1. Towards a computational representation of
host-pathogen interaction networks
J. Grzebyta1 , A. Splendiani1 , M. Urban2 , K.E. Hammond-Kosack2 ,
C.J. Rawlings1 , M. Saqi1
1
Dept of Biomathematics and Bioinformatics, Rothamsted Research
2
Dept of Plant Pathology and Microbiology, Rothamsted Research
Second SICSA Workshop on Biological Networks
21th October
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2. What is PHI-base?
http://www.phibase.org/
97
Pathogens
When? 2005 76 Hosts
1065 173
Genes Organisms
How many 1335
PHI-base records? Interactions
Fusarium
graminearum
720 64
References Diseases
Why? Magnaporthe
oryzae
Mycosphaerella
graminicola
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3. Terms cloud
Protein function Pathogenicity
Gene Disease
Protein
Infection development
GO terms
Resistance
AA sequence
NT sequence Organism Organism function
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4. Domain model
Curation Metadata
(7 tables)
Temporary Tables
(2 tables)
Experiment Specific System
(17 tables)
Reference System
(18 tables)
Output
(2 tables)
Perturbated System
(7 tables)
Controlled Vocabulary
(2 tables)
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5. Data network
Data internal life
Osmosensing
Cell wall
integrity
Pathogenicity
Three conserved intracellular signalling transduction protein kinase pathways in pathogenic fungi.
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6. Data pathway
Generation 0
Terms cloud
PHI-base
domain model
Exported data
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7. Data pathway
Generation 1
or PHI-base is friendly
Terms cloud
PHI-base
domain model
Web links
External databases
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8. Data pathway
Generation 2
or data freedom
Terms cloud
PHI-base
domain model
SPARQL
External databases
cloud
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9. Whole big world
Linked
LOV User Slideshare tags2con
Audio
Feedback 2RDF delicious
Moseley Scrobbler Bricklink Sussex
Folk (DBTune) Reading St.
GTAA
Magna- Lists Andrews
Klapp-
tune stuhl- Resource NTU
DB club Lists Resource
Tropes Lotico Semantic yovisto
John Music Man- Lists
Music Tweet chester
Hellenic Peel Brainz NDL
(DBTune) (Data Brainz Reading
subjects
FBD (zitgist) Lists Open
EUTC Incubator) Linked
Hellenic Library Open t4gm
Produc- Crunch-
PD Surge RDF info
tions
Discogs base Library
Radio Ontos Source Code
Crime ohloh Plymouth (Talis)
(Data News LEM
Ecosystem Reading RAMEAU
Reports business Incubator)
Crime data.gov. Portal Linked Data Lists SH
UK Music Jamendo
(En- uk
Brainz (DBtune) LinkedL
Ox AKTing) FanHubz gnoss ntnusc
(DBTune) SSW CCN
Points Thesau-
Last.FM Poké- Thesaur
Popula- artists pédia Didactal us rus W LIBRIS
tion (En- (DBTune) Last.FM ia theses. LCSH Rådata
reegle research patents MARC
AKTing) (rdfize) my fr nå!
data.gov. data.go Codes
Ren.
