eXframe: A Semantic Web Platform for Genomic Experiments

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eXframe is a reusable framework for creating online repositories of genomics experiments. It uses Drupal to structure annotations of experiments, biomaterials, and assays. eXframe automatically publishes this data as RDF and provides a SPARQL endpoint. The first instance is the Stem Cell Commons, which deeply annotates experiments, organisms, tissues, and more using ontologies. It allows flexible querying of the data via SPARQL and integration with other endpoints. eXframe creates both public and private RDF stores to selectively share experimental data with researchers.

Technology Education

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

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
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

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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)

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) • )

7. Sample RDF from Stem Cell Commons Stem Cell Commons

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

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