Annotation Conf. Call 2016-06-28

Bluejeans URL

https://bluejeans.com/993661940

Agenda

Annotation Consistency Exercise

• Drosophila SLC22A Transporter Is a Memory Suppressor Gene that Influences Cholinergic Neurotransmission to the Mushroom Bodies.

Abstract The mechanisms that constrain memory formation are of special interest because they provide insights into the brain's memory management systems and potential avenues for correcting cognitive disorders. RNAi knockdown in the Drosophila mushroom body neurons (MBn) of a newly discovered memory suppressor gene, Solute Carrier DmSLC22A, a member of the organic cation transporter family, enhances olfactory memory expression, while overexpression inhibits it. The protein localizes to the dendrites of the MBn, surrounding the presynaptic terminals of cholinergic afferent fibers from projection neurons (Pn). Cell-based expression assays show that this plasma membrane protein transports cholinergic compounds with the highest affinity among several in vitro substrates. Feeding flies choline or inhibiting acetylcholinesterase in Pn enhances memory, an effect blocked by overexpression of the transporter in the MBn. The data argue that DmSLC22A is a memory suppressor protein that limits memory formation by helping to terminate cholinergic neurotransmission at the Pn:MBn synapse.

• How to capture biological process aspects of memory?
  • The paper identifies a ‘memory suppressor gene’ (Solute Carrier 22A of Drosophila (DmSLC22A) (FlyBase:CG7442; FBgn0037140). How to capture the biology described - memory, learning, conditioning? What new terms are needed to capture the process? Alternatively, is it better to capture these experiments only as phenotypes?
  • Leave the expression/mechanistic sections and have a look at these four sections of this paper:
    • Drosophila CG7442 Is a Memory Suppressor Gene Functioning in MBn and DAn
    • Drosophila CG7442 Overexpression Impairs Memory
    • DmSLC22A Regulates Both Memory Acquisition and Retention
    • DmSLC22A Modulates Memory Strength by Regulating Cholinergic Neurotransmission in the MB Calyx

Protein Binding Annotations

• Review Protein Binding Annotation Guidelines
• The following statement in our protein binding annotation guidelines does not hold for some annotation groups:

 The 'with' column (8) and the annotation extension column (16) should be used only for direct interactions and only when the binding 
 relationship is not already included in the GO term and/or definition. See "column 16 documentation for relationship types to use when 
 adding IDs in the annotation extension column (16). 

• Some groups do annotate protein binding from experiments that do not assess direct physical interactions, such as co-IP.
• Proposal has been made to update documentation to be clearer about how the GOC members annotate protein binding.
• Any objections to updating the documentation? Suggestions for clearer wording?