Sub-branch review: Stress related behavior #123
Comments
Hopefully final version before open review process.
|
I've started reviewing these, and the first three seem to be based on physiology rather than behavior. In particular, stress related behavior seems to be defined in terms of mechanism (allostatic overload). The next two are defined in terms of the general adaptation syndrome model. If defining this in terms of mechanism is the best way to do so, then I'm fine, but maybe we need a physiology ontology (or GO additions?) to handle these. The term id for agonistic alarm indicates it came from the ABO, and it does have a definition there: "Behavior signaling awareness of and or fear of danger, triggered by agonistic actions or postures of a conspecific rather than a predator." I don't have a source for that, maybe @aclark-binghamton-edu, who worked with a collaborator to develop the ABO definitions from established reference sources could find it. I'll keep looking through these. I do appreciate your effort in proposing these definitions, I think the role of physiology and its relation to behavior, in particular in NBO, is something worth working through. |
|
I appreciate your reviewing these. But fundamentally, I'm asking if my labelling and defining method is valid; these are more like pedantic examples: we may never want to go through with these exact redefinitions. My main effort is currently going into producing a theoretically sound behaviour model with the prospect of totally rebooting the NBO - look out for that soon hopefully. Then if that won't float, I'd come back in earnest to the sub-branch reviews like the stress one above. The physiology question is exactly the kind of observation I'm most looking for though:
|
|
The labeling and defining method looks good to me, it's certainly an improvement over the haphazard state of things. This and the other issues have convinced me to review the pages and blog posts you linked, both for NBO and what I have been doing with the spiders. I will wait to see what you come up with in a behavior model. You might want to look at ABO as well - it's an ontology a group of animal behaviorists developed about 15 years ago, there's a copy in this project. |
Will do - thanks. |
|
To enter this conversation as one of the animal behaviorists/behavioral
ecologists who developed the ABO and then worked on the merger--and forgive
me if some of what I say below is obvious:
Definitions in NBO were often missing when we were merging the two
ontologies and I did write many, where clear and appropriate, to follow ABO
definitions; every ABO term had a definition. However, before ABO was
merged into NBO, I reformatted ABO definitions or modified ABO terms (e.g.
noun form vs verb or gerund form) to follow the patterns set up by NBO.
That is where the "Behavior of..." or "xxx Behavior" comes from. In NBO,
a behavior that ABO termed "sucking" was termed in NBO "sucking behavior".
Furthermore, where ABO had, e.g. "urinate", NBO 's possible equivalent was
"Behavioral Control of urination".
I still have my spreadsheets showing equivalencies or assumed equivalencies
of terms, as well as definitions for ABO terms (and thus for equivalent NBO
terms). Reasoning across the two hierarchies was sometimes difficult
because parent-child relationships were often different. There were many
terms in NBO that did not apply to ABO, which emphasized normal or
ecologically relevant behaviors. It attempted to describe what was
observable visually or auditorily (e.g. for vocalizations). It also left
out aspects that could be added as a modifier for a particular study or
context: quality or strength of behavior, by male vs female, etc. And of
course, it had to stop at a fairly high level of description to accommodate
many different species.
An ontology emphasizing the ABO goals would be most welcome. I am using
the ABO as represented in its pre-merger form to organize my American Crow
Ethogram; this is being used and will be made further available to those
working with other crow species.
…On Mon, Jan 16, 2023 at 3:31 PM Ditch Townsend ***@***.***> wrote:
You might want to look at ABO as well - it's an ontology a group of animal
behaviorists developed about 15 years ago, there's a copy in this project.
Will do - thanks.
—
Reply to this email directly, view it on GitHub
<#123 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ADUXTFQSPHMHQ3SN53XBJATWSWVZVANCNFSM6AAAAAATUAV5BE>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
--
Anne B. Clark, Ph.D.
Biological Sciences
Binghamton University
Binghamton, NY 13902-6000
(607) 222-0905 (cell)
(607) 777-6521 (fax-Dept office)
(607) 777-2438 (Biol Sci office)
|
|
Thanks Anne. I need to get into the ABO stuff in detail, but I am certainly leaning in your direction by the sound of it. |
We absolutely need to keep behaviour in here. Stress is a physiological state that triggers many non-behavioural processes, the behavioural term is for behaviours in response to stress. The proposed definition makes it indistinguishable from the GO term you xref when it should be a subclass. IIRC, ABO maintained a clean division between observed behaviour and functional/causal interpretation. We should still support this - after all, interpretation of function/cause may change with no change to the observation. In merging with NBO, we allowed for behavioural classes that included cause/function. These should be considered OWL compound classes with behaviour as the genus and slots for cause/function. When we merged in NBO, we discussed formalising such patterns, but in the absence of funding/resources, this never happened. |
|
Really helpful, although I don't understand xrefs technically. My knowledge of OWL is also near zero: doubtless, "OWL compound classes with... slots..." is what I would suggest if I knew it was what I meant (and don't worry, I really am not being sarcastic). For the forseeable future, I see my time and motivation as a key resource for NBO and I hope you can help me, alongside Nico, to do what I can technically. But I certainly agree that the ABO is a good direction to look in. |
|
I'd forgotten that we have a partial write-up of the workshop where we decided to merge ABO and NBO. This outlines the approach pretty well I think. https://docs.google.com/document/d/1eSCjQfR5BujtUYw4W2pYOL6rhPPMycJd8u95X1-5U7Q/edit# Apologies for not sharing earlier. Unfortunately I think this clashes with many of your suggestions. e.g.
