the semantic web for life sciences
DESCRIPTION
TRANSCRIPT
The Semantic Web for Life Sciences
Egon Willighagen <http://chem-bla-ics.blogspot.com/>
Bioclipse & Proteochemometric Group (Prof. J. Wikberg)Until 2010-09-30
Department of Pharmaceutical Biosciences (Prof. E. Brittebo)
Uppsala University
2010-09-22
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Drug-Protein Binding
patented:ELW00356
binds to
uniprot:CYP1B1
2010-09-22 Bioclipse & Proteochemometric Group - 2 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Drug-Protein Binding
patented:ELW00356
binds to
uniprot:CYP1B1
Where was this published? How measured?Other measurements?What about similar molecules and proteins?What haplotype, SNP, or missense mutation?
2010-09-22 Bioclipse & Proteochemometric Group - 3 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Semantic Web
Current World Wide Web
hyperlinked web pages
Semantic Web
machine-readable hyperlinked (web) pages
2010-09-22 Bioclipse & Proteochemometric Group - 4 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Semantic Web 4 Life Sciences??
Is this relevant to drug discovery?
knowledge discovery, ...
data consistency checking
model validation
2010-09-22 Bioclipse & Proteochemometric Group - 5 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Applications
2010-09-22 Bioclipse & Proteochemometric Group - 6 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
OpenMolecules RDF: linked data
2010-09-22 Bioclipse & Proteochemometric Group - 7 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
OpenMolecules RDF
http://rdf.openmolecules.net/?InChI=1/CH4/h1H4
2010-09-22 Bioclipse & Proteochemometric Group - 8 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Linked Data
As of July 2009
LinkedCTReactome
Taxonomy
KEGG
PubMed
GeneID
Pfam
UniProt
OMIM
PDB
SymbolChEBI
Daily Med
Disea-some
CAS
HGNC
InterPro
Drug Bank
UniParc
UniRef
ProDom
PROSITE
Gene Ontology
HomoloGene
PubChem
MGI
UniSTS
GEOSpecies
Jamendo
BBCProgrammes
Music-brainz
Magna-tune
BBCLater +TOTP
SurgeRadio
MySpaceWrapper
Audio-Scrobbler
LinkedMDB
BBCJohnPeel
BBCPlaycount
Data
Gov-Track
US Census Data
riese
Geo-names
lingvoj
World Fact-book
Euro-stat
flickrwrappr
Open Calais
RevyuSIOCSites
Doap-space
Flickrexporter
FOAFprofiles
CrunchBase
Sem-Web-
Central
Open-Guides
Wiki-company
QDOS
Pub Guide
RDF ohloh
W3CWordNet
OpenCyc
UMBEL
Yago
DBpediaFreebase
Virtuoso Sponger
DBLPHannover
IRIT Toulouse
SWConference
Corpus
RDF Book Mashup
Project Guten-berg
DBLPBerlin
LAAS- CNRS
Buda-pestBME
IEEE
IBM
Resex
Pisa
New-castle
RAE 2001
CiteSeer
ACM
DBLP RKB
Explorer
eprints
LIBRIS
SemanticWeb.org
Eurécom
RKBECS
South-ampton
CORDIS
ReSIST ProjectWiki
NationalScience
Foundation
ECS South-ampton
LinkedGeoData
BBC Music
CC-BY-SA2010-09-22 Bioclipse & Proteochemometric Group - 9 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Linked Data: the Life Science corner
CC-BY-SA
2010-09-22 Bioclipse & Proteochemometric Group - 10 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Proteochemometrics
Data: protein sequences, molecular structures, binding a�nities
E.L. Willighagen et al., J. Biomed. Sem., 2010, in print
2010-09-22 Bioclipse & Proteochemometric Group - 11 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Proteochemometrics: RDF input
2010-09-22 Bioclipse & Proteochemometric Group - 12 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Substructure mining: ChEMBL
Annso�e Andersson, M.Sc. project2010-09-22 Bioclipse & Proteochemometric Group - 13 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
OpenTox
Open Standards around Computation Toxicology
Web services
Public Data Repository
Bioclipse integration
downloading/uploading data
run descriptor calculation
future: build QSAR models
E.L Willighagen, N. Jeliazkova, O. Spjuth, in preparation
2010-09-22 Bioclipse & Proteochemometric Group - 14 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
OpenTox: downloading
2010-09-22 Bioclipse & Proteochemometric Group - 15 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Hyperlinked Data
How do we put our semantic data online?
2010-09-22 Bioclipse & Proteochemometric Group - 16 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
XHTML+RDFa
Embedded in web pages
2010-09-22 Bioclipse & Proteochemometric Group - 17 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
SPARQL end point
Query the data directly
2010-09-22 Bioclipse & Proteochemometric Group - 18 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Semantic Wikis
Bootstrapping Life Sciences Knowledge Bases
Samuel Lampa et al., in preparation
2010-09-22 Bioclipse & Proteochemometric Group - 19 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Other Building Blocks
2010-09-22 Bioclipse & Proteochemometric Group - 20 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
The Chemistry Development Kit
A Family of Projects
CDK-Taverna (chemoinformatics work�ows)
JChemPaint (semantic 2D editor)
ChemoJava (GPL-ed extension)
Goals
library of cheminformatics algorithms
educational
Usage
CDK: 140+ times cited in scienti�c literature
Bioclipse, KNIME, CDK-Taverna, Jumbo (CML), AMBIT,...
C. Steinbeck et al., J.Chem.Inf.Comput.Sci, 2003
C. Steinbeck et al., Curr.Pharm.Design, 2006
2010-09-22 Bioclipse & Proteochemometric Group - 21 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
More detail on the CDK
Tomorrow, during the presentation from 13:00-14:00
2010-09-22 Bioclipse & Proteochemometric Group - 22 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Bioclipse-RDF
Linking the Semantic Web to Cheminformatics
local RDF storage (memory, on disk)
read/write RDF/XML, N3
run SPARQL queries (local and remote)
extract RDF from XHTML/RDFa
Thanx to Open Source projects including Jena, SWI-Prolog,and Pellet.
E.L. Willighagen et al., J. BioMed. Sem., in press
O. Spjuth et al., BMC Bioinformatics 2007
O. Spjuth et al., BMC Bioinformatics 2010
2010-09-22 Bioclipse & Proteochemometric Group - 23 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
MyExperiment: Bioclipse ScriptingLanguage
myexperiment.search("RDF")
myexperiment.downloadWork�ow(937)
2010-09-22 Bioclipse & Proteochemometric Group - 24 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Semantic Web
The new building block...
It's already 10+ years old...
2010-09-22 Bioclipse & Proteochemometric Group - 25 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Why are Open Standards Important?
Standards: We speak the same langauge
Open: Social contract: you can use it, now and in thefuture
2010-09-22 Bioclipse & Proteochemometric Group - 26 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
The Semantic Web Stack
The Semantic Web is more than RDF
(From Wikipedia)
2010-09-22 Bioclipse & Proteochemometric Group - 27 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Resource Description Framework
hyperlinked, machine-readable knowledge
hyperlinked Universal Resource Identi�er (URI)
machine-readable knowledge markup with triple
2010-09-22 Bioclipse & Proteochemometric Group - 28 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
RDF: the URI
Universal Resource Identi�er (URI)
e.g. URL: http://www.pharmbio.org/
Too long? Use pre�xes
http://www.semanticweb.org/ontologies/cheminf.owl#Molecule
cheminf:Molecule
2010-09-22 Bioclipse & Proteochemometric Group - 29 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
RDF: the triple
Type 1: resource - predicate - resource
heavierthan
Ethane Methane
Type 2: resource - predicate - literal
boilingpoint
-161Methane
2010-09-22 Bioclipse & Proteochemometric Group - 30 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
RDF: graphs
Linked triples create a graph
heavierthan
Ethane Methane
boilingpoint
-161-89
boilingpoint
2010-09-22 Bioclipse & Proteochemometric Group - 31 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
RDF Schema & Web Ontology Language
RDF Schema: taxonomies
rdfs:Class, rdfs:Property
rdfs:label, rdfs:comment
rdfs:subClassOf, rdfs:subPropertyOf
Web Ontology Language (OWL)
owl:equivalentClass
owl:sameAs
and a lot more ...
