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This repository hosts the tracker for issues pertaining to GO annotations.
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Review annotations to transporters involved in synaptic BP #4955

Open pgaudet opened 7 months ago

pgaudet commented 7 months ago

GO:0099520 | monoatomic ion antiporter activity involved in regulation of presynaptic membrane potential GO:0099582 | neurotransmitter receptor activity involved in regulation of presynaptic cytosolic calcium ion concentration GO:0099580 | monoatomic ion antiporter activity involved in regulation of postsynaptic membrane potential GO:0099583 | neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration GO:0099529 | neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential GO:1905056 | P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration GO:0099530 | G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential GO:1905059 | P-type calcium transporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration GO:0099626 | voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels GO:1905057 | voltage-gated calcium channel activity involved in regulation of postsynaptic cytosolic calcium levels GO:0099635 | voltage-gated calcium channel activity involved in positive regulation of presynaptic cytosolic calcium levels GO:1905054 | calcium-induced calcium release activity involved in regulation of presynaptic cytosolic calcium ion concentration GO:1905058 | calcium-induced calcium release activity involved in regulation of postsynaptic cytosolic calcium ion concentration GO:0099102 | G-protein gated potassium channel activity involved in regulation of postsynaptic membrane potential GO:0099507 | ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential GO:1905055 | calcium:monoatomic cation antiporter activity involved in regulation of presynaptic cytosolic calcium ion concentration GO:0099508 | voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential GO:1905060 | calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration GO:1905030 | voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential GO:0098695 | inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels GO:1904315 | transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential GO:0150047 | G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential GO:0140232 | intracellular cAMP-activated cation channel activity involved in regulation of presynaptic membrane potential GO:0098872 | G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration GO:0099579 | G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential GO:0140233 | intracellular cAMP-activated cation channel activity involved in regulation of postsynaptic membrane potential GO:0098697 | ryanodine-sensitive calcium-release channel activity involved in regulation of postsynaptic cytosolic calcium levels GO:0099521 | ATPase coupled ion transmembrane transporter activity involved in regulation of presynaptic membrane potential GO:0099581 | ATPase coupled ion transmembrane transporter activity involved in regulation of postsynaptic membrane potential

deustp01 commented 7 months ago

Any possibility of generating a basic list of current usage of these terms - for each user and each term, e.g., Reactome and GO:0099521, do we use it? At least for us, generating that list is labor-intensive and really inefficient. In contrast, if you give us a list of specific terms that we have actually used, it is easier, and definitely in-scope, to review and evaluate the usages (as in the case of the deprecated calcium channel terms earlier today).

pgaudet commented 7 months ago

Hi Peter,

As far as I can tell, you only use GO:0099635, see https://github.com/geneontology/go-annotation/blob/master/reports/4955/mappings_GO_0098695-GO_0098697-GO_0098872-GO_0099102-GO_0099507-GO_0099508-GO_0099520-GO_0099521-GO_0099529_etc.tsv

However Reactome have a number of TAS annotations, are we generally missing those?

Generally, if you are not assigned, please consider there is nothing to do on your end. I run these queries to see the scope of the task, not necessarily because any work is requested - at least not before you are assigned.

Thanks, Pascale

deustp01 commented 7 months ago

However Reactome have a number of TAS annotations, are we generally missing those?

TAS annotations arise because we associate evidence only with reaction instances so that there is no automatic way to determine which bit of published evidence supports which assertion about a gene product involved in the reaction, much like a standard GO annotation where the evidence is a review. And based on that analogy there was historically an agreement that Reactome-derived GO annotations would get a TAS evidence code with the Reactome reaction instance itself (R-HSA-###) as the evidence. So, yes, TAS annotations should be included in your surveys if that is possible.

if you are not assigned, please consider there is nothing to do on your end.

Thanks. Got it.