Cell Type Progress Report (LBNL) December 2009

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This report has been subsumed into the Cell Ontology Progress Report December 2009.


Item 1 - Quarterly Activities


Aim 1: REFORMING THE STRUCTURE OF THE CL

  • Assist devising new structure of CL.
    • Estimated start month: 1
    • Estimated duration: 3 months
    • Working with the Jackson group, we have been prototyping the new CL structure using the hematopoeitic branch as a test case. 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.
  • Add formal logical axioms to the CL.
    • Estimated start month: 3
    • Estimated duration: 3 months
    • 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.
  • Implement automated reasoner strategy
    • Estimated start month: 6
    • Estimated duration: 3 months
    • Although we did 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.
  • 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 THE CL

  • We are now actively assisting the Jackson group in preparation for a CL workshop.



Aim 3: APPLYING THE CL TO THE GO

  • This work is to commence in month 6

Item 2 - Percent Complete

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

Item 3 – New Hire

  • A programmer was hired into this position at LBNL in November 2009


[Return to 2009 Progress Reports]