Function-process Pilot Studies

First implementation meeting: To be decided.

Technology: webex and skype.

Personnel:

• Chris Mungall (define relationships)
• Amelia Ireland (Steering)
• David Hill and Midori Harris (Managers)

Biochemical experts:

• Harold Drabkin
• Ben Hitz
• Chris Tissier
• Hartmut Foerster
• Peifen Zhang
• Martha Arnaud
• Cindy Krieger
• Jennifer Deegan

Areas:

• Glycolysis Process-Function Links
• TCA Cycle Process-Function Links
• Electron transport
• Regulation of molecular function
• Single-step biological processes

Mailing List:

• subscribe
• archives

Test files checked into CVS under:

• go/scratch/fp-links

Implementation plan:

• Define relationships and enter them into the OBO_REL ontology. (Chris Mungall and Amelia Ireland)
  • See the 'realizes' relation in ro_proposed
  • See also Function-Process_Use_Cases
  • Has_part
• Decide methodology for representation of the links.
  • Hard wired into the ontology?
  • Separate file?
• Begin with metabolic processes. Assign different areas of metabolism to biochemical experts. Resources will be:
  • KEGG
  • Reactome
  • Metacyc

Additional material:

• Minutes from FIGS meeting (May 2006; Michael Ashburner, Suzanna Lewis, Chris Mungall; Jane Lomax, Midori Harris)
• Media:F-P-stcroix.ppt Function-process slides from St Croix (Chris)
• Media:Processing_Function.ppt Refacotoring MF and BP (St Croix, Amelia)

Display of links:

• AmiGO:Inter-ontology links

Mining links from pathway databases

• SWUG:Mining_function_process_links_from_pathway_databases
• Mining Process Function Links