2010-09-22 Bioclipse & Proteochemometric Group - 32 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
SPARQL
SPARQL RDF Query Language
SELECT DISTINCT * WHERE {
SERVICE <http://uu3.org:8888/7tm_receptors> {
?iuphar iface:family ?family .
?iuphar iface:code ?code .
?iuphar iface:iupharName ?iupharNm .
?human iface:iuphar ?iuphar .
?human iface:geneName "GABBR1" .
?human iface:entrezGene ?humanEntrez .
}
SERVICE <http://dbpedia.org/sparql> {
_:gene dbp:entrezgene ?humanEntrez ;
rdfs:label ?label ;
FILTER (lang(?label) = "en")
}
GRAPH <http://hcls.deri.org/atag/data/gabab_example.html> {
?topic rdfs:label ?label .
?post sioc:topic ?topic
}
}
2010-09-22 Bioclipse & Proteochemometric Group - 33 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
The Players
Who are working with RDF?
2010-09-22 Bioclipse & Proteochemometric Group - 34 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
W3C
World Wide Web Consortium
Coordinates standard development
Builds user communities
Health Care and Life Sciences Interest Group
Linked Open Drug Data (LODD)
Transitional Medican O? (TMO)
Scienti�c Discourse
2010-09-22 Bioclipse & Proteochemometric Group - 35 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Bio2RDF / Chem2Bio2RDF
Bio2RDF
Proteins, DNA, ...
Open Source
Canada, Virtuoso, ...
Chem2Bio2RDF
More towards molecules...
Indiana University
2010-09-22 Bioclipse & Proteochemometric Group - 36 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Talis & Virtuoso
The companies that provide triple store support.
Very supportive of Open initiatives...
2010-09-22 Bioclipse & Proteochemometric Group - 37 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
ACS Meeting
Boston, 22-23 August 2010
Topics lipidomics, text mining, drug discovery, ontologies
Thematic Issue submit before 2010-11-28
http://egonw.github.com/acsrdf2010/
2010-09-22 Bioclipse & Proteochemometric Group - 38 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Summary
RDF
New Open Standards for knowledge exchange
Simplies sharing data
RDFS + OWL
Machine-readable knowledge
Disambiguation
SPARQL, etc
Application Programming Interfaces
2010-09-22 Bioclipse & Proteochemometric Group - 39 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
What does this bring us?
Platform to integrate the RDF with the computation world
Bioclipse as single point of access
Scripting, sharing of scripts with MyExperiment.org
Bridging Names to Numbers
2010-09-22 Bioclipse & Proteochemometric Group - 40 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
Acknowledgements
Maris Lapins, Martin Eklund: statistics
Annso�e Andersson: ChEMBL + MoSS integration
Samuel Lampa: reasoning (Pellet/Prolog) and RDFIO
Nina Jeliazkova: OpenTox integration
John Overington: ChEMBL database
Ola Spjuth
2010-09-22 Bioclipse & Proteochemometric Group - 41 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
The Details: PharmBio course
http://www.pharmbio.org/
Book in preparation ...
2010-09-22 Bioclipse & Proteochemometric Group - 42 - Egon Willighagen | chem-bla-ics.blogspot.com
Why RDF?
Applications
Online
BuildingBlocks
RDF
The Players
Conclusion
The Details: Molecular Chemometrics
http://www.citeulike.org/user/
egonw/tag/papers
http:
//chem-bla-ics.blogspot.com
http://egonw.github.com
waveto:
2010-09-22 Bioclipse & Proteochemometric Group - 43 - Egon Willighagen | chem-bla-ics.blogspot.com