Manager 22Sep10: Difference between revisions

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==Discussion topics==
==Discussion topics==
===From BHB meeting===
===From BHB meeting===
# Exp. extrapolation by family annotation proposal: WG: (aka "broad" but the use of the word "broad" is deprecated)
# Proposal for rapidly propagating exp. annotations in each protein family: WG: (aka "broad" but the use of the word "broad" is deprecated)
# evidence codes: proof of principle for chain of evidence: WG:
# evidence codes: proof of principle for chain of evidence: WG:
# dealing with column 16 in AmiGO : software? is the documentation finished? create a WG?  
# dealing with column 16 in AmiGO : software? is the documentation finished? create a WG?  
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==Ref Genome Group Priorities==
==Ref Genome Group Priorities==
* We had a phone call yesterday (Pascale, Kara, Mike L, Paul, Mike C, Rama) ; see notes [[21_SEPT_2010_RefGen_Priorities_Discussion]]
* We had a phone call yesterday (Pascale, Kara, Mike L, Paul, Mike C, Rama) ; see notes [[21_SEPT_2010_RefGen_Priorities_Discussion]]
* The goal of the reference genome project is to provide detailed functional annotations capturing experimental data for each gene of the 12 reference genome species.  
* The goal of the reference genome project is
* There are several possible possible ways to do this: one is on a family by family basis (PANTHER10001, PANTHER10002, etc). Another one is based on known biological/cellular processes - see document: [[GO_broad_coverage_of_processes]].
*# First to provide detailed functional annotations capturing experimental data for each and every gene in the 12 reference genome species where such data is available.
*# Second, to propagate these exp. annotations to other species (including other ref. genomes) based on phylogenetic relationships.
* To achieve biological coverage for the first goal is to base our approach on known biological/cellular processes - see document: [[GO_broad_coverage_of_processes]].
* To achieve rapid propagation to other protein family members is still a work in progress

Revision as of 20:37, 21 September 2010

Discussion topics

From BHB meeting

  1. Proposal for rapidly propagating exp. annotations in each protein family: WG: (aka "broad" but the use of the word "broad" is deprecated)
  2. evidence codes: proof of principle for chain of evidence: WG:
  3. dealing with column 16 in AmiGO : software? is the documentation finished? create a WG?

Other discussion topics

  1. Code for updated ontology terms: can we improve TXN_OH? this is very cryptic.
  2. Protein binding : what do we do next?

Annotation Group Priorities

  1. educate annotators; new monthly annotation conference call: Rama to send an email about monthly call.
  2. change annotation jamborees: everyone does the same paper? Plan is to do it the next one in November
  3. loading GAF files - how can we help groups identify appropriate files, procedures
  4. improvements to documentation on the website
  5. 1st phase of QC checks is almost in place, by October probably still working out with Chris how to do soft QC checks, e.g. communicating with groups what they need to do, including keeping track of things that have already been checked; tracking things that have actually been removed (so that we can give some stats for the grant showing actual improvement)

Ref Genome Group Priorities

  • We had a phone call yesterday (Pascale, Kara, Mike L, Paul, Mike C, Rama) ; see notes 21_SEPT_2010_RefGen_Priorities_Discussion
  • The goal of the reference genome project is
    1. First to provide detailed functional annotations capturing experimental data for each and every gene in the 12 reference genome species where such data is available.
    2. Second, to propagate these exp. annotations to other species (including other ref. genomes) based on phylogenetic relationships.
  • To achieve biological coverage for the first goal is to base our approach on known biological/cellular processes - see document: GO_broad_coverage_of_processes.
  • To achieve rapid propagation to other protein family members is still a work in progress