with semantic web technologies - BiGCaT Wiki 2G

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21 Οκτ 2013 (πριν από 4 χρόνια και 22 μέρες)

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Department of Bioinformatics - BiGCaT
1
Bioinformatics
with semantic web technologies
Department of Bioinformatics - BiGCaT
2
The context
Department of Bioinformatics - BiGCaT
3
Bioinformatics
1.

Using
information
to
understand
biology
2.

Tools:
1.

Automation
2.

Multivariate statistics
(Cheminformatics: using information to understand biology)
Department of Bioinformatics - BiGCaT
4
What is
information
? #1

Human language

Protein X binds
to inhibitor Y ...”
Huh?

Tables: CSV,
Excel, …
1,5,CDK3,4.1,...
-1,7,CDK3,4.2,...
Huh?
Department of Bioinformatics - BiGCaT
5
What is
information
? #2

Names are not enough to understand
the biology or chemistry

What did the mean in the first place?

What measurement is behind that
metabolite name?

What was the genotype of that cell line
used for that dose-response assay?

How did they get
that
logP for glucose??
Department of Bioinformatics - BiGCaT
6
Meaning

Controlled vocabulary

things have a description

Thesaurus

things have a description, and are
hierarchical organized

Ontology

things have a description, are hierarchical
organized, and have implications
Department of Bioinformatics - BiGCaT
7

a solution
Department of Bioinformatics - BiGCaT
8
Resource Description Framework

A simple framework to express
knowledge

no prescribed syntax

works in HTML, JSON, XML, and many more

decouples meaning from assertions

Web Ontology Language (OWL) is a layer

technology independent

dereferencable (
semantic web
)
Department of Bioinformatics - BiGCaT
9
RDF in HTML?
O. Jankowski,
http://www.pharmash.com/posts/2010-09-27-sparql-to-chart.html
, 2010
Department of Bioinformatics - BiGCaT
10
Five Stars (T. Berners-Lee)
http://5stardata.info/
Department of Bioinformatics - BiGCaT
11
Resource Description Framework

Two kinds of facts:
<subject> <relatesTo> <object> .
<subject> <hasValue> “value” .
Department of Bioinformatics - BiGCaT
12

working out solutions
Department of Bioinformatics - BiGCaT
13
Toxicity Prediction
Department of Bioinformatics - BiGCaT
14
Malaria data set ...
Department of Bioinformatics - BiGCaT
15
OpenTox: running models
models =
opentox
.listModels(ontologyService);
model = models.get(3);
// third model
js
.say(

opentox
.predictWithModel(

service,

model,

molecules

)
);
Department of Bioinformatics - BiGCaT
16
Bayesian statistics
Department of Bioinformatics - BiGCaT
17
Linked (Open) Drug Data
M. Samwald et al. JChemInf, 2011, ...
Department of Bioinformatics - BiGCaT
18
ChEMBL
Department of Bioinformatics - BiGCaT
19
Department of Bioinformatics - BiGCaT
20
Combining data sets
WHERE {

?sider sider:cid [pubchem:std_inchi ?inchi] .

?sider sider:side_effect ?side_effect . FILTER regex(?side_effect,"hypertension","i") .

?mol bo:inchi ?inchi .


?act chembl:forMolecule ?mol .

?act chembl:type ?type ;

cito:citesAsDataSource ?paper ;

chembl:standardValue ?value ;

chembl:standardUnits "nM";

chembl:type "IC50";

chembl:onAssay ?assay .

FILTER (xsd:float(?value)<10000) .

?assay chembl:hasTarget ?target .

?target dc:title ?title .

?target chembl:organism "Homo sapiens" .

?target owl:sameAs ?target_bio2rdf .


?interaction hprd:Uniprot_A [owl:sameAs ?target_bio2rdf] .

?interaction hprd:uniprot_B [owl:sameAs ?target_b] .
}
Department of Bioinformatics - BiGCaT
21
Linked Open Data
Department of Bioinformatics - BiGCaT
22
Domain Ontologies

PRotein Ontology (PRO)

Chemical Entities of Biological Interest (ChEBI)

Cheminformatics Ontology (CHEMINF)

Bibliography Ontology (BIBO)

Citation Typing Ontology (CiTO)

Cell Type Ontology

PRotein Ontology

Next: BioAssay Ontology (BAO), Cell Line Ontology
(CLO)
Department of Bioinformatics - BiGCaT
23
Units reasoning→
ops:Nanomolar

rdf:type qudt:MolarConcentrationUnit ,

qudt:SIDerivedUnit ;

rdfs:label "Nanomolar"^^xsd:string ;

qudt:abbreviation "nM"^^xsd:string ;

qudt:conversionMultiplier

0.000001 ;

qudt:conversionOffset

"0.0"^^xsd:double ;

qudt:symbol "nmol/dm^3"^^xsd:string .
Department of Bioinformatics - BiGCaT
24

summary
Department of Bioinformatics - BiGCaT
25
Summary

Complements other bioinformatics
methods

replacing XML (huh?), SQL (huh?)

Single (set of) standard(s)

thus: tools available for any environment

Helps us understand biology

by supporting explanations of strange
patterns

Greatly improved expressiveness!
Department of Bioinformatics - BiGCaT
26
Thanx

ChEMBL-RDF contributors (Janna
Hastings, Peter Ansell, Mark Davies)

Bioclipse team (Ola Spjuth, Jonathan
Alvarsson, Samuel Lampa, Martin
Eklund, ...)

OpenTox team (Nina Jeliazkova, Barry
Hardy, Roland Grafstrom…)

W3C HCLS team (many)
Department of Bioinformatics - BiGCaT
27
Further detail
http://www.sciencedirect.com/science/article/pii/S1570826812000376?v=s5
http://www.jcheminf.com/content/3/1/19
http://www.jbiomedsem.com/content/2/S1/S6
http://www.biomedcentral.com/1756-0500/4/487
http://chem-bla-ics.blogspot.com/