Visualisation andAnalysis 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Interfaces

PartsWhole
Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumInterfaces

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

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

RDFScapeAndrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

RDFScape = Interface
Using Cytoscapefor interaction
on the SemanticWeb

Using theSemantic Web
for the analysisof networks inCytoscapeAndrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

RDFScape = Interface
Inspection

Mapping

Analysis
Query

Reasoning

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

RDFScape = Interface
Inspection

Mapping

Analysis
Query

Reasoning

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

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

Andrea Splendiani,Visualisation and Analysis of Biological Networks on the WebBioHackathon3 SymposiumInspection

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

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

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

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

RDFScape = Interface
Inspection

Mapping

AnalysisQueryReasoning

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

QueryAndrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

QueryAndrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

QueryAndrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

QueryAndrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

QueryAndrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

QueryAndrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

QueryAndrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

RDFScape = Interface
Inspection

Mapping

Analysis
Query

Reasoning

Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumMapping• selection/

colouring by
namespace• datatype
properties as
attributes• URIsrepresented
as multiple
nodes
Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumMapping• selection/

colouring by
namespace• datatype
properties asattributes• URIsrepresented
as multiple
nodes
Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumMapping• selection/colouring by
namespace• datatype
properties as
attributes• URIsrepresented
as multiple
nodes
Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumMapping• selection/colouring by
namespace• datatype
properties as
attributes• URIsrepresented
as multiple
nodes
Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumMapping• selection/=ATP, H2O...

colouring by
namespace• datatype
properties as
attributes• URIsrepresented
as multiple
nodes

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

RDFScape = Interface
Inspection

Mapping

Analysis
Query

Reasoning

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

Reasoning?x6

new:interacts?x7

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

Reasoning
A collection of pathways:
biological facts
Visualization

An ontology: a meaning
for facts (interpretation)i ?
?
Abstraction of pathways
as interactions[Skip-Context1:(?i an:directp ?p) <- (?i bp:PARTICIPANT ?p)(?p rdf:type bp:entity)]

Queries[Skip-Context2:(?i an:directp ?p) <- (?i bp:PARTICIPANTS ?pep)(?pep bp:PHYSICAL’ENTITY ?p)(?p rdf:type bp:entity)][Interacts:(?x an:interacts ?y) <- (?z rdf:type bp:interaction)(?z and:directp ?x) (?z an:directp ?y)inference rules:
more meaning...

Analysis“Semantic-enabled”
Interface (RDFScape)Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

Reasoning

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

Reasoning
bp:interaction

rdf:type?x6?x3
bp:PARTICIPANTS
?x2

?x1

YSICALïENTITY?x5

bp:PARTICIPANTS

new:interacts?x7

bp:PHYSICALïENT

?x4[Direct-interaction:(?interactor new:dirInt ?p)<(?x rdf:type bp:interaction)(?x bp:PARTICIPANTS ?px)(?px bp:PHYSICAL-ENTITY ?p)]

[Define-interaction:(?pe1 new:interacts ?pe2)<(?x rdf:type bp:interaction)(?x new:dirInt ?pe1)(?x new:dirInt ?pe2)]

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

RDFScape = Interface
Inspection

Mapping

AnalysisQueryReasoning

Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumAnalysis(Reasoning on pathways)[influence: (?x ak:influences ?y) <- (?p1 rdf:type
View of pathways as an influence graphbp:biochemicalReaction)(?p2 rdf:type bp:biochemicalReaction)(?p1 bp:RIGHT ?k1)(?k1 bp:PHYSICAL-ENTITY ?k)(?p2 bp:LEFT ?k2)(?k2 bp:PHYSICAL-ENTITY ?k)inference rules:(?p1 bp:LEFT ?k3)(?k3 bp:PHYSICAL-ENTITY ?x)(?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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Analysis(Ontologies and data)• Ontologies• General• A-priori• Data• Specific• A-posteriori
The user open a correlation network in Cytoscape, andthis is connected (through RDFScape) to ontologies
Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumAnalysis(Ontologies and data)

Definingthemapping

Name: sgd
Pattern: (?x <bp:XREF> ?y)(?y <bp:DB> ?z) (?y <bp:ID> ?w)
AND ?z eq <SGD>
ID: ?w
URI: ?x

Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumAnalysis(Queries on ontologies and data)

Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumAnalysis(Queries on ontologies and data)

All possible relations (in theontology) between?x and ?y (in the a network)

Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 SymposiumAnalysis(Queries on ontologies and data)

All possible relations (in theontology) 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Analysis(Queries on ontologies and data)

All possible relations (in theontology) 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Analysis(Information overlay)
Selected elements in thisp-p interaction graphs
correspond to“controllers” in Kegg.
The size of the nodes isproportional to thevariance in gene
expression

Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium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Analysis(Using ontologies for data analysis)

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

Conclusions@Hackathon

RDFScape:
Interaction+Query+Mapping+Reasoning+Analysis=
Interface

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

Conclusions@Hackathon

RDFScape:
Interaction+Query+Mapping+Reasoning+Analysis=
Interface

RDFScape today
Andrea Splendiani,Visualisation and Analysis of Biological Networks on the Web
BioHackathon3 Symposium

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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

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