• Share
  • Email
  • Embed
  • Like
  • Save
  • Private Content
eXframe: A Semantic Web Platform for Genomic Experiments
 

eXframe: A Semantic Web Platform for Genomic Experiments

on

  • 148 views

 

Statistics

Views

Total Views
148
Views on SlideShare
123
Embed Views
25

Actions

Likes
0
Downloads
0
Comments
0

4 Embeds 25

http://mindinformatics.org 10
http://localhost 7
http://live-mind-informatics.gotpantheon.com 4
http://www.mindinformatics.org 4

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

    eXframe: A Semantic Web Platform for Genomic Experiments eXframe: A Semantic Web Platform for Genomic Experiments Presentation Transcript

    • 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