NHS uk v.uk Good- Experi-
Classical List
Energy (En- win flickr ment
(DB Pokedex Family Norwe-
Genera- AKTing) Mortality BBC wrappr Sudoc PSH
Tune) gian
(En-
tors Program MeSH
AKTing) semantic
mes BBC IdRef GND
CO2 educatio OpenEI web.org SW
Energy Sudoc ndlna
Emission n.data.g Music Dog VIAF
EEA (En- Chronic- Linked
(En- ov.uk Portu- Food UB
AKTing) ling Event MDB
AKTing) guese Mann- Europeana
BBC America Media
DBpedia Calames heim
Ord- Recht- Wildlife Deutsche
Open Revyu DDC
Openly spraak. Finder Bio- lobid
Election nance
legislation Local nl RDF graphie
Resources NSZL Swedish
Data Survey Tele- data Ulm
EU New Book
Project data.gov.uk graphis bnf.fr Catalog Open
Insti- York
URI Open Mashup Cultural
tutions Times Greek P20
UK Post- Burner Calais Heritage
codes DBpedia ECS Wiki
statistics lobid
GovWILD data.gov. Taxon iServe South- Organi-
LOIUS BNB
Brazilian
uk Concept ECS ampton sations
Geo World OS BibBase STW GESIS
Poli- ESD South- ECS
Names Fact- (RKB
ticians stan- reference ampton
data.gov.uk book Freebase Explorer) Budapest
dards data.gov. NASA EPrints
uk intervals Project OAI
Lichfield transport (Data DBpedia data
Guten- Pisa
Spen- data.gov. Incu- dcs RESEX Scholaro-
ISTAT ding bator) Fishes berg DBLP DBLP
uk Geo
meter
Immi- Scotland of Texas (FU (L3S)
Pupils & Uberblic DBLP
gration Species Berlin) IRIT
Exams Euro- dbpedia data- (RKB
London TCM ACM
stat lite open- Explorer) NVD
Gazette (FUB) Gene IBM
Traffic Geo ac-uk
Scotland TWC LOGD Eurostat Daily DIT
Linked UN/
Data UMBEL Med ERA
Data LOCODE DEPLOY
Gov.ie CORDIS YAGO New-
lingvoj Disea-
(RKB some SIDER RAE2001 castle LOCAH
CORDIS Explorer) Linked Eurécom
Eurostat Drug CiteSeer Roma
(FUB) Sensor Data
GovTrack (Ontology (Kno.e.sis) Open Bank Pfam Course-
Central) riese Enipedia
Cyc Lexvo LinkedCT ware
Linked PDB
UniProt VIVO
EURES EDGAR dotAC
US SEC Indiana ePrints IEEE
(Ontology totl.net
(rdfabout)
Central) WordNet RISKS
(VUA) Taxono UniProt
US Census EUNIS Twarql HGNC
Semantic Cornetto (Bio2RDF)
(rdfabout) my VIVO
FTS XBRL PRO- ProDom STITCH Cornell LAAS
SITE NSF
PHI-base
Scotland KISTI
Geo- GeoWord LODE
graphy Net WordNet WordNet JISC
(W3C) (RKB
Climbing
Linked Affy- KEGG
SMC Explorer) SISVU Pub VIVO UF
Piedmont GeoData metrix Drug
ECCO-
Finnish Journals PubMed Gene SGD Chem
Munici-
Accomo- El AGROV Ontology TCP Media
dations Alpine bible
palities Viajero OC
Ski ontology
Tourism KEGG
Ocean
Austria
Enzyme PBAC Geographic
Metoffice GEMET ChEMBL
Italian Drilling OMIM KEGG
Weather Open
public Codices AEMET Linked MGI Pathway
schools Forecasts
Data
Open InterPro GeneID Publications
EARTh Thesau- KEGG
Turismo
rus Colors Reaction
de
Zaragoza Product Smart KEGG
User-generated content
Weather DB Link Medi Glycan
Janus Stations Product Care KEGG
AMP UniParc UniRef UniSTS Government
Types Italian
Homolo Com-
Yahoo! Airports Museums pound
Ontology Google
Gene
Geo Art
Planet National
wrapper
Chem2 Cross-domain
Radio- Bio2RDF
activity UniPath
JP Sears Open Linked OGOLOD way
Life sciences
Corpo- Amster- Reactome
dam medu- Open
rates Numbers
Museum cator
As of September 2011
Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/
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10. Acknowledgements
PHI-base 4.x is partly funded by the BBSRC within the BBR initiative (Grant
”PhytoPath: an integrated resource for comparative phytopathogen
genomics”. Ref. BB/I000488/1) held jointly with the EBI Cambridge, UK and
partly from core BBSRC funding to Rothamsted (Research).
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11. Thank you
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