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slides from talk given at Bio-ontologies 2013, Berlin DE, 20 July 2013 Emily Merrill*, Stephane Corlosquet*, Paolo Ciccarese†*, Tim Clark*†‡, Sudeshna Das†* * Massachusetts General Hospital † Harvard Medical School ‡ School of Computer Science, University of Manchester
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A Semantic Web Platform for Genomics
ExperimentsEmily Merrill1, Stéphane Corlosquet1, Paolo Ciccarese1,2,
Tim Clark1,2,3 & Sudeshna Das1,2
1Massachusetts General Hospital 2Harvard Medical School
3University of Manchester
†Authors contributed equally
What is eXframe?• reusable framework for creating online data
repositories• upgraded version based on Drupal 7 (drupal.org)• structured annotation of experiments, bio-
materials and assays• publishes Semantic Web data automatically (RDF
& SPARQL endpoint)• first instance of upgraded version - Stem Cell
Commons (http://stemcellcommons.org)
Architecture
• re-factored second generation of eXframe
• updated experimental model mapped to ontologies
• Drupal RDF modules used to generate RDF
• RDF store (SPARQL endpoint) powered by ARC2 PHP library
Data Model• experiment
(obi:investigation); meta-data mapped to Dublin Core (dc)
• researchers & citations mapped to foaf & bibo respectively
• experiments are comprised of bioassays (obo:assay)
• bioassays have replicates (efo:replicate)
• replicates are associated with biomaterials (obo:specimen)
Biomaterials• biomaterials are deeply annotated, key examples:- organism (NCBI Taxonomy)- tissue (FMA: Foundation Model of Anatomy)- cell type (CL: Cell Type ontology)- disease state (DO: Disease ontology)- treatment compound (CheBI: Chemical Entities of
Biological Interest)• )
Sample RDF from Stem Cell Commons
SPARQL queries• flexible query system with
SPARQL
• allows graph queries
• integration with other endpoints
• sample query on right: “find experiments done on mouse, hematopoietic stem cells”.
Security• Stem Cell Commons: selected experiments
are accessible only to researchers from Harvard Stem Cell Institute
• created two stores: - public with limited data- private with all data
Conclusion• groups & institutions can create databases
simply by configuring eXframe• structured repository serves as institutional
memory and facilitates publication• automatic RDF generation & SPARQL
endpoint lowers barrier to Semantic Web adoption