I don't think we can avoid appending 'behaviour' in the case of general grouping classes - function/cause + behaviour. I also think we need to step back a bit an detail use cases for NBO before we attempt anything radical. This is particularly important when it comes to assertions of redundancy. Apparently redundant terms may not really be redundant when we look at use cases. Use case 1: Ethology - ABO approachObservations need to be recorded separately from interpretations (cause/function). I think that the best way to do this is with separate terms for function/cause (as ABO). This may also be appropriate for observational work on model organisms (e.g. home cage experiments in mice or FlyBowl in Drosophila) Use case 2: Behavioural studies of model organisms centred on behavioural testing paradigms.Here we mostly want to use phenotype terms, but need a behaviour ontology to defined phenotypes. A mix of observational behavioural classes and those combined with some function is needed for non-controversial, well studied paradigms. e.g. Drosophila biologists would expect to see the dipteran jump response classified as an escape response. The compound term approach in the above doc supports this. There are some tricky boundary problems around mental events & processes vs behaviour (e.g. learning and memory). NBO glosses these, which may be fine given that we need these classes and upper ontology fussiness is likely to get in the way of supporting this use case. Use case 3: Clinical use casesLots more expert input is needed here. We need to support classes for behaviours caused by internal mental state or external stimulus (needed for other animals too - just much more so here). e.g. - maybe we need to broaden, not narrow the definition here so that it more explicitly covers cases where the stimulus is internal (maybe it does already cover this in an triggering stimulus may be a mental state):
Suggestion: We collect use-cases, with examples, in the README of this repo and use these to assess proposed changes. |
|
Thanks. I think I understand the term 'use case' but can you give me some examples and where to find them, so I don't get the wrong end of the stick? I suspect 'we' means 'me'. |
Sorry - it was right in front of me and I didn't notice (Use case 1, Use case 2, Use case 3)! |
|
Method
With reference to the principles and guidelines named in issue #122, I have reviewed the 17 subclasses in the stress related behavior sub-branch of the behavior process branch of NBO. I do not propose to go into such detailed explanations in any future sub-branches, but this is an opportunity to demonstrate my method.
Apologies
I have made changes to a fork in my repository using Protege for a pull request in due course, and look forward to modifying it on the basis of discussions here. This is my first time doing all this, so apologies in advance for doing it wrong or appearing to criticise anyone with the changes I have suggested.
Analysis
I have split my notes up into a task list below, in case they need to be broken down into individual issues.
NBO Style and Conventions
For general discussions about NBO style and conventions which refer to the S1 bullet below (i.e. not specific to a stress related class definition), I am copying it into issue #122 and suggest continuing it there.
NBO:0000469
stress related behavior
ORIGINAL (definition): "G1aBehavior related toG6.1a how the bodyG5.1a reacts to a stressorG7a (a stimulusG3.1.2a that causes stressG7b),G6.2a real or imagined."G5.1b,P6a,S1a,S11a [wikipedia: Stress_(biological)]G2a,G2b
PROPOSED (definition): A processG2c,S3.1.1a thatP6a responds toG3.1.3a allostatic overload.G5a,G6.1a,G7c
NBO:0000470
behavioral alarm
ORIGINAL (definition): "G1aBehavior related to the identification or realizationG3.1.3b of a threatG6.1b or a stressor."G3.1a,P6a,S11a [wikipedia: Stress_(biological)]G2a,G2b
PROPOSED (definition): A response to allostatic overloadG2c,G3.1b,G3.1.1a thatP6a manages the first stageG9.2a of adaptation.G9a,S5a
NBO:0000088
acute stress response
ORIGINAL (definition): "G1aBehavior related toG6.1a the preparation of the body to "fight" or "flee" from perceivedG1.1a attack, harm or threat."G3.1a,P6a,S11a [NBO:GVG]
