Difference between revisions of "Annotation Conf. Call 2016-07-26"

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(LEGO Model for FlyBase Annotation Consistency Exercise Paper)
(Minutes)
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=Minutes=
 
=Minutes=
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*On call: Antonia, Bob, Chris, David H., David O-S., Giulia, Helen, Judy, Kimberly, Li, Melanie, Midori, Peter, Petra, Ruth, Sabrina, Shur-Jen, Val 
  
  
 
[[Category: Annotation Working Group]]
 
[[Category: Annotation Working Group]]

Revision as of 08:37, 27 July 2016

Bluejeans URL: https://bluejeans.com/993661940

Agenda

Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016

  • Please indicate on the Meeting Logistics Page if you plan to come.
  • We are also gauging interest in a one- or half-day Noctua/LEGO workshop at USC (either before or after the main consortium meeting) so have added two additional column to the table to see if people can also attend that, and if so, when.
  • Please add your information as soon as possible so we can make arrangements.

Annotation Consistency Exercise for the Remainder of 2016

  • Thanks to everyone who agreed to select and present a paper for the remainder of this year:
  • August 23 - SGD
  • September 27 - dictyBase
  • October 25 - RGD
  • November 22 - Zfin
  • If you have thoughts about the exercises, please send them along to David and Kimberly. At the end of the year, we will again evaluate how this is working and if we need to make any changes to the format to keep these exercises useful for people.

Revised Protein Binding Documentation

  • GO website has been updated with the following guideline on protein binding annotations:
 Proposed New Guideline: The Molecular Function (MF) ontology can be used to capture macromolecular interactions, such as protein-
 protein, protein-nucleic acid, protein-lipid interactions, etc.  While GO annotations are not considered to be a repository of all 
 protein-protein interactions, many gene products are annotated to 'protein binding' (GO:0005515) or one of its child terms.  In making 
 these annotations, contributing groups may follow slightly different practices with respect to the types of experimental evidence used 
 to support these inferences, e.g. some groups may use co-immunoprecipitation as supporting evidence for a protein binding annotation 
 between two gene products, others not.  However, all groups generally adhere to the principle that, when annotated, protein binding 
 interactions inform what is believed to be the normal biological role of a gene product, i.e. the protein-protein interactions support 
 an author's hypothesis about how the gene product is thought to execute its molecular function in the context of a normal biological 
 process.  Protein-protein interactions for which there is not yet sufficient biological context are discouraged as sources of GO MF 
 annotations.
  • Also, the GO FAQs have been updated to document how protein-protein interactions curated by IntAct are exported to GO as protein binding (GO:0005515) annotations.

Questions about Membrane Cellular Component Annotations

  • This annotation issue was raised by Rebecca and concerns annotation to membrane child terms, e.g. integral to synaptic vesicle membrane, given different types of experimental results.
  • We will resume discussion of this issue when Rebecca is back.
  • In the meantime, there is a nice summary from Rebecca on the 2016-07-11 minutes.
  • Please take a look and review the discussion and proposal so we can move towards creating guidelines on the 2016-08-09 call.

LEGO Model for FlyBase Annotation Consistency Exercise Paper

  • Review annotations to paper on memory and relations between them in LEGO model
  • Review resulting GAF (from Model drop-down menu, select Export GAF)
  • Review additional annotations desired from a GAF output.
  • Review use of directly_inhibits relation between acetylcholine transporter and receptor activities in LEGO model and annotation to inhibitor activity based on the definition.
  • Compare with annotations submitted from consistency exercise
  • GREEN = Noctua GAF , BLUE = desired GAF annotations, MAGENTA = GAF annotations that would be made based on the current model if logical defs were in place for the inhibitor activity, but are questionable.
Gene Name (col 2) GO ID and term name (col 5) Evidence (col 7) Annotation Extension (col 16) With/From (col 8)
CG7442 Dmel GO:0005277, acetylcholine transmembrane transporter activity IDA negatively_regulates(GO:0007271, synaptic transmission, cholinergic),negatively_regulates(GO:0007613, memory),RO:0002408(GO:0015464, acetylcholine receptor activity),positively_regulates(GO:0008355, olfactory learning)
CG7442 Dmel GO:0051630, acetylcholine uptake IDA occurs_in(GO:0098794), postsynapse
CG7442 Dmel GO:000030425, dendrite IDA
Ace Dmel GO:0003990, acetylcholineterase activity TAS negatively_regulates(GO:0007271, synaptic transmission, cholinergic),negatively_regulates(GO:0007613, memory),RO:0002408(GO:0015464, acetylcholine receptor activity)
Ace Dmel GO:0006581, acetylcholine catabolic process TAS occurs_in(GO:0043083, synaptic cleft)
Ace Dmel GO:0043083, synaptic cleft TAS
CG7442 Dmel GO:0005277, acetylcholine transmembrane transporter activity IDA occurs_in(GO:000030425, dendrite)
CG7442 Dmel GO:0051630, acetylcholine uptake IDA occurs_in(GO:0098794), postsynapse
CG7442 Dmel GO:000030425, dendrite IDA
CG7442 Dmel GO:0051241, negative regulation of multicellular organismal process IMP
CG7442 Dmel GO:0090328, regulation of olfactory learning IMP
CG7442 Dmel GO:0032223, negative regulation of synaptic transmission, cholinergic IMP
CG7442 Dmel GO:0031645, negative regulation of neurological system process IMP
CG7442 Dmel GO:0048521, negative regulation of behavior IMP
Ace Dmel GO:0003990, acetylcholinesterase activity TAS occurs_in(GO:0043083, synaptic cleft)
Ace Dmel GO:0006581, acetylcholine catabolic process TAS occurs_in(GO:0043083, synaptic cleft)
Ace Dmel GO:0043083, synaptic cleft TAS
Ace Dmel GO:0032223, negative regulation of synaptic transmission, cholinergic IMP
Ace Dmel GO:0051241, negative regulation of multicellular organismal process IMP
Ace Dmel GO:0090328, regulation of olfactory learning IMP
Ace Dmel GO:0031645, negative regulation of neurological system process IMP
Ace Dmel GO:0048521, negative regulation of behavior IMP
Ace Dmel GO:0030550, acetylcholine receptor inhibitor activity IC occurs_in(GO:0098794), postsynapse With/From: GO:0003990, acetylcholinesterase activity
CG7442 Dmel GO:0030550, acetylcholine receptor inhibitor activity IC occurs_in(GO:0098794), postsynapse With/From: GO:0005277, acetylcholine transmembrane transporter activity

Minutes

  • On call: Antonia, Bob, Chris, David H., David O-S., Giulia, Helen, Judy, Kimberly, Li, Melanie, Midori, Peter, Petra, Ruth, Sabrina, Shur-Jen, Val