exFrame: a Semantic Web Platform for Genomics Experiments

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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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exFrame: a Semantic Web Platform for Genomics Experiments

  1. 1. A Semantic Web Platform for Genomics Experiments Emily Merrill1 , Stéphane Corlosquet1 , Paolo Ciccarese1,2 , Tim Clark1,2,3 & Sudeshna Das1,2 1 Massachusetts General Hospital 2 Harvard Medical School 3 University of Manchester †Authors contributed equally
  2. 2. 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)
  3. 3. 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
  4. 4. 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)
  5. 5. 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) • )
  6. 6. Sample RDF from Stem Cell Commons Stem Cell Commons
  7. 7. 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”.
  8. 8. 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
  9. 9. 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

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