Bio Hackaton Symposium

Visualisation and Analysis of Biological

Networks on the WebAndrea Splendiani

Centre for Mathematical and Computational Biology Rothamsted Research, UK

The parts

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

The parts

The whole

Interfaces

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

=RDFScape

=RDFScape = Interface

Using the Semantic Web for the analysis of networks in

Cytoscape

Using Cytoscape for interaction

on the Semantic Web

Inspection

Mapping

Reasoning

Analysis

RDFScape = Interface

Inspection

Mapping

Reasoning

Analysis

Inspection

Mapping

Reasoning

Analysis

Inspection

Mapping

Reasoning

Analysis

Mapping• selection/ colouring by namespace• datatype properties as attributes• URIs represented as multiple nodes

ATP, H2O...

Inspection

Mapping

Reasoning

Analysis

Reasoning

new:interacts?x7

ReasoningA collection of pathways:

biological facts

An ontology: a meaning for facts (interpretation)

[Skip-Context1: (?i an:directp ?p) <- (?i bp:PARTICIPANT ?p)(?p rdf:type bp:entity)]

[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...

“Semantic-enabled” Interface (RDFScape)

? i ?Abstraction of pathways

as interactions

Queries

Visualization

Analysis

Reasoning

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

new:interacts?x7

bp:PHYSICAL ENT

bp:PARTICIPANTSbp:PARTICIPANTS

YSICAL ENTITY

rdf:type

bp:interaction

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

Inspection

Mapping

Reasoning

Analysis

[influence: (?x ak:influences ?y) <- (?p1 rdf:type bp:biochemicalReaction) (?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) (?p2 bp:RIGHT ?k4)(?k4 bp:PHYSICAL-ENTITY ?y) ]

inference rules:definition of “influence”

View of pathways as an influence graph

Analysis (Reasoning on pathways)

• Ontologies• General• A-priori

• Data• Specific• A-posteriori

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

Analysis

Name: sgdPattern: (?x <bp:XREF> ?y) (?y <bp:DB> ?z) (?y <bp:ID> ?w) AND ?z eq <SGD>ID: ?wURI: ?x

Defining the

mapping

Analysis

Analysis (Queries on ontologies and data)

Analysis

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

Analysis

Such that ?y follows ?x (inferred)

Analysis

Such that ?y follows ?x (inferred)

Such ?x is differentially expressed and ?y has variance>0.2 (from data)

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

Analysis (Information overlay)

Source:http://biit.cs.ut.ee/vishic/

Analysis (Using ontologies for data analysis)

Analysis

Can generic analysis tools be brought on the Semantic Web ?

Source:http://ondex.org/

Conclusions@Hackathon

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

RDFScape todayAndrea Splendiani, Visualisation and Analysis of Biological Networks on the Web

BioHackathon3 Symposium

RDFScape today RDFScape after the HackatonAndrea 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

The end

Thanks

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