eXframe: A Semantic Web Platform for Genomic Experiments
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. 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.
4. 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
5. 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)
6. 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)
• )
8. 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”.
9. 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
10. 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
