Project
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Personnel
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January
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February
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March
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April
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May
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June
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July
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August
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September
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October
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November
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December
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Chemical terms in GO. Phase I: metabolism, binding, transport
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Harold, David, Tanya, Jane, Chris, Becky, Paola
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Fix GO/goche misalignments - add CHEBI xps to GO
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Chemical terms in GO. Phase II: improve enzyme functions, align with external databases inc. Rhea, MF-BP links for enzymes/metabolic processes
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Amelia, Chris, David, Jane, Tanya, Becky, Paola
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- 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.
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- 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)
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- 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?
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- 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?
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Chemical terms in GO. Phase III: biological roles
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Chris, David, Jane, Tanya, Becky, Paola
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Cell ontology cross-products
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Paola, Chris, Jane, Alex
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Review and improve biological_process_xp_cell
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Make TG templates
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Incorporate cell xps into GO
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Internal Cross Products
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David, Tanya, Jane, Chris, Paola, Becky
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Behaviour: GO/NBO integration
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Jane, Chris, George, Janna, David OS
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Survey ontology consumers to examine the implications of including non-GO ids in GO
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Generate file of mismatches between GO and NBO
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Fix GO (and NBO) so they align
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Replace GO ids with equivalent NBO ids and definitions
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Signaling overhaul
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Becky, Alex, Sandra, Peter, Ruth and others
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Representing GPCR and second messenger signaling
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Ligand-gated ion channels that signal
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Define intracellular signaling start and stops
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Ligand-mediated signaling pathways and receptor-mediated signaling pathways
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Neurological processes and components
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Jane, Chris, David and Paola
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Cardiac Conduction Ontology Development
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Ruth, Stan, Doug, David, Tanya, Becky, Paola and community experts
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Apoptosis
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Emily, Becky, Paola, Pablo and community experts
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Revisiting second-level terms: feedback from experts
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Revisiting existing annotations to second-level terms
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Final overall structure: sanity checks and completion
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Write paper
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Viral processes
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Jane, Philippe Le Mercier (SIB) and community experts
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