Regulation Main Page: Difference between revisions

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*[[Regulation cross-products]]
*[[Regulation cross-products]]
*[[Meeting Minutes 1]]
*[[Meeting Minutes 1]]
*[[Meeting Minutes 2]]

Revision as of 15:07, 7 December 2007

First implementation meeting: Technology: webex and skype.

Personnel:

  • Chris Mungall
  • Jane Lomax
  • Amelia Ireland
  • David Hill
  • John Day-Richter
  • Tanya Berardini

Implementation plan:

  • Enable reasoner to create implied links. (Chris Mungall and John Day-Richter)
    • Sort regulation cross-products:
  • Biologists categorize unassignable (David Hill, Amelia Ireland, Jane Lomax)
    • David has gone through this list and noted the following.
      • Terms where the 'regulation of...' is a regulation of a molecular function. RoMF
      • Terms where the 'regulation of...' is a regulation of a biological quality.RoBQ
      • Terms where the 'regulation of...' is a valid subtype of another 'regulation of...' term and we probably do not want to make subtypes of the original BP term. Terms like 'regulation of transcription involved in....' are examples of this. The transcription is basically the same, but it is the regulation that differs.
      • Terms where the 'regulation of...' and the BP parent need to be made univocal or there is a missing BP type.
      • Terms that are still questionable. I have noted suggestions about what to do with these.
    • The file with David's notes and questions can be found here. Regulation Worksheet
  • Rerun reasoner
    • Requirements for reanalysis
  1. Do not report any terms that are is_a children of 'regulation of molecular function' or 'regulation of biological quality'.
  2. Do not report any terms in Worksheets 2 or 3 where it says 'ok subchild/subtype of xxxx'.
  3. For terms that are is_a children of RoMF, check to be sure that the corresponding MF exists.
  4. For terms that are is_a children of RoBQ, check if they correspond to PATO terms.
  • Outstanding questions/thoughts
    • For biological qualities, it makes sense to have positive and negative regulation be a part of the parent regulation term, but does this make sense with biological processes?
    • Should we make relationships between the RoMF terms and the processes in which the execution of the functions take part? For example, should 'regulation of epidermal growth factor receptor activity' relate to the epidermal growth factor receptor signaling pathway? If so, how?
    • In some cases, a regulation process can be a bona-fide part of another process, or be a bona-fide type of another process. We need to be careful about which part-ofs are replaced by regulates.
    • Do we want to instantiate all of the implied regulates relationships that are generated by legitimate 'regulation of ...' subtypes?
  • Export to instantiate implied links.
  • Remove redundant links (Requires OBO-Edit feature, John Day-Richter)
  • Add Chris Mungall's logical definitions to gene_ontology_edit.obo file.