Introduction to Semantic Technologies (SPARQL, GRDDL, RDFa, OWL, SPASQL, SPDL …)

HCLS BioRDF Projects.

Eric Prud'hommeaux, Sanitation Engineer.
Last modified: $Date: 2009/01/21 14:33:03 $

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This work is licensed under a Creative Commons Attribution 3.0 License, with attribution to W3C.

Drug discovery

Using the Semantic Web: Precise Answers to Complex Questions:

Find me genes involved in signal transduction that are related to pyramidal neurons.

223,000 results from google

223K responses for previous query

2580 results from pubmed

223K responses for previous query

0 from PathGuide

223K responses for previous query

Integrate databases ...

Mesh
Pubmed
Entrez Gene
Gene Ontology
...

... so that one query ...

... (trivially) spans several DBs ...

SenseLab Database headings and representation graph

... to yield cross-specialty inforation

Alzgene query results

What was the trick?

Good-enough modeling.
- RDFS - simple subclass/subproperty relationships
- OWL - inference and more expressive modeling
Query interface tailored to data model.
- SPARQL - RDF query language
Agreement on common terms and relations.
- RDF - flexible underlying data model
- URI - unambiguous naming

Unification needed in lots of places

Protein/Gene identifiers
Biological processes
Publication abstracts
Publication metadata

W3C Notes