Upload
others
View
5
Download
0
Embed Size (px)
Citation preview
Analysis and visualisation of RDF resources in Ondex
Catherine [email protected]
Nat
ure
Pre
cedi
ngs
: doi
:10.
1038
/npr
e.20
10.5
430.
1 : P
oste
d 23
Dec
201
0
Motivation
Biomedical resources provide info on the Semantic Web
Potential to advance biomedical research Need for tools
Data reduction Data visualization Interactive analysis capabilities
Nat
ure
Pre
cedi
ngs
: doi
:10.
1038
/npr
e.20
10.5
430.
1 : P
oste
d 23
Dec
201
0
Ondex: a platform to exploit the Semantic Web
1) all information can be represented as a graph
2) all elements of the graph can be annotated with ontologies
3) data model conformant to Semantic Web framework, in particular to RDF
Ondex ideally positionedNat
ure
Pre
cedi
ngs
: doi
:10.
1038
/npr
e.20
10.5
430.
1 : P
oste
d 23
Dec
201
0
Data integration and visualisation in Ondex
Data analysisData Integration
Data Input
HypothesisNew experiments
Ontologies & Free Text
Biological Databases
Experimental DataData alignment
• Concept mapping
• Sequence analysis
• Text mining
Graph of concepts and
relations
Parse Export
Nat
ure
Pre
cedi
ngs
: doi
:10.
1038
/npr
e.20
10.5
430.
1 : P
oste
d 23
Dec
201
0
Data reduction and representation methods
Filter on centrality
Filter on confidence
Nat
ure
Pre
cedi
ngs
: doi
:10.
1038
/npr
e.20
10.5
430.
1 : P
oste
d 23
Dec
201
0
Nat
ure
Pre
cedi
ngs
: doi
:10.
1038
/npr
e.20
10.5
430.
1 : P
oste
d 23
Dec
201
0
Demo
Interactive importer based on SPARQL Querydriven construction of datasets Bring information from different RDF data
resources into Ondex
Welcome feedback on our prototype
Nat
ure
Pre
cedi
ngs
: doi
:10.
1038
/npr
e.20
10.5
430.
1 : P
oste
d 23
Dec
201
0
Data used in demointegrated by Keywan Hassani-Pak
AHD
Poplar KB
1. Input 45778 predicted poplar genes
2. Data IntegrationPoplarCyc, Poplar TFDB
3. Comparative GenomicsBLAST against UniProt PlantsHMMer against PfamInparanoid to Arabidopsis
4. Autom. Function PredictionGene, Plant and Trait Ontology
5. Text MiningCooccurrence of genes and traits in Medline abstracts
Nat
ure
Pre
cedi
ngs
: doi
:10.
1038
/npr
e.20
10.5
430.
1 : P
oste
d 23
Dec
201
0
Connecting and queryingN
atur
e P
rece
ding
s : d
oi:1
0.10
38/n
pre.
2010
.543
0.1
: Pos
ted
23 D
ec 2
010
Right-click pre-defined queriesN
atur
e P
rece
ding
s : d
oi:1
0.10
38/n
pre.
2010
.543
0.1
: Pos
ted
23 D
ec 2
010
Filling attributesN
atur
e P
rece
ding
s : d
oi:1
0.10
38/n
pre.
2010
.543
0.1
: Pos
ted
23 D
ec 2
010
Proteins related to shoot branchingN
atur
e P
rece
ding
s : d
oi:1
0.10
38/n
pre.
2010
.543
0.1
: Pos
ted
23 D
ec 2
010
Colour proteins by taxonomy IDN
atur
e P
rece
ding
s : d
oi:1
0.10
38/n
pre.
2010
.543
0.1
: Pos
ted
23 D
ec 2
010
Scale relation based on BLASTN
atur
e P
rece
ding
s : d
oi:1
0.10
38/n
pre.
2010
.543
0.1
: Pos
ted
23 D
ec 2
010
Acknowledgements
Artem Lysenko
Andrea Splendiani
Matthew Pocock
Chris RawlingsNat
ure
Pre
cedi
ngs
: doi
:10.
1038
/npr
e.20
10.5
430.
1 : P
oste
d 23
Dec
201
0