HCLSIG/SWANSIOC/Actions/SWANmyExpArray

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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.


Objectives

  • 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


Ontology

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]

Participants

  • 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)