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Discourse, Data & Experiment

This is a new HCLS Scientific Discourse task, which will integrate (intially) the SWAN, myExperiment, and OBI ontologies. It is a joint task with HCLS BioRDF's MicroArray Use Case led by Scott Marshall. The objective of this task is to provide a general semantic model for linking experimental data, workflows, scientific claims + hypothesis, and publications. The approach will be via stepwise integration of existing ontologies with some gap filling. Initial integration targets will be SWAN, myExperiment, MGED and ResearchObjects.


  • Integrate SWAN/MyExperiment/MO/OBI
  • Address BioRDF micro-array use case
  • Provide ability to properly link experimental results and analysis to a publication/claim/hypothesis
  • Find all relevant data to a given biomedical research objective
  • Integrate with ISA-TAB

Use Cases

  • Capture experimental and computational information for gene lists generated in micro-array experiment
  • Capture meta-data and analysis of various types of biomedical experiments
    • high-throughput screening assays done in a pharma company
    • gene association studies
    • ChIP-Seq studies
  • Integrate ChIP-Seq and micro-array data


First cut at integration of SWAN, MyExperiment and MGED DRAFT
Second cut at integration of SWAN, MyExperiment and OBI 2nd DRAFT
The first DRAFT of Ontology in OWL v 0.1 [1]


  • Paolo Ciccarese (Mass General Hospital, Harvard Medical School)
  • Tim Clark (Mass General Hospital, Harvard Medical School)
  • Kei Cheung (Yale Medical School)
  • Sudeshna Das (Mass General Hospital, Harvard Medical School)
  • Matt Gamble (University of Manchester)
  • Carole Goble (University of Manchester)
  • M. Scott Marshall (Leiden University Medical Center / University of Amsterdam)
  • David R Newman (University of Southampton)
  • Philippe Rocca-Serra (University of Oxford)
  • Satya Sahoo (Wright State University)
  • Susanna-Assunta Sansone (University of Oxford)
  • Jun Zhao (University of Oxford)