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.


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, hired 10-2009)
  • Programmer
    • Nomi Harris, LBNL (75% effort, hired 11-2009)
  • 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.

Item 1 - Quarterly Activities

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.
    • Started month: 1
    • Estimated duration: 6 months
  • Add formal logical axioms to the CL.
    • We have made the first steps towards adding logical axioms to theCL. The first is the formal definition of the capable_of relation, required for linking cell types to biological processes (for example, Tr1 cells to IL-10 production). The LBL group has created the formal definition in terms of the Basic Formal Ontology (BFO) "disposition" class, and whilst the Jackson group has applied this in the prototype ontology.
    • Started month: 1
    • Estimated duration: 6 months
  • 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)
      • PATO - Phenotypic Quality Ontology
      • Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.
    • Started month: 1
    • Estimated duration: 6 months
  • Implement automated reasoner strategy
    • Although we do not estimate commencing this until month 6 we have made some preliminary steps, partially implementing the MIREOT methodology within OBO-Edit. This allows the CL editors at Jackson to select classes from external ontologies and bring in only the subset of those ontologies that pertain to these referenced classes. This improves reasoner performance.
    • Estimated start month: 6
    • Estimated duration: 3 months
  • General software support
    • Support with managing ontology versions in Open Bio-Ontologies repository
    • OBO-Edit bug fixes
    • OBO-Edit tutorials for CL curators


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

  • This work is to commence in month 6


Item 2 -- Percent Completion

  • Based on current progress towards completion of our aims we are on track, with 10-15% of the work accomplished.


Related Publications for 2009

Alexander D. Diehl, Alison Deckhut Augustine, Judith A. Blake, Lindsay G. Cowell, Elizabeth S. Gold, Timothy A. Gondré-Lewis, Anna Maria Masci, Terrence F. Meehan, Penelope A. Morel, NIAID Cell Ontology Working Group, Anastasia Nijnik, Bjoern Peters, Bali Pulendran, Richard H. Scheuerman, Q. Alison Yao, Martin S. Zand, and Christopher J. Mungall. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. In Proceedings of the First International Conference on Biomedical Ontology, 2009

Anna Maria Masci, Cecilia Arighi, Alexander Diehl, Anne Lieberman, Chris Mungall, Richard Scheuermann, Barry Smith, and Lindsay Cowell. An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics, 10(1):70, 2009

Christopher J. Mungall, Michael Bada, Tanya Z. Berardini, Jennifer Deegan, Amelia Ireland, Midori A. Harris, David P. Hill, and Jane Lomax. Cross-Product Extensions of the Gene Ontology. In Proceeeings of the First International Conference on Biomedical Ontology, July 2009


[Return to 2009 Progress Reports]