Towards a computational representation of     host-pathogen interaction networksJ. Grzebyta1 , A. Splendiani1 , M. Urban2 ...
What is PHI-base?http://www.phibase.org/                                                                                  ...
Terms cloud        Protein function                                 Pathogenicity                                     Gene...
Domain model                                                  Curation Metadata                                           ...
Data networkData internal life                                                                                 Osmosensing...
Data pathwayGeneration 0                                       Terms cloud                                                ...
Data pathwayGeneration 1or PHI-base is friendly                                           Terms cloud                     ...
Data pathwayGeneration 2or data freedom                                          Terms cloud                              ...
Whole big world                                                                                                           ...
AcknowledgementsPHI-base 4.x is partly funded by the BBSRC within the BBR initiative (Grant”PhytoPath: an integrated resou...
Thank youTowards a computational ...               Grzebyta et all   11 / 11
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Towards a computational representation of host-pathogen interaction networks

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Towards a computational representation of host-pathogen interaction networks

  1. 1. Towards a computational representation of host-pathogen interaction networksJ. 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 Towards a computational ... Grzebyta et all 1 / 11
  2. 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 Towards a computational ... Grzebyta et all 2 / 11
  3. 3. Terms cloud Protein function Pathogenicity Gene Disease Protein Infection development GO terms Resistance AA sequence NT sequence Organism Organism function Towards a computational ... Grzebyta et all 3 / 11
  4. 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) Towards a computational ... Grzebyta et all 4 / 11
  5. 5. Data networkData internal life Osmosensing Cell wall integrity Pathogenicity Three conserved intracellular signalling transduction protein kinase pathways in pathogenic fungi. Towards a computational ... Grzebyta et all 5 / 11
  6. 6. Data pathwayGeneration 0 Terms cloud PHI-base domain model Exported data Towards a computational ... Grzebyta et all 6 / 11
  7. 7. Data pathwayGeneration 1or PHI-base is friendly Terms cloud PHI-base domain model Web links External databases Towards a computational ... Grzebyta et all 7 / 11
  8. 8. Data pathwayGeneration 2or data freedom Terms cloud PHI-base domain model SPARQL External databases cloud Towards a computational ... Grzebyta et all 8 / 11
  9. 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/ Towards a computational ... Grzebyta et all 9 / 11
  10. 10. AcknowledgementsPHI-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). Towards a computational ... Grzebyta et all 10 / 11
  11. 11. Thank youTowards a computational ... Grzebyta et all 11 / 11

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