NTR: recoil (branch)

[DitchingIt]

I would be pleased to have access to a number of new movement qualities related to a behaviour ontology. As well as the branch class, I need two subclasses each with their own three subclasses (9 classes in total). A single source is proposed for defining all terms, so I am putting all terms into this one Issue.

BRANCH

1. Label: recoil

• Parent: movement quality PATO:0001906
• Definition: Destabilizing force generated by the inherent characteristics of a given mode of propulsion.
• Source (interpolated): doi:10.1242/jeb.204.8.1459

SUB-BRANCH A

2. Label: rotation

• Parent: recoil
• Definition: Rotatory movements about an axis that passes through the center of mass.
• Source (copied): doi:10.1242/jeb.204.8.1459

SUB-SUB-BRANCH A1

3. Label: pitch

• Parent: rotation
• Definition: Rotatory movements about the center of mass in the transverse plane.
• Source (interpolated): doi:10.1242/jeb.204.8.1459
• Property: has_part transverse plane BSPO:0000018

SUB-SUB-BRANCH A2

3. Label: roll

• Parent: rotation
• Definition: Rotatory movements about the center of mass in the sagittal plane.
• Source (interpolated): doi:10.1242/jeb.204.8.1459
• Property: has_part sagittal plane BSPO:0000417

SUB-SUB-BRANCH A3

4. Label: yaw

• Parent: rotation
• Definition: Rotatory movements about the center of mass in the horizontal plane.
• Source (interpolated): doi:10.1242/jeb.204.8.1459
• Property: has_part horizontal plane BSPO:0000019

SUB-BRANCH B

2. Label: translational recoil (NB: the term 'translation' is already used in PATO with a different meaning)

• Parent: recoil
• Definition: Deviation in a plane containing the center of mass.
• Source (copied): doi:10.1242/jeb.204.8.1459

SUB-SUB-BRANCH B1

3. Label: heave

• Parent: translational recoil
• Definition: Vertical deviation of the center of mass.
• Source (interpolated): doi:10.1242/jeb.204.8.1459

SUB-SUB-BRANCH B2

3. Label: slip

• Parent: translational recoil
• Definition: Lateral deviation of the center of mass.
• Source (interpolated): doi:10.1242/jeb.204.8.1459

SUB-SUB-BRANCH B3

3. Label: surge

• Parent: translational recoil
• Definition: Antero-posterior deviation of the center of mass.
• Source (interpolated): doi:10.1242/jeb.204.8.1459

[Clare72]

I think some of these labels should be much more specific - maybe include the parent labels in the child labels and/or make labels reflect the movement type and direction. I think 'heave', 'slip' and 'surge' are particularly unhelpful in conveying the term meanings given that not everyone searching PATO will be experts in movement types.

Recoil is defined as a force, everything below it is defined as a movement

Are these intended to be characteristics of organism movements? - if not, 'sagittal plane' maybe doesn't make much sense, if so, this should be in the definitions (and maybe put them under PATO:0002076 'movement behavioural quality')?

[DitchingIt]

Thanks for the rapid review @Clare72 . These are indeed intended to be characteristics of organism movements and I appreciate the pointer to PATO:0002076 'movement behavioural quality'. I have attempted to rewrite my efforts incorporating all your suggestions, but I may not have fully understood you; please do edit them if you want. I would also appreciate direct editing by anyone who understands the concepts better. (I am trying to get them into PATO so I can use them, not because I am an expert in them per se.)

Sorry about the numbering by the way, but it seemed to slip after hitting the comment button - it looked fine (1-9) on the preview. I am not expert in using markup. I hope I have solved it below:

BRANCH

1 Label: motion recoil

• Parent: movement behavioral quality PATO:0002076
• Definition: A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting a destabilizing motion caused by the reaction from its particular fluid medium, caused by the inherent characteristics of its particular mode of propulsion.
• Source (interpolated): doi:10.1242/jeb.204.8.1459

SUB-BRANCH A

2 Label: rotational recoil motion

• Parent: motion recoil
• Definition: A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting destabilizing rotatory movements about an axis that passes through its center of mass, as it uses its own propulsion to move through, or resist surrounding flow from, its fluid medium.
• Source (partially copied): doi:10.1242/jeb.204.8.1459

SUB-SUB-BRANCH A1

3 Label: pitching rotation

• Parent: rotational recoil motion
• Definition: A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting upwards or downwards rotary movements, about its center of mass.
• Source (interpolated): doi:10.1242/jeb.204.8.1459
• Property: has_part transverse plane BSPO:0000018

