#11241 Rubidium Biological Role?

[Harold J. Drabkin]

I just came across some terms that I am suspicious of.

rubidium ion transmembrane transporter activity

negative regulation of rubidium ion transmembrane transporter activity
negative regulation of rubidium ion transport
positive regulation of rubidium ion transmembrane transporter activity
positive regulation of rubidium ion transport
regulation of rubidium ion transmembrane transporter activity
regulation of rubidium ion transport
renal rubidium ion absorption
renal rubidium ion transport
rubidium ion transport

From what I can tell, rubidium ion is often used to measure transport (86Ru uptake).
It is used as a measure of K+ transport I think. So these terms are about an assay and not a true biological function and process...? We have 11 annotations to the processes, but across the GOC, maybe around 84 non-iea to processes, around 8 to the activity terms.
Should these be fixed and the terms obsoleted? I have a feeling this has been addressed in the past.

[Tanya Berardini]

Editor's discussion:

Removal of 'assay' terms as we discover them.

Annotate to the intended transported molecule, in this case, K+. Then add the
OBI, BAO, or bioassay term - measure of K+ transport using rubidium, in the with field. (IDA + evidence with allowed where with field contains the assay term).

[rach_huntley]

Hi,

Wouldn't the correct way to annotate be to use a specific ECO term for the assay? Also, you cannot add anything into the with/from field of an IDA annotation.

Rachael.

[Tanya Berardini]

The suggestion from Chris was to modify the requirements so that IDA annotations would be allowed to have entries in the with/from and that in this case the with/from field would be populated with a specific assay term.

[rach_huntley]

I would hope that Chris will bring this to an annotation call as we have already gone through the exercise of deciding when with strings are mandatory/not acceptable etc. for each evidence code earlier this year. We need to know if this is going to change. Also, I don't understand what the difference is between ECO and OBI and when we should use a specific ECO term vs. an OBI ID in the with field - maybe it's an interim measure to use OBI until groups can use ECO? We definitely need clear guidelines on this.

[Valerie Wood]

At PomBase we would just make an IDA to the substrate which was the authors intent. There is enough knowledge/evidence for a curator to capture the authors intent and annotate to potassium transport with IDA. Anybody who went back to the paper would immediately see why. We have been doing it this way for ever and it works fine...why make it more complicated?

Val

[Tanya Berardini]

Specifics of how to capture the 'rubidium transport assay bit' can be punted to another time and place. The suggestion to capture the experimental conditions in the with field was an idea of how this might be done. Maybe, as Val says, we're overly complicating things. The main point of the discussion was to annotate to what the authors were trying to show. Nothing is going to change without discussion with annotators.