Cell Ontology Progress Report December 2009

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Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL. Please refer to Cell Type Progress Report (LBNL) December 2009 for additional information regarding the progress of the LBNL-based work.

Personnel

  • Project Leaders
    • Alexander Diehl, The Jackson Laboratory (50% effort)
    • Christopher Mungall, LBNL (10% effort)
  • Cell Ontology Curator
    • Terrence Meehan, The Jackson Laboratory (100% effort)
  • Senior Advisors
    • Judith Blake, The Jackson Laboratory
    • Suzanna Lewis, LBNL
  • External Consultants
    • Lindsay Cowell, Duke University
    • Anna Maria Masci, Duke University


Collaborations

  • Martin Zand, University of Rochester, cross-product definition of B cells
  • Caroline Kane, Berkeley, use of CL terms as metadata for the Virtual Library of Cell Images
  • Alan Ruttenberg, Science Commons, computational identification of cell types in the literature
  • Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL
  • INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.

Aim 1: Reforming the Structure of the Cell Ontology

  • Devise new structure for the Cell Ontology
    • We have been prototyping the new CL structure using the hematopoeitic cell types as a test case.
  • Add logical definitions using other OBO ontologies
    • We have identified the following ontologies as key to defining cell types:
      • PRO - Protein Ontology
      • GO - Gene Ontology (particularly biological processes such as immune response)
    • We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types define by location in the body.


Aim 2: Improving and extending the content of CL

  • We have begun planning for a Cell Ontology workshop, to be held May 18-19, 2009 at the Jackson Laborotory, Bar Harbor, Maine. The workshop will be used for discussion of general issues involved in the revision of the Cell Ontology.
  • We are implementing the cross-product/logical definition formulation of the hematopoietic terms. As part of this work, we are improving definitions for a number of cell types, and adding new cell types.
  • We are working to add is_a parents to all terms in the CL.
  • We are preparing definitions for current nervous system terms in the CL that lack them.


Aim 3: Applying the CL to the GO

Please refer to Cell Type Progress Report (LBNL) December 2009 for progress in this area.