Cell Ontology Progress Report December 2009: Difference between revisions

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** Christopher Mungall, LBNL (10% effort)
** Christopher Mungall, LBNL (10% effort)


* '''Ontology Curator'''
* '''Cell Ontology Curator'''
** Terrence Meehan, The Jackson Laboratory (100% effort)
** Terrence Meehan, The Jackson Laboratory (100% effort)


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** Lindsay Cowell, Duke University
** Lindsay Cowell, Duke University
** Anna Maria Masci, Duke University
** Anna Maria Masci, Duke University


==Collaborations==
==Collaborations==

Revision as of 17:23, 14 December 2009

{NOTE: This report is will be finished later on December 14, 2009 -- still incomplete]


Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. The funding notice was received on September 30, 2009, and work commenced immediately.

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 Ruttanberg, 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.