New terminology - biological process

[UlrikeS91]

This came up in issue openMetadataInitiative/openMINDS_controlledTerms#151 and it is easier to follow-up on it when it has it's own issue.

I can make a first PR for the schema and some instances. I've looked through the term suggestions that we currently have in the Knowledge Graph and found quite some a few terms that may fall under this terminology. Some are straight-forward (as far as I can tell) and should be added, but others require some discussions.

Should be added:

• action potential
• alpha activity
• beta activity
• gamma activity
• BOLD signal
• cortico-cortical evoked potential
• local field potential
• multi-unit activity
• single-unit activity
• slow oscillation

Terms that might be measured quantities:

• miniature inhibitory postsynaptic current
• spontaneous inhibitory postsynaptic current
• evoked potential?

Terms that describe biological processes which can occur both naturally and/or be induced e.g. with drugs:

• fast receptor inhibition
• slow receptor inhibition
• DNA methylation
• RNA expression
• glucose uptake
• hemodynamic response

"Far fetched" terms that should be discussed, but we probably do not want to add as biological processes:

• consciousness
• motor behavior
• visual perception
• perturbed activation
• rapid-eye movement sleep
• slow wave sleep
• eye movement

These are the exact labels from the Knowledge Graph! These can be changed and some really need to change, but this will make it easier to re-map them later on.

Any feedback/thought are appreciated, @tgbugs , @lzehl, @apdavison (and other if you wish to include more).

[ehennestad]

I added a comment in https://github.com/HumanBrainProject/openMINDS_controlledTerms/issues/151 and my point is that it would be better to call many of these concepts BiologicalPhenomenon than BiologicalProcess, especially those under the list "should be added". Out of the far fetched terms, rapid-eye movement sleep, slow wave sleep, eye movement are definitely observable phenomenons.

[UlrikeS91]

I added a comment in openMetadataInitiative/openMINDS_controlledTerms#151 and my point is that it would be better to call many of these concepts BiologicalPhenomenon than BiologicalProcess, especially those under the list "should be added". Out of the far fetched terms, rapid-eye movement sleep, slow wave sleep, eye movement are definitely observable phenomenons.

Unless, @tgbugs strongly objects, the terminology will be called BiologicalPhenomenon instead of BiologicalProcess. I found it better fitting and @lzehl did not seem to object.

[lzehl]

I don't mind using BiologicalPhenomenon :smile:

[lzehl]

@tgbugs @UlrikeS91 @ehennestad Did we agree here now on how to proceed?

Adding terminology BiologicalPhenomenon with the following instances (??? TBD):

category	term
process	action potential
process measure	alpha activity
process measure	beta activity
process measure	gamma activity
process measure	BOLD signal
process measure	cortico-cortical evoked potential
process measure	local field potential
process measure	multi-unit activity
process measure	single-unit activity
process	slow oscillation
process	fast receptor inhibition
process	slow receptor inhibition
process	DNA methylation
process	RNA expression
process	glucose uptake
process	hemodynamic response
process	motor behavior
process	visual perception
process	rapid-eye movement sleep
process	slow wave sleep
process	eye movement
?	consciousness
?	perturbed activation

https://en.wikipedia.org/wiki/Consciousness#The_problem_of_definition

[lzehl]

@tgbugs could we go over this?

[tgbugs]

For most of these biological process is the correct parent class, and may of them are in GO already.

[lzehl]

@tgbugs @aeidi89 I discussed the terminology terms with @apdavison and we would like to suggest to not use "process" but keep the term "phenomenon". Meaning we would group terms under "BiologicalPhenomenon" and "MeasuredPhenomenon". Is there anything speaking against this suggestion?

[MBAbrams]

I am in favor of phenomenon

[aeidi89]

As far as I can tell, a process refers to something that is being carried on, it is moving/happening, leading towards something ref, while a phenomenon is an observed status, an observation or a fact ref. In my personal opinion, anything that is per definition biological is not static but moving, however, I do not feel strongly for one or the other. I hope this helps.