PROPOSED (definition): The second phase of the first stageS9.4a of adaptationG2c,G3.1b,G3.1.1a that activates the sympathetic nervous system.S5a
NBO:0000471
predator avoidance behavior
ORIGINAL (definition): NoneP6b
PROPOSED (definition): NAG6a
NBO:0020145
agonistic alarm
ORIGINAL (definition): Alarm behavior triggered by agonistic actions or postures.G1.1b, G5b
PROPOSED (definition): NAG6c
NBO:0000472
behavioral exhaustion
ORIGINAL (definition): "G1aBehavior related toG6.1a the depletion of the bodyG5.1a resources for coping toG11.1a stress."G3.1a,P6a,S11a [NBO:GVG]
PROPOSED (definition): One of two pathways through the third stage of adaptation,G2c that decompensates from normal function.S5a
NBO:0000103
coping behavior
ORIGINAL (definition): "G1aBehavioral response to the presidencyG1b of the stressor where it becomes necessary to attempt some means of coping with the stress."G3.1a,G5.1b,P6a,S11a [NBO:GVG]
PROPOSED (definition): A response to allostatic overloadG2c,G3.1b,G3.1.1a thatP6a attempts to compensate in the second stageG9.2b of adaptation.G9a,S5a
NBO:0000018
ORIGINAL (label): fear/anxiety related behaviorP12a
PROPOSED (label): threatened behaviorP12b
ORIGINAL (definition): "G1aEmotional behavior related to fear or anxiety."G3.1a [NBO:GVG]
PROPOSED (definition): A response to allostatic overload,G2c,G3.1b,G3.1.1a thatP6a is social and emotional.G9a,S5a
NBO:0000092
anxiety-related behavior
ORIGINAL (definition): "G1aAn emotional behavior related toG6.1a a feeling of uneasiness orG3.1.3b nervousness triggered by an identifiable triggeringG7d stimulus."G2h,G3.1a,G5c,P6a,S11a [NBO:GVG]
PROPOSED (definition): An emotional responseG2c,G3.1b,G3.1.1a thatP6a is triggered by an imagined future danger.S5a
NBO:0000091
fear-related behavior
ORIGINAL (definition): "G1aAn emotional behavior related toG6.1a a feeling of uneasiness orG3.1.3b nervousness triggered by a specified triggeringG7d stimulus such as pain or the threat of danger."G2h,G3.1a,G5c,G9.2c,P6a,S11a [NBO:GVG]
PROPOSED (definition): An emotional responseG2c,G3.1b,G3.1.1a thatP6a is triggered by a real present danger.S5a
NBO:0000095
fear behavior towards living things
ORIGINAL (definition): "G1aAn emotional behavior related toG6.1a a feeling of uneasiness orG3.1.3b nervousness in respect to a living thing."G3.1a,G5d [NBO:GVG]
PROPOSED (definition): NAG5d
OR
PROPOSED (definition): A triggered responseG2c,G3.1b,G3.1.1a thatP6a is about an animate danger.S5a
NBO:0000093
fear behavior towards objects
ORIGINAL (definition): "G1aAn emotional behavior related toG6.1a a feeling of uneasiness orG3.1.3b nervousness in respect to an object."G3.1a,G5d [NBO:GVG]
PROPOSED (definition): NAG5d
OR
PROPOSED (definition): A triggered responseG2c,G3.1b,G3.1.1a thatP6a is about an inanimate danger.S5a
NBO:0000094
fear behavior towards situation/environmentP12c
ORIGINAL (definition): "G1aAn emotional behavior related toG6.1a a feeling of uneasiness orG3.1.3b nervousness in respect to a particular situation or environment."G3.1a,G5d [NBO:GVG]
PROPOSED (definition): NAG5d
OR
PROPOSED (definition): A triggered responseG2c,G3.1b,G3.1.1a thatP6a is about an environmental danger.S5a
NBO:0000096
agoraphobia behaviorP12c
ORIGINAL (definition): "G1aA phobia characterised by fear of open spaces."G2j,G3.1a,G6.2a [NBO:GVG]
PROPOSED (definition): NAG2j
NBO:0002569
ORIGINAL (label): stress-induced hypothermiaG11.1b
PROPOSED (label): stress-induced hyperthermiaG11.1b
ORIGINAL (definition): "G1aIncrease in core body termperature in response to stress or anticipatory anxiety."G3.1.3c, Xb [NBOC:GVG]
PROPOSED (definition): Core temperature change that is hotter.G6e
NBO:0040004
ORIGINAL (label): surface breathingG6.1c
PROPOSED (label): aquatic surface respirationG6.1c, G6.2b
ORIGINAL (definition): A behavior involving an organismG5.1a (especially fish or tadpoles)G9.2c breathing at orG3.1.3b near the surface of water where the concentration of dissolved oxygen is highest.G2c,G5.1b,G6.1c,P6a [NBO:EJS]
PROPOSED (definition): Increased oxygenation that comes from surface water.G6.1c
NBO:0000102
fear-related retropulsion
ORIGINAL (definition): "G1aMoving backwards in response to a fear stimulus."G5e [NBO:GVG]
PROPOSED (definition): NAG5e
The text was updated successfully, but these errors were encountered: