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Visualisation and
Analysis of Biological
Networks on the Web
                Andrea Splendiani
Centre for Mathematical and Computational Biology
            Rothamsted Research, UK
The parts




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                                 BioHackathon3 Symposium
The parts




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                                 BioHackathon3 Symposium
The parts




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                                 BioHackathon3 Symposium
The parts




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                                 BioHackathon3 Symposium
The whole




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          BioHackathon3 Symposium
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Bio Hackaton Symposium

  • 1. Visualisation and Analysis of Biological Networks on the Web Andrea Splendiani Centre for Mathematical and Computational Biology Rothamsted Research, UK
  • 2. The parts Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 3. The parts Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 4. The parts Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 5. The parts Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 6. The whole Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 7. Interfaces Parts Whole Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 8. Interfaces Source: http://relfinder.dbpedia.org/ Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 9. RDFScape Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 10. RDFScape = Interface Using Cytoscape for interaction on the Semantic Web Using the Semantic Web for the analysis of networks in Cytoscape Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 11. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 12. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 13. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 14. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 15. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 16. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 17. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 18. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 19. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 20. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 21. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 22. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 23. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 24. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 25. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 26. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 27. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 28. Mapping • selection/ colouring by namespace • datatype properties as attributes • URIs represented as multiple nodes Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 29. Mapping • selection/ colouring by namespace • datatype properties as attributes • URIs represented as multiple nodes Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 30. Mapping • selection/ colouring by namespace • datatype properties as attributes • URIs represented as multiple nodes Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 31. Mapping • selection/ colouring by namespace • datatype properties as attributes • URIs represented as multiple nodes Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 32. Mapping • selection/ colouring by namespace • datatype = properties as attributes • URIs represented as multiple nodes ATP, H2O... Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 33. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 34. Reasoning ?x6 new:interacts ?x7 Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 35. Reasoning A collection of pathways: biological facts Visualization Analysis An ontology: a meaning for facts (interpretation) ? iof pathways Abstraction ? [Skip-Context1: (?i an:directp ?p) <- (?i bp:PARTICIPANT ?p) as interactions (?p rdf:type bp:entity)] [Skip-Context2: (?i an:directp ?p) <- (?i bp:PARTICIPANTS ?pep) (?pep bp:PHYSICAL’ENTITY ?p) Queries (?p rdf:type bp:entity)] “Semantic-enabled” [Interacts: (?x an:interacts ?y) <- (?z rdf:type bp:interaction) (?z and:directp ?x) (?z an:directp ?y) inference rules: Interface (RDFScape) more meaning... Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 36. Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 37. Reasoning bp:interaction rdf:type ?x3 ?x6 new:interacts bp:PARTICIPANTS bp:PARTICIPANTS ?x7 ?x2 ?x1 YSICAL ENTITY bp:PHYSICAL ENT ?x5 ?x4 [Direct-interaction: [Define-interaction: (?interactor new:dirInt ?p) (?pe1 new:interacts ?pe2) <- <- (?x rdf:type bp:interaction) (?x rdf:type bp:interaction) (?x bp:PARTICIPANTS ?px) (?x new:dirInt ?pe1) (?px bp:PHYSICAL-ENTITY ?p)] (?x new:dirInt ?pe2)] Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 38. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 39. Analysis (Reasoning on pathways) [influence: (?x ak:influences ?y) <- (?p1 rdf:type bp:biochemicalReaction) View of pathways as an influence graph (?p2 rdf:type bp:biochemicalReaction) (?p1 bp:RIGHT ?k1)(?k1 bp:PHYSICAL-ENTITY ?k) (?p2 bp:LEFT ?k2)(?k2 bp:PHYSICAL-ENTITY ?k) (?p1 bp:LEFT ?k3)(?k3 bp:PHYSICAL-ENTITY ?x) inference rules: (?p2 bp:RIGHT ?k4)(?k4 bp:PHYSICAL-ENTITY ?y) ] definition of “influence” Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 40. Analysis (Ontologies and data) • Ontologies • General • A-priori • Data • Specific • A-posteriori Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 41. Analysis (Ontologies and data) • Ontologies • General • A-priori • Data • Specific • A-posteriori The user open a correlation network in Cytoscape, and this is connected (through RDFScape) to ontologies Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 42. Analysis (Ontologies and data) Name: sgd Pattern: (?x <bp:XREF> ?y) (?y <bp:DB> ?z) (?y <bp:ID> ?w) AND ?z eq <SGD> ID: ?w URI: ?x Defining the mapping Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 43. Analysis (Queries on ontologies and data) Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 44. Analysis (Queries on ontologies and data) All possible relations (in the ontology) between ?x and ?y (in the a network) Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 45. Analysis (Queries on ontologies and data) All possible relations (in the ontology) between ?x and ?y (in the a network) Such that ?y follows ?x (inferred) Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 46. Analysis (Queries on ontologies and data) All possible relations (in the ontology) between ?x and ?y (in the a network) Such that ?y follows ?x (inferred) Such ?x is differentially expressed and ?y has variance>0.2 (from data) Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 47. Analysis (Information overlay) Selected elements in this p-p interaction graphs correspond to “controllers” in Kegg. The size of the nodes is proportional to the variance in gene expression Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 48. Analysis (Using ontologies for data analysis) Source: http://biit.cs.ut.ee/vishic/ Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 49. Analysis (Using ontologies for data analysis) Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 50. Analysis Source: http://ondex.org/ Can generic analysis tools be brought on the Semantic Web ? Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 51. Conclusions @Hackathon RDFScape: Interaction+Query+Mapping+Reasoning+Analysis= Interface Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 52. Conclusions @Hackathon RDFScape: Interaction+Query+Mapping+Reasoning+Analysis= Interface RDFScape today Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 53. Conclusions @Hackathon RDFScape: Interaction+Query+Mapping+Reasoning+Analysis= Interface RDFScape today RDFScape after the Hackaton Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 54. References RDFScape and network analysis (inference): http://www.biomedcentral.com/1471-2105/9/S4/S6/ Semantic Web user interfaces (discussion): http://CEUR-WS.org/Vol-544/ andrea.splendiani@bbsrc.ac.uk Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  • 55. The end Thanks Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium