Expanding the Pathway and Interaction Knowledge in Linked Life Data

Ontotext AD
Expanding the Pathway and Interaction Knowledge in Linked Life Data
10/23/2009

Holistic View of the Scientific Problems
Link data between different silos applications
Put the information into context
Analyze the knowledge locked into unstructured data
Environmental Factors
10/23/2009
Semantic Web Challenge 2009

The Challenge of the Holistic View
Extreme amount of data
Data is supported by different organizations
Information is highly distributed and redundant
Tons of flat file formats with special semantics
Knowledge is locked in vast data silos
Isolated communities which could not reach cross-domain understanding
10/23/2009

Ontologies and Thesauri
Unified Medical Language System®
Drugs
The Open Biomedical Ontologies
Linked Open Drug Data
Text-Analysis
Interactions and Pathways
Linked Life Data
RDF Warehouse
Biological Pathway Exchange
Semantic Annotations
Genes and Proteins
Documents
5 billion RDF statements!

LLD Integration Process
Data Source Identification
Flat files
OBO files
XML
RDBMS
RDF
Special tailored transformer
OBO to SKOS converter
Custom XSLT
RDBMS to RDF formatter
RDF warehouse
Reasoner
Instance Mappings
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Complex Cross-Domain Queries
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Physiological
process
Molecular Technique
filter human genes
Gene
participate in
cause
Molecular Interaction
Disease
analyzed by
express protein
Protein
Drugs
curated interaction
treated
with
target

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TODO Put a nice screenshot

Instance Alignment
Redundancy is removed by human crafted declarative rules
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CD40L_HUMAN
biopax-2:SHORT-NAME
cpath:CPATH-94138
CD40L_HUMAN
biopax-2:DB
biopax-2:XREF
UNIPROT
uniprot:mnemonic
biopax-2:PHYSICAL-ENTITY
biopax-2:ID
uniprot:mnemonic
TNF5_HUMAN
P29965
biopax-2:PHYSICAL-ENTITY
uniprot:P29965
uniprot:mnemonic
TNFL5_HUMAN
cpath:CPATH-LOCAL-8467065
uniprot:mnemonic
cpath:CPATH-LOCAL-8749236
CD4L_HUMAN

db
X
Y
X
Y
ns-x: id
ns-y: id
id
db: id
X
X
Y
accession
term
db: accession
db: id
Y
text to describe name
Y
X
Y
X
name

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Respiration Disorders
umls:C0035204
Chronic Obstructive Airway Diseases
broader
Bronchial Diseases
umls:C0006261
Asthma and chronic obstructive pulmonary disease (COPD) are chronic airway diseases characterized by airflow obstruction. The beta(2)-adrenoceptormediates bronchodilatation in response to exogenous and endogenous beta-adrenoceptor agonists. Single nucleotide polymorphisms in the beta(2)-adrenoceptorgene (ADRB2) cause amino acid changes (e.g. Arg16Gly, Gln27Glu) that potentially alter receptor function. Recently, a large cohort study found no association between asthma susceptibility and beta(2)-adrenoceptor polymorphisms. In contrast, asthma phenotypes, such as asthma severity and bronchial hyperresponsiveness, have been associated with beta(2)-adrenoceptor polymorphisms.
broaderTransitive
COPD
broader
broader
broaderTransitive
Asthma
mentions
umls:C000496
mentions
journal
pmid:17714090
author
Clinical and experimental pharmacology …
Ian A Yang

Multiple information extraction views
High-recall annotations
lifeskim:mentions
705,338,334 statements
High-precision annotations
lifeskim:mentionsStrict
263,323,164 statements
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lifeskim:mentions
rdfs:subPropertyOf
lifeskim:mentionsStrict

Distribution of RDF Triples
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Conclusion
Linked Life Data is a public and free service
There are many more interesting queries
Multi-paradigm search
Concept co-occurrence
Combine text with structured search
Easy integrates information from the public linked data cloud
Why not give a try?
10/23/2009

Acknowledgement
AstraZeneca
Bosse Andersson
LODD
BioRDF
HCLSIG
Ontotext
Deyan Peychev
Georgi Georgiev
Todor Primov
OWLIM team
10/23/2009
The development of PIKB and Linked Life Data is partially funded by FP7 215535