2010 Bar Harbor Action items

Action items

1. ANNOTATION GROUP. The annotation group will consider whether GO should even be making protein binding annotations or whether these interactions are better left to specialized databases, such as BioGrid, focusing specifically on interactions, and then interaction data can be used in conjunction with GO, rather than GO needing to represent these interactions as "protein binding" interactions
2. ANNOTATION GROUP. Chain of evidence: Background: the conclusion the researchers make, which the annotation is trying to represent, is not based on any single piece of evidence, but a combination of multiple lines of evidence. Everybody agreed that in order to increase the annotation expressivity, we should come up with a way to represent the chaing of evidence. Action item: Rama et al will form a working group on chain of evidence/LEGO and come up with a proposal to move forward with this idea. She will consult/include Michelle. This may require changing the GAF format.
3. ANNOTATION GROUP Signalling group:
   1. Add a comment to the signaling term to also consider annotating to its sibling term signaling pathway : This is no longer valid since the signaling pathway/signaling process split has been removed.
   2. Update documentation on signaling: A signaling curation manual is in progress, and will be completed once the edits are in the ontology.
   3. Add synonyms using word 'ligand' for the receptor agonist and antagonist terms. Done.
   4. cytokines can be both agonist and antagonists. Cytokine isn't linked to 'receptor agonist' or 'receptor antagonist' in the ontology, and its current definition allows for both, so this is not a problem.
   5. reword the term epidermal growth factor receptor activity so that it is clear. Will be reworded to 'epidermal growth factor-activated receptor activity.
4. ONTOLOGY DEV GROUP (Chris, David). Term Genie: For the example that Jane demo'd there is an issue with the placement in the ontology. It was too high. Chris and David were to look into, and if needed fix, the placement of the term Jane used for the Term Genie demo
5. ONTOLOGY DEV GROUP Transcription overhaul:
   1. Make sure that common use phrases get put in as synonyms for complex transcription factor terms (txnOH group)
   2. Decide whether or not this refinement to how GO defines functions, using transcription as a model, should be written up as a paper (?)
6. REFERENCE GENOME: Define resources required for broad annotation coverage via phylogenetic annotation methods (ie, need to understand how much person-power would be needed to be effective in making progress in this)
7. REFERENCE GENOME: Development of stable IDs for Panther families (Paul)