exFrame: a Semantic Web Platform for Genomics Experiments
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ExFrame is a reusable framework for creating online genomic data repositories, upgraded from Drupal 7, that enables structured annotation and automatic publication of semantic web data. It features a flexible architecture, a comprehensive data model, and ensures secure access to sensitive experiments through differentiated public and private stores. The framework is designed to streamline the management of genomics data and support the integration of information across various platforms.
exFrame: a Semantic Web Platform for Genomics 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)
- 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