[tgbugs]

phenomenon is not correct, biological process is literally the base class name for all of these things in GO, changing it to something else will only confuse the matter, phenomenon is ambiguous with regard to whether something is a continuant or an occurrent, so process should be used

[apdavison]

I'm not fully convinced that all of the items in the list are continuants. "Local field potential", for example, refers to a single voltage measured at a given point in space at a point in time and/or to certain characteristics of the filtering in the acquisition process. "Local field potential recording", however, would certainly be a continuant. Given a careful choice of terms, however, I think all of the items could be considered as continuant.

My second quibble is whether these are all biological processes. For example, the BOLD signal comes from the interaction of a strong magnetic field and some radio waves with haemoglobin in the blood. "Variation of blood oxygenation levels" is a biological process, I'm not sure "BOLD signal" is.

Similar remarks apply to "multi-unit activity", "single-unit activity" where there is an interaction of an underlying biological process with a measurement activity, and to "slow oscillation", "alpha activity", "beta activity", etc., which are descriptive of recorded signals, but are agnostic as to whether the signal is biological or not.

[apdavison]

On re-reading the thread, I don't know that we actually disagree. @tgbugs comment from March 14th was that "For most of these biological process is the correct parent class", and that I agree with. Just not all.

So let's use "BiologicalProcess" where it fits, and some other term(s) for cases that don't fit there.

[tgbugs]

Yes, and IIRC everything that is marked as process in the table has an existing GO term.

[apdavison]

For those that don't fit in BiologicalProcess, I'm not happy with "Measurement", which to me implies a single value (with uncertainty) at a single point in time. How about:

• "MeasuredSignalType" for "BOLD signal", "local field potential", "multi-unit activity", "single-unit activity", "cortico-cortical evoked potential"
• "SignalProperty" or "SignalCharacteristic" for "alpha/beta/gamma activity" and "slow oscillation"?

[tgbugs]

In terms of naming MeasuredSignalType is ok in the openMINDS context, the parent class for the ontology would likely need to be thought out a bit more carefully. I wonder if there is a more general term, but we can add it in the future as needed since all the examples we have right now fit MeasuredSignalType.

I don't think SignalProperty is needed because alpha/beta/gamma activity etc. are the same type of thing as local field potential, that is, power in a certain frequency band.

[lzehl]

@apdavison @tgbugs did we come to a conclusion here and formulate a TODO list that someone could tackle?

[tgbugs]

biological process + measured signal type are the two categories, and measured signal type (which includes alpha/beta/gamma) and biological process can both also be put as a study target. @apdavison

[lzehl]

@apdavison are you confirming this approach?

[apdavison]

I can live with this for the v3 release, although I'm still not happy with putting "alpha/beta/gamma activity" and "slow oscillation" in MeasuredSignalType as they say nothing about the source/recording modality of the signal (e.g. you can measure beta activity with an electrode or with voltage-sensitive dye imaging; to me, these would be two different measured signal types. "single/multi-unit activity" are implicitly electrophysiology signals, so I think they're ok).

[lzehl]

@apdavison thanks for the feedback. I understand now better your concern. I actually never thought about it that way and in my head explicitly decoupled technique from signal type (which should have the same characteristic features independent of the technique, e.g. beta, alpha etc have a certain frequency range in which the signals oscillate). Let's keep this discussion point in mind and for now go with the suggested split. We should revisit this if we run into problems with future use cases.

@aeidi89 (if you have time) TODO:

• [x] add new terminology "MeasuredSignalType"
  • add schema file (schemas/measuredSignalType.schema.tpl.json)
• [x] add new terminology "BiologicalProcess"
  • add schema file (schemas/measuredSignalType.schema.tpl.json)
• [ ] add new terms for new terminologies (see above)
  • add instance file of terminology to terminology:
    • instances/terminology/measuredSignalType.jsonld
    • instances/terminology/biologicalProcess.jsonld
  • add instances files for each terminology:
    • instances/measuredSignalType/XXX.jsonld (see above)
    • instances/biologicalProcess/XXX.jsonld (see above)

[UlrikeS91]

This is almost done. We only need to add:

• [ ] instances/terminology/biologicalProcess.jsonld
• [ ] instances/biologicalProcess/XXX.jsonld (see above)

Since all parts related to the controlledTerms-repo are complete and only instances in the instances-repo are missing, I will move this to the instances-repo.