spring Framework
I Hibernate
I XML – Java Object Mapping
Jacek Grzebyta PHI-base 4