exframe: a semantic web platform for genomic experiments

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