2012 Timeline

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2011_Timeline

Project Personnel January February March April May June July August September October November December
Chemical terms in GO. Phase I: metabolism, binding, transport Harold, David, Tanya, Jane, Chris, Becky, Paola Fix GO/goche misalignments - add CHEBI xps to GO
Chemical terms in GO. Phase II: improve enzyme functions, align with external databases inc. Rhea, MF-BP links for enzymes/metabolic processes Amelia, Chris, David, Jane, Tanya, Becky, Paola
  • Manual: Identify MF reaction terms that can't be expressed using has_input: CHEBI:XXX / has_output: CHEBI:XXX; manually research and review
  • Automated: set up or augment script to produce has_input/has_output data for all rxns with RHEA xrefs (RHEA = EC rxns with CHEBI terms)
  • Automated: create system to check GO rxns are up to date wrt RHEA, EC, MetaCyc data. Alert on clashes between sources.
  • Manual: continue review of non-conformant MF rxn terms
  • Automated: continue development of system to check GO rxns are up to date wrt RHEA, EC, MetaCyc data. Look at incorporating KEGG and UM-BBD data (no bulk downloads available)
  • Manual: continue review of non-conformant MF rxn terms
  • Automated: continue development of GO rxn update system.
  • Automated: pull in MetaCyc pathway data - how to fit with GO BP?
  • Manual: continue review of non-conformant MF rxn terms
  • Automated: look at other p'way databases (esp. those with BioPAX output) - fit with GO BP?
  • Manual: continue review of non-conformant MF rxn terms
  • Manual: continue review of non-conformant MF rxn terms
Chemical terms in GO. Phase III: biological roles Chris, David, Jane, Tanya, Becky, Paola
Cell ontology cross-products Paola, Chris, Jane, Alex Review and improve biological_process_xp_cell Make TG templates Incorporate cell xps into GO
Internal Cross Products David, Tanya, Jane, Chris, Paola, Becky
Behaviour: GO/NBO integration Jane, Chris, George, Janna, David OS Survey ontology consumers to examine the implications of including non-GO ids in GO Generate file of mismatches between GO and NBO Fix GO (and NBO) so they align Replace GO ids with equivalent NBO ids and definitions
Signaling overhaul Becky, Alex, Sandra, Peter, Ruth and others Representing GPCR and second messenger signaling Ligand-gated ion channels that signal Define intracellular signaling start and stops Ligand-mediated signaling pathways and receptor-mediated signaling pathways
Neurological processes and components Jane, Chris, David and Paola
Cardiac Conduction Ontology Development Ruth, Stan, Doug, David, Tanya, Becky, Paola and community experts
Apoptosis Emily, Becky, Paola, Pablo and community experts Revisiting second-level terms: feedback from experts Revisiting existing annotations to second-level terms Final overall structure: sanity checks and completion Write paper
Viral processes Jane, Philippe Le Mercier (SIB) and community experts