Function involved in process to OBSOLETE

[pgaudet]

GO:0099582 neurotransmitter receptor activity involved in regulation of presynaptic cytosolic calcium ion concentration

GO:0099626 voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels

GO:1903264 nitrate reductase activity involved in anaerobic electron transport chain

GO:0098663 transmembrane transporter activity involved in import into cell GO:0039632 RNA translocase activity involved in viral RNA genome packaging |
GO:0039631 DNA translocase activity involved in viral DNA genome packaging GO:1902945 metalloendopeptidase activity involved in amyloid precursor protein catabolic process GO:0098697 ryanodine-sensitive calcium-release channel activity involved in regulation of postsynaptic cytosolic calcium levels GO:1905057 voltage-gated calcium channel activity involved in regulation of postsynaptic cytosolic calcium levels GO:1905056 calcium-transporting ATPase activity involved in regulation of presynaptic cytosolic calcium ion concentration |
GO:1905059 calcium-transporting ATPase activity involved in regulation of postsynaptic cytosolic calcium ion concentration

GO:0099507 ligand-gated ion channel activity involved in regulation of presynaptic membrane potential GO:0099508 voltage-gated ion channel activity involved in regulation of presynaptic membrane potential GO:0099581 ATPase coupled ion transmembrane transporter activity involved in regulation of postsynaptic membrane potential GO:0099579 G-protein coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential GO:0099102 G-protein gated potassium channel activity involved in regulation of postsynaptic membrane potential GO:0099107 ion channel regulator activity involved in G-protein coupled receptor signaling pathway GO:0099108 potassium channel activator activity involved in G-protein coupled receptor signaling pathway GO:0097364 stretch-activated, cation-selective, calcium channel activity involved in regulation of action potential
GO:0097365 stretch-activated, cation-selective, calcium channel activity involved in regulation of cardiac muscle cell action potential GO:0086086 voltage-gated potassium channel activity involved in AV node cell action potential repolarization GO:0086058 voltage-gated calcium channel activity involved in Purkinje myocyte cell action potential GO:0086088 voltage-gated potassium channel activity involved in Purkinje myocyte action potential repolarization

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Note that @dosumis wants to keep

• GO:0099582 neurotransmitter receptor activity involved in regulation of presynaptic cytosolic calcium ion concentration zero

  • GO:0099626 voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels zero (see #14278)

[dosumis]

I'd rather you held off on obsoleting anything in subset: goslim_synapse or anything that classifies a term that is. You should at least discuss with the synapse group before obsoleting any of these.

CC @RLovering @BarbaraCzub @Pimmelorus

[pgaudet]

Thanks @dosumis, will do.

[paolaroncaglia]

@pgaudet

Related to this ticket, @RLovering emailed you some time ago. I’m copying her message here in case it fell through the cracks :-)

“Hi Pascale

I am emailing you because I noticed that the github ticket about this has been closed

There are 75 cardiac electrophysiology terms that have the word 'involved' (there might be less but there are definately more than 50). Although many of these are process involved in process terms

eg

GO:1903763 | gap junction channel activity involved in cell communication by electrical coupling

GO:0086080 | protein binding involved in heterotypic cell-cell adhesion

GO:0086008 | voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization

GO:0086072 | AV node cell-bundle of His cell adhesion involved in cell communication

We are about to resubmit a paper describing the improvement of the ontology in this domain. [In fact, the paper was resubmitted last week]

Some of these terms do not have any annotations associated at this time because we have not yet captured the role of hormones etc in regulating heart conduction

Thanks

Ruth

@dosumis @paolaroncaglia @ukemi”

@pgaudet could you please consider holding off on obsoleting the cardiac-relevant terms above (and similar ones). Thanks!

[pgaudet]

@dosumis @RLovering

I agree we should not obsolete all these terms; however one that jumps to me is the protein binding: 'GO:0086080 | protein binding involved in heterotypic cell-cell adhesion' this may lead to an explosion of terms if we allow this pattern (unless there is something specific about this term that isn't immediately obvious). In this case would the MF term 'cell-cell adhesion mediator activity' represent the function you are trying to capture ?

Thanks, Pascale

[pgaudet]

I am also concerned about terms such as 'GO:0086008 | voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization' because if you mix all types of channels with all possible nervous system responses again you'll have a large number of terms. This does seems more suited for a GO-CAM model.

I'm adding this to the next editors discussion.

Thanks, Pascale

[pgaudet]

@cmungall @thomaspd suggest that these terms could automatically be converted to GO-CAM models, so the pre-composed version of the term would not be necessary anymore.

[pgaudet]

Hi all,

We'd like to have minimally one reference for each of these terms. I'll go though the list and ask for the missing ones.

Thanks, Pascale

[pgaudet]

Hi @dosumis @RLovering I went over the list of terms above, here are the ones that don't have a reference. While you are working on the paper can you provide the references ?

GO:0099582 neurotransmitter receptor activity involved in regulation of presynaptic cytosolic calcium ion concentration No pubmed

GO:0098697 ryanodine-sensitive calcium-release channel activity involved in regulation of postsynaptic cytosolic calcium levels No pubmed

GO:0099508 voltage-gated ion channel activity involved in regulation of presynaptic membrane potential No pubmed

GO:0099581 ATPase coupled ion transmembrane transporter activity involved in regulation of postsynaptic membrane potential No pubmed

GO:0099579 G-protein coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential No pubmed

GO:0099107 ion channel regulator activity involved in G-protein coupled receptor signaling pathway No pubmed

GO:0086086 voltage-gated potassium channel activity involved in AV node cell action potential repolarization No pubmed

GO:0086058 voltage-gated calcium channel activity involved in Purkinje myocyte cell action potential No pubmed

GO:0086088 voltage-gated potassium channel activity involved in Purkinje myocyte action potential repolarization No pubmed

Thanks, Pascale

[dosumis]

Hi @Pimmelorus We need to add PMIDS for these. Do you have refs?

GO:0099582 neurotransmitter receptor activity involved in regulation of presynaptic cytosolic calcium ion concentration No pubmed

GO:0098697 ryanodine-sensitive calcium-release channel activity involved in regulation of postsynaptic cytosolic calcium levels No pubmed

GO:0099508 voltage-gated ion channel activity involved in regulation of presynaptic membrane potential No pubmed

GO:0099581 ATPase coupled ion transmembrane transporter activity involved in regulation of postsynaptic membrane potential No pubmed

GO:0099579 G-protein coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential No pubmed

GO:0099107 ion channel regulator activity involved in G-protein coupled receptor signaling pathway No pubmed

[pgaudet]

@Pimmelorus Is it possible to provide references for these terms ?

Thanks, Pascale