non-regulation term has odd regulation parent/release of sequestered calcium ion into cytosol by Golgi

[ValWood]

release of sequestered calcium ion into cytosol by Golgi can be used for example for a Golgi transmembrane transporter.

However it's parent is "negative regulation of sequestering of calcium ion"

Implying the process of releasing calcium ions is regulating itself? Does this seem odd?

release of sequestered calcium ion into cytosol by Golgi

[raymond91125]

I would read this as: releasing calcium ion from target site of sequestration negatively_regulates calcium ion sequestration. That seems reasonable. Doesn't it?

[ValWood]

I guess so but it seems kind of odd. Also the entities that would be annotated wouldn't be "regulation of" in the GO sense, they would be part_of.

MAybe we should ignore this for now.

[ValWood]

I think my problem was that this transporter https://www.pombase.org/gene/SPBC31E1.02c becomes annotated to "negative regulation of sequestering of calcium ion (GO:0051283)" but the transporter isn't "regulating" in the GO sense.

[pgaudet]

The calcium terms are problematic because there is a lot of redundancy. We had decided that sequestering was a MF , so:

1. GO:0051208 sequestering of calcium ion should be obsolste with 'consider' GO:0140314 calcium ion sequestering activity
2. I suggest we revise all these terms: (I dont think we can do the obsoletion suggested above and keep these: GO:0061454 release of sequestered calcium ion into cytosol by Golgi GO:1903514 release of sequestered calcium ion into cytosol by endoplasmic reticulum GO:0014808 release of sequestered calcium ion into cytosol by sarcoplasmic reticulum GO:0051209 release of sequestered calcium ion into cytosol GO:0099586 release of sequestered calcium ion into postsynaptic cytosol GO:0099585 release of sequestered calcium ion into presynaptic cytosol GO:0051282 regulation of sequestering of calcium ion GO:0010880 regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum GO:0051279 regulation of release of sequestered calcium ion into cytosol GO:0051283 negative regulation of sequestering of calcium ion GO:0051284 positive regulation of sequestering of calcium ion GO:0051280 negative regulation of release of sequestered calcium ion into cytosol GO:0051281 positive regulation of release of sequestered calcium ion into cytosol GO:0008377 light-induced release of internally sequestered calcium ion GO:0014809 regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion GO:0014811 negative regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion GO:0014810 positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion

• The BPs in many cases would be either calcium ion homeostasis (either cytoplasmic or in an organelle) OR calcium ion signaling.
• Probably 'release of sequestered calcium ion into cytosol by endoplasmic reticulum' and similar terms should be annotated as to a transport term such 'transport of calcium from endoplasmic reticulum to cytosol' (although we only have a term for the other direction, 'calcium ion transport from cytosol to endoplasmic reticulum'.

@raymond91125 Do you want to tackle this?

[raymond91125]

How to revise the terms in 2, obsoleting them all?

For example, GO:0051282 regulation of sequestering of calcium ion, cannot regulate an MF. Perhaps some annotations may be moved to a term 'regulation of intracellular calcium ion concentration' (NEW). But that's not equivalent. Sequestering means taken into a protected compartment, that can be anywhere.

[ValWood]

Possibly the problem here is that "sequestering" is used in a couple of different ways. First to describe the "activity" of binding and sequestering something (preventing it from moving or interacting). Sometimes researchers refer to the transport step as part_of 'sequestering'. I.e. you need to move something into a location (like the Golgi, or ER), before it can be "sequestered", or maybe the transport itself is sufficient to sequester, which makes this quite complicated to model.

Mostly, it seems that calcium-binding proteins are involved. In might therefore be possible to model:

the transporter activity -> sequestering activity as part of a broader process of homeostasis. If not it becomes more complicated because sequestration would need to be modelled as a process.

Perhaps this should be dealt with as part of the larger discussion about transport/homeostasis later?

The reason I brought this up was that I was reviewing PomBase regulation annotations and I didn't think this was regulation: https://www.pombase.org/term/GO:0061454 One option would be to change this annotation to "Golgi calcium ion transmembrane transport" (the non-regulation parent) but then I lose the transport direction. @pgaudet do you prefer that the transport direction is captured on the MF or BP, I forgot?

[raymond91125]

PMID:23595672 Intracellular Calcium Homeostasis and Signaling reviews cellular calcium ion transport and homeostasis.

[raymond91125]

There are 381 EXP annotations to regulation of sequestering of calcium ion and descendant terms. I think many of them will have to be reviewed if we start to remove 'sequester terms'. I feel it's rather drastic.