Towards a computational representation of host-pathogen interaction networks
description
Transcript of Towards a computational representation of host-pathogen interaction networks
Towards a computational representation ofhost-pathogen interaction networks
J. Grzebyta1, A. Splendiani1, M. Urban2, K.E. Hammond-Kosack2,C.J. Rawlings1, M. Saqi1
1Dept of Biomathematics and Bioinformatics, Rothamsted Research2Dept of Plant Pathology and Microbiology, Rothamsted Research
Second SICSA Workshop on Biological Networks21th October
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What is PHI-base?http://www.phibase.org/
PHI-base
Why? Magnaportheoryzae
Mycosphaerellagraminicola
Fusariumgraminearum
When? 2005
How manyrecords?
1065Genes
173Organisms
97Pathogens
76 Hosts
1335Interactions
64Diseases
720References
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Terms cloud
GeneProtein
GO termsAA sequence
Protein function
NT sequence Organism Organism function
PathogenicityDisease
ResistanceInfection development
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Domain model
Curation Metadata(7 tables)
Reference System(18 tables)
Experiment Specific System(17 tables)
Perturbated System(7 tables)
Controlled Vocabulary(2 tables)
Temporary Tables(2 tables)
Output(2 tables)
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Data networkData internal life
Osmosensing
Cell wallintegrity
Pathogenicity
Three conserved intracellular signalling transduction protein kinase pathways in pathogenic fungi.
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Data pathwayGeneration 0
Terms cloud
PHI-basedomain model
Exported data
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Data pathwayGeneration 1or PHI-base is friendly
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PHI-basedomain model
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Data pathwayGeneration 2or data freedom
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PHI-base
domain model
External databases
cloud
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Whole big world
As of September 2011
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PHI-base
Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/
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Acknowledgements
PHI-base 4.x is partly funded by the BBSRC within the BBR initiative (Grant”PhytoPath: an integrated resource for comparative phytopathogengenomics”. Ref. BB/I000488/1) held jointly with the EBI Cambridge, UK andpartly from core BBSRC funding to Rothamsted (Research).
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Thank you
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