Regulation Main Page

First implementation meeting: Technology: webex and skype.

Personnel:

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

Implementation plan:

• Enable reasoner to create implied links. (Chris Mungall and John Day-Richter)
  • Sort regulation cross-products:
    • Molecular function
    • Biological process
    • Biological quality
    • Unassignable
      • Chris has run the reasoner and there is a report in the go/scratch directory that list all of the 'regulation of...' terms where the target of the regulation is not a valid biological process. ftp://ftp.geneontology.org/pub/go/scratch/regulation-of-non-process.txt
• 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.
  • 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 eipdermal 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?
• Rerun reasoner
• 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.

• Regulation cross-products