(http://sgtp.net/AndreaSplendiani)

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