NTR: perturbation

[beckyjackson]

• Parent: 'planned process'
• Definition: A planned process that disrupts the function of a biological system through external or internal means. [doi:10.1007/978-1-4419-9863-7]
• Other (potential) axioms:
  • 'has participant' some 'perturbation device'
  • realizes some 'perturb function'

For ECO mappings, we need the actual process of perturbation to apply as the independent variable of an assay. If this isn't desired in OBI, we can always just use something like 'planned process' and (realizes some 'perturb function'), though that's a bit messier.

[bpeters42]

How is this related to 'study intervention'? I suspect it is quite similar? Can we see some examples?

On Fri, Nov 22, 2019 at 10:40 AM Becky Jackson [email protected] wrote:

• Parent: 'planned process'
• Definition: A planned process that disrupts the function of a biological system through external or internal means. [doi:10.1007/978-1-4419-9863-7]
• Other (potential) axioms:
  • 'has participant' some 'perturbation device'
  • realizes some 'perturb function'

For ECO mappings, we need the actual process of perturbation to apply as the independent variable of an assay. If this isn't desired in OBI, we can always just use something like 'planned process' and (realizes some 'perturb function'), though that's a bit messier.

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[beckyjackson]

Here are some ECO terms that it would be used for:

• anatomical perturbation evidence
  • A type of experimental phenotypic evidence resulting from the disruption of a structural feature.
• environmental perturbation phenotypic evidence
  • A type of experimental phenotypic evidence resulting from modification to the surroundings or conditions in which an organism lives or operates.

The anatomy or environment of an organism is disrupted by the perturbation, which theoretically results in changes to the biological system(s).

the part of the execution of an intervention design study which is varied between two or more subjects in the study

I would suspect that any assay involving a perturbation has a control subject, so the 'study intervention' could perhaps be the parent instead...?

[bpeters42]

We have "in vivo intervention experiment"

http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0001980

Which already pointed out that we have an issue with the border of 'assay' and 'study'. This requires some thought and discussion. Some thoughts:

• a perturbation (or intervention) is associated with a physical act (mostly), which remains the same regardless if we consider it a 'study intervention' or a variable in an experiment.
• distinctions between assay/experiment vs. study are inherent to the overall plan of an investigation, not in the perturbation itself
• OBI should cover catalogs of 'planned interventions/perturbations'
• many of these perturbations can also occur naturally. Some planned perturbations mimic such natural occurrences. Such as exposure to a pathogen.

Stopping here. My strawman proposal would be to subtype "in vivo intervention experiment" with the types of interventions (anatomical perturbation experiment etc.), to give Rebecca/ECO something quick to reference. And catalog the types of intervenetions done (anatomical perturbation, environmental perturbation etc) in a neutral setting (=not under planned processes) so that we can refer to them as part of an investigation and as part of a life course.

On Fri, Nov 22, 2019 at 7:52 AM Becky Jackson [email protected] wrote:

Here are some ECO terms that it would be used for:

• anatomical perturbation evidence
  • A type of experimental phenotypic evidence resulting from the disruption of a structural feature.
• environmental perturbation phenotypic evidence
  • A type of experimental phenotypic evidence resulting from modification to the surroundings or conditions in which an organism lives or operates.

The anatomy or environment of an organism is disrupted by the perturbation, which theoretically results in changes to the biological system(s).

the part of the execution of an intervention design study which is varied between two or more subjects in the study

I would suspect that any assay involving a perturbation has a control subject, so the 'study intervention' could perhaps be the parent instead...?

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-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[beckyjackson]

Proposal to follow suggestion above and create specific types of perturbation experiments under "in vivo intervention experiment" -> e.g., "in vivo anatomical perturbation experiment", "environmental perturbation experiment"...

I will move forward with these experiment terms.

We need to spend more time discussing the actual perturbation process that is applied in these experiments. @rvita - Process of transferring T cells/antibodies (adoptive transfer experiments) falls under this discussion as well.

[beckyjackson]

@mgiglio99 - it doesn't look like @nsuvarnaiari has permissions for the OBI repo so I've assigned this issue to you for now.

[jamesaoverton]

I just invited @nsuvarnaiari to the OBI Developer team on GitHub.

[mgiglio99]

Discussed on May 13, 2024 call - decided to keep things simple and not make the granular terms. ECO can just use 'in vivo intervention experiment'