A presentation given at the University of Toronto on June 18, 2009 describing the current state of Bio2RDF with respect to biological knowledge representation on the semantic web as linked data with services to describe and answer questions.
12. What is the semantic web?
The Semantic Web is a web of knowledge.
It is about standard formats for
representing and querying
knowledge drawn from
diverse sources and
making statements
about real
objects.
13. Goals for the Semantic Web
• Provide a common knowledge representation
• syntax & semantics
• Facilitate publishing, data integration and
information retrieval
• Make possible semantically interoperable web
applications and services
• Enable the answering of questions across global
repositories of knowledge
14. Resource Description Framework (RDF)
• Allows one to express propositions, and reason
about them
• Uniform Resource Identifier (URI) are entity names
• i.e http://purl.uniprot.org/uniprot/Q16665
• A RDF statement consists of:
– Subject: resource identified by a URI u:Q16665
– Predicate: resource identified by a URI rdf:type
– Object: resource or literal
Protein
15. Semantic Knowledge Base
fact
Q16665
rdf:type
Protein rdf:type
rdfs:subClassOf
Molecule
ontology
Knowledge base
17. Syntactic Data Integration
depends on consistent naming
has name
u:Q16665 HIF1-alpha
HIF1-alpha
UniProt
has name
+
located in located in
u:Q16665 go:nucleus u:Q16665 go:nucleus
Gene Ontology
+ interacts with
u:vhl
interacts with
u:Q16665 u:vhl Unified view
BIND
31. Services
• Describe a resource
– http://bio2rdf.org/ns:id
• Global services over federated endpoints
– http://bio2rdf.org/links/ns:id
– http://bio2rdf.org/search/term
• Targeted services to a specific endpoint
– http://bio2rdf.org/linksns/ns/ns2:id
– http://bio2rdf.org/searchns/ns/term
46. Bioinformatics Discovery Registry
• Part of SharedName initiative to provide stable URI
patterns for data records.
• We add the relationship between entities and records
Discovery Service
• Registry links entities to data records, their formats
(RDF/XML, HTML, etc) and provider (Bio2RDF, Uniprot)
http://registry.semanticscience.org/ns:id
Redirection Service
• Automatic redirection to data provider document
http://registry.semanticsience.org/doc/provider/format/ns:id
50. The Knowledge Web
• Merging data & services
• Reasoning & question answering
• Persistent (RESTful)
• Trust & Security
Data consumers must be able
to rely upon your data to use it
as a foundation for their own
applications.
51. 2009 Goals
• Add more data!
– Standardize RDFizers
– Enrichment from small producer data!
• Design more RESTful services (Workflow)
• Start using Virtuoso 6 cluster
• Add mirrors
• Approval from data providers to distribute RDF
dump and publish SPARQL endpoints
– Confirmed: UniProt, BioCyc, Pathway Commons, BIND
55. Thanks To:
• The Bio2RDF community
• Dumontier Lab
– Alex De Leon, Jose Cruz, Natalia Villanueva-Rosales
• Quebec Reseachers
– Francois Belleau, Marc-Alexandre Nolin
• Australian Researchers
– Peter Ansell
• Openlink Virtuoso Team