Function-Process Links

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Archive: Function-process Pilot Studies


  • Chris Mungall
  • Tanya Berardini
  • David Hill
  • Jane Lomax

Implementation plan:

  • Use part_of as described in Eugene ppt presentation slides
  • We will work on the live file, gene_ontology_write.obo
  • Chris' script will filter out all inter-ontology links.
  • Begin working on the 1:1 function-process part-of links. We will work in both directions, looking at functions to see if they correspond to processes and looking at processes to see if they contain a certain type of function.
  • First round:
    • Jane: metabolism
    • Tanya and David: enzyme regulator activity, structural molecule activity, transporter activity and children
  • We will start from the top down, splitting up the categories as we go.
    • While doing the transporters/transport, we noticed that it is easier to work from the bottom up. This way a renderer can be set in OBO-Edit to easily identify MF terms that do not have a direct part_of relationship to BP.
  • Once we make a first pass, we (Chris) will create a new 'gene_association file' to prove to the world that this is a good thing.
  • After 'easy' metabolic processes are done, move on to mining metabolic pathway databases for links (face to face meeting for finalization of method/implementation?). Possibly involve Peter D'Eustacio at this point to deal with issues involving Reactome and GO. Resources will be:
    • KEGG
    • Reactome
    • Metacyc

Mining links from pathway databases

Display of links:

See also: