Annotation Conf. Call 2016-06-28
Bluejeans URL
https://bluejeans.com/993661940
Agenda
Annotation Consistency Exercise
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
Annotations
Gene/Marker Name | GO term | Evidence Code | With/From | Annotation Extension | Comment |
---|---|---|---|---|---|
Biological Process | |||||
SLC22A | NT:negative regulation of olfactory memory retention | (not forgetting)? | |||
SLC22A | NT:positive regulation of memory acquisition | (learning?) | |||
SLC22A | NT:negative regulation of memory retention | (memory) | |||
SLC22A | NT:negative regulation of memory | IMP | |||
SLC22A | NT:regulation of memory acquisition | IMP | |||
SLC22A | NT:regulation of memory retention | IMP | |||
SLC22A | NT:negative regulation of memory | IMP | |||
SLC22A | NT:negative regulation of anesthesia-resistant memory | IMP | |||
SLC22A | regulation of olfactory learning (GO:0090328) | IMP | |||
SLC22A | NT:positive regulation of rate of learning | IMP | |||
AChE | NT:negative regulation of memory | IMP | |||
SLC22A | NT:negative regulation of memory | IGI | AChE | ||
AChE | NT:negative regulation of memory | IGI | SLC22A | ||
SLC22A | negative regulation of synaptic transmission, cholinergic (GO:0032223) | IMP | |||
SLC22A | NT:neurotransmitter transport involved in regulation of memory | IC | GO:0015220|GO:NT: negative regulation of memory | ||
SLC22A | NT:cholinergic synaptic transmission involved in regulation of memory | This one's a "maybe" | |||
SLC22A | NT:negative regulation of memory | IMP/IDA | part_of (olfactory learning) | ||
SLC22A | NT:negative regulation of olfactory learning | IMP/IDA | |||
SLC22A | memory (GO:0007613) | IMP | occurs_in(DAn),happens_during(adult life stage) | ||
SLC22A | NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine uptake involved in memory acquisition rate enhancement? | occurs_in(DAn),happens_during(adult life stage) | |||
SLC22A | NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine uptake involved in memory retention suppression? | occurs_in(DAn),happens_during(adult life stage) | |||
AChE | memory (GO:0007613) | IMP | How to express an extracellular synaptic region between two different neurons via annotation extensions? | ||
AChE | NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine catabolism involved in memory acquisition rate enhancement? | ||||
AChE | NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine catabolism involved in memory retention suppression? | ||||
SLC22A | NT:negative regulation of olfactory memory | IMP | acts_on_population_of mushroom body neuron; dopamine neuron | olfactory memory,pos. reg., children of olfactory learning (GO:0008355). From Fig1,2 (MbN and DpN need to be component terms). | |
SLC22A | NT:positive regulation of olfactory learning | IMP | child of olfactory learning (GO:0008355). From fig 5c. Rate of learning is impaired in knockdown. | ||
SLC22A | regulation of synaptic transmission, cholinergic (GO:0032222) | IMP | |||
SLC22A | NT: choline uptake? | IDA | |||
SLC22A | dopamine uptake (GO:0015872) | IDA | |||
SLC22A | histamine uptake (GO:0051615) | IDA | |||
SLC22A | NT: amino-acid betaine uptake? | IDA | |||
Molecular Function | |||||
SLC22A | amino-acid betaine transmembrane transporter activity (GO:0015199) | IDA | |||
SLC22A | acetylcholine transmembrane transporter activity (GO:0005277) | IDA | |||
SLC22A | choline transmembrane transporter activity (GO:0015220) | IDA | |||
SLC22A | dopamine transmembrane transporter activity (GO:0005329) | IDA | |||
SLC22A | NT: histamine transmembrane transporter activity | IDA | |||
SLC22A | acetylcholine transmembrane transporter activity (GO:0005277) | IDA/IMP | |||
SLC22A | choline transmembrane transporter activity | IDA | |||
SLC22A | acetylcholine transmembrane transporter activity | IDA | |||
SLC22A | choline transmembrane transporter activity (GO:0015220) | IDA | |||
SLC22A | acetylcholine transmembrane transporter activity (GO:0005277) | IDA | |||
Cellular Component | |||||
SLC22A | dendrite (GO:0030425) | IDA | part_of (calyx of adult mushroom body) | ||
SLC22A | plasma membrane (GO:0005886) | IDA | |||
SLC22A | dendrite (GO:0030425) | IDA | part_of(cholinergic neuron), part_of (calyx of adult mushroom body) | ||
SLC22A | dendrite (GO:0030425) | IDA | part_of(a/b MBn),part_of(a'/b' MBn) | ||
SLC22A | NT:dendrite plasma membrane | IC | GO:0030425,GO:0005277,GO:0051630 | part_of(a/b MBn),part_of(a'/b' MBn) | Would need to use GO_REF:0000036 |
- Other comments: "Not clear what the differences between memory retention and learning."
I really don't understand the stuff about interference and forgetting. Overall I'm not fully convinced the set of memory BP annotations is self-consistent and sensible. Annotations like increased/decreased olfactory memory for RNAi and overexpressors should be phenotype annotation
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?
Minutes
- On call: Alice, Bob, David OS, Edith, Elena, Giulia, Helen, Kimberly, Li, Melanie, Midori, Paola, Petra, Rebecca, Sabrina, Shur-Jen, Stacia, Stan, Tanya
Annotation Consistency Exercise
- Molecular Function and Cellular Component annotations were all generally the same; no problems there
- Biological Process annotations generated more discussion
- Consensus seemed to be that this is an area of the ontology that would benefit from further development, with input from experts in the learning and memory field
- There is a NeuroBehavior Ontology - who uses that ontology and would it be helpful for GO to work with that?
- Paper raises the issue of what specific aspects of memory we want to capture in GO
- Memory acquisition?
- Memory retention?
- Memory interference?
- We also want to make sure we understand how the results of assays used to assess different aspects of learning and memory inform BP term choice
- Tentative plan: compare learning and memory papers across organisms to find commonalities that could be used to develop GO BP
- Consensus seemed to be that this is an area of the ontology that would benefit from further development, with input from experts in the learning and memory field
Protein Binding Documentation
- Review of different group's practices for capturing protein binding annotations indicates that there are still some differences with respect to what interactions groups capture
- Some groups are more inclusive than others based largely on methodology and interpretation of author intent
- Another contributing factor is whether or not groups have another mechanism in place, e.g. BioGrid or IntAct, to capture these physical interactions. Would be good to follow-up with IntAct to confirm what interactions they export to GOC and why.
- Consensus was, though, that this is an area of annotation where it is okay to have some differences but the documentation should reflect this
- ACTION ITEM: Draft new statement explaining diverse GOC approach to protein binding annotations. Review at a future call to make sure everyone is okay with it.