Visualisation and
Analysis of Biological
Networks on the Web
                Andrea Splendiani
Centre for Mathematical and...
The parts




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




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




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




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




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          Bio...
Interfaces


Parts




                                                                Whole
 Andrea Splendiani,Visualisat...
Interfaces




Source:
http://relfinder.dbpedia.org/

     Andrea Splendiani,Visualisation and Analysis of Biological Netwo...
RDFScape




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          BioH...
RDFScape = Interface
Using Cytoscape
 for interaction
on the Semantic
       Web
                                         ...
RDFScape = Interface

  Inspection                                   Mapping
                              Analysis

     ...
RDFScape = Interface

Inspection                                     Mapping
                              Analysis

     ...
Inspection




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          Bi...
Inspection




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          Bi...
Inspection




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          Bi...
Inspection




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          Bi...
Inspection




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          Bi...
Inspection




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          Bi...
RDFScape = Interface

  Inspection                                   Mapping
                              Analysis

     ...
Query




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          BioHack...
Query




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          BioHack...
Query




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          BioHack...
Query




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          BioHack...
Query




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          BioHack...
Query




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          BioHack...
Query




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          BioHack...
RDFScape = Interface

  Inspection                                Mapping
                              Analysis

        ...
Mapping
                                                            • selection/
                                         ...
Mapping
                                                            • selection/
                                         ...
Mapping
                                                            • selection/
                                         ...
Mapping
                                                            • selection/
                                         ...
Mapping
                                                              • selection/
                                       ...
RDFScape = Interface

  Inspection                                   Mapping
                              Analysis

     ...
Reasoning


                                                ?x6
                                                       new...
Reasoning
A collection of pathways:
     biological facts
                                                                ...
Reasoning




Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
                          Bio...
Reasoning
                     bp:interaction



                        rdf:type



                            ?x3
     ...
RDFScape = Interface

  Inspection                                   Mapping

                           Analysis
        ...
Analysis
                              (Reasoning on pathways)




[influence: (?x ak:influences ?y) <- (?p1 rdf:type
bp:bio...
Analysis
                            (Ontologies and data)

• Ontologies
• General
• A-priori

                           ...
Analysis
                            (Ontologies and data)

• Ontologies
• General
• A-priori

                           ...
Analysis
                        (Ontologies and data)




                                              Name: sgd
       ...
Analysis
                (Queries on ontologies and data)




Andrea Splendiani,Visualisation and Analysis of Biological N...
Analysis
                     (Queries on ontologies and data)

All possible relations (in the
ontology) between
?x and ?y...
Analysis
                     (Queries on ontologies and data)

All possible relations (in the
ontology) between
?x and ?y...
Analysis
                     (Queries on ontologies and data)

All possible relations (in the
ontology) between
?x and ?y...
Analysis
                        (Information overlay)


                                               Selected elements ...
Analysis
               (Using ontologies for data analysis)




                                                         ...
Analysis
               (Using ontologies for data analysis)




Andrea Splendiani,Visualisation and Analysis of Biologica...
Analysis




                                                                          Source:
                           ...
Conclusions
                        @Hackathon
     RDFScape:
     Interaction+Query+Mapping+Reasoning+Analysis=
     Inte...
Conclusions
                        @Hackathon
     RDFScape:
     Interaction+Query+Mapping+Reasoning+Analysis=
     Inte...
Conclusions
                        @Hackathon
     RDFScape:
     Interaction+Query+Mapping+Reasoning+Analysis=
     Inte...
References
RDFScape and network analysis (inference):
http://www.biomedcentral.com/1471-2105/9/S4/S6/

Semantic Web user i...
The end


                         Thanks

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

  1. 1. Visualisation and Analysis of Biological Networks on the Web Andrea Splendiani Centre for Mathematical and Computational Biology Rothamsted Research, UK
  2. 2. The parts Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  3. 3. The parts Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  4. 4. The parts Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  5. 5. The parts Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  6. 6. The whole Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  7. 7. Interfaces Parts Whole Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  8. 8. Interfaces Source: http://relfinder.dbpedia.org/ Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  9. 9. RDFScape Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  10. 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. 11. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  12. 12. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  13. 13. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  14. 14. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  15. 15. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  16. 16. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  17. 17. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  18. 18. Inspection Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  19. 19. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  20. 20. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  21. 21. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  22. 22. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  23. 23. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  24. 24. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  25. 25. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  26. 26. Query Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  27. 27. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  28. 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. 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. 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. 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. 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. 33. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  34. 34. Reasoning ?x6 new:interacts ?x7 Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  35. 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. 36. Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  37. 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. 38. RDFScape = Interface Inspection Mapping Analysis Query Reasoning Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  39. 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. 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. 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. 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. 43. Analysis (Queries on ontologies and data) Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  44. 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. 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. 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. 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. 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. 49. Analysis (Using ontologies for data analysis) Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  50. 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. 51. Conclusions @Hackathon RDFScape: Interaction+Query+Mapping+Reasoning+Analysis= Interface Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium
  52. 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. 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. 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. 55. The end Thanks Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web BioHackathon3 Symposium

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