SUB-SUB-BRANCH A2

4 Label: rolling rotation

• Parent: rotational recoil motion
• Definition: A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting corkscrewing rotatory movements around its long axis, about its center of mass.
• Source (interpolated): doi:10.1242/jeb.204.8.1459
• Property: has_part sagittal plane BSPO:0000417

SUB-SUB-BRANCH A3

5 Label: yawing rotation

• Parent: rotational recoil motion
• Definition: A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting 'spinning top' rotatory movements around a vertical axis, about its center of mass.
• Source (interpolated): doi:10.1242/jeb.204.8.1459
• Property: has_part horizontal plane BSPO:0000019

SUB-BRANCH B

6 Label: pushback recoil motion

• Parent: motion recoil
• Definition: A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting a deviational translation along a plane containing its center of mass, as it uses its own propulsion to move through, or resist surrounding flow from, its fluid medium.
• Source (partially copied): doi:10.1242/jeb.204.8.1459

SUB-SUB-BRANCH B1

7 Label: heaving pushback

• Parent: pushback recoil motion
• Definition: A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting up or down (vertical) pushback of its center of mass, without necessarily losing its orientation, as it uses its own propulsion to move through, or resist surrounding flow from, its fluid medium.
• Source (interpolated): doi:10.1242/jeb.204.8.1459

SUB-SUB-BRANCH B2

8 Label: slipping pushback

• Parent: pushback recoil motion
• Definition: A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting sideslip (lateral) pushback of its center of mass, without necessarily losing its orientation, as it uses its own propulsion to move through, or resist surrounding flow from, its fluid medium.
• Source (interpolated): doi:10.1242/jeb.204.8.1459

SUB-SUB-BRANCH B3

9 Label: surging pushback

• Parent: pushback recoil motion
• Definition: A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting boosting or checking (antero-posterior) pushback of its center of mass, without necessarily losing its orientation, as it uses its own propulsion to move through, or resist surrounding flow from, its fluid medium.
• Source (interpolated): doi:10.1242/jeb.204.8.1459

[Clare72]

I think these labels are better and good to have everything defined as 'behavioural quality'.

Definitions sound quite fish-specific (I know that comes from your source article), however I am not an expert in animal movement types and I am not sure of the right way to generalise them.

[DitchingIt]

Thanks.

• I have tried to ensure the language includes aerial environments.
• It is still the fluid layer above a hard surface that will have the key impact on runners (like the American coackroach which can experience enough pitch from air resistance at high speed to allow it to run on its rear pair of legs only), or punters (like wilderbeest crossing a river by pushing off along the bottom, which can slip downstream if the flow is strong, into the crocodiles).
• Interfacing environments like a water-strider rowing, or Portuguese man-o-war sailing along, are still facing fluid issues, just across a viscidity layer.
• I don't think we need to cater for hard surface disruptions; tripping, slipping, surface collapse, burrowing, and side-winding can be dealt with elsewhere.

[matentzn]

Thanks @DitchingIt, and thanks @Clare72 for the earlier review. Before we get into wording, I want to step back to the question of fit.

The reusable core of your request is the six rigid-body degrees of freedom (pitch/roll/yaw for rotation, heave/slip/surge for translation). Those are generic and a plausible fit for PATO.

But the terms as proposed aren't those primitives: every definition bakes in some causal story ("destabilizing motion caused by the reaction from its fluid medium, caused by the inherent characteristics of its mode of propulsion").

That ties them to one paper and one scenario, which is what an application or behaviour ontology is for, not the broadly reusable qualities PATO is built around. The fact that the whole branch hangs on a single source points the same way.

So my suggestion is to split this:

• Propose the generic degrees of freedom to PATO (or check whether movement qualities for them already exist), defined simply: pitch as rotation about the transverse axis, etc., with no fluid medium or propulsion in the definition.
• Build the "recoil" layer (the fluid-medium destabilization framing) in your behaviour ontology, importing the PATO terms.

Two concrete modeling points:

• has_part <plane> isn't right: a rotation isn't composed of a plane, it's about an axis (and occurs in a plane). The current assignments are also crossed, e.g. pitch is rotation about the transverse axis with motion in the sagittal plane, not the transverse plane. If you want the spatial reference, point at the BSPO axis with an appropriate relation rather than has_part a plane.
• Drop the causal mechanism from the definitions. PATO definitions are genus plus a simple differentia; the "why it happens" belongs in the issue or the source, not the logical definition.

What do you think?

[DitchingIt]

I have attempted a simple, generic reformulation for definitions, with the original labels, and only the six core terms.

I have reverted to movement quality PATO:0001906 here because of the generic nature of the terminology, but I agree with @Clare72 that fluid-related recoil has a movement behavioral quality about it.

Aside from the note below for 'pitch', I couldn't find similar terms with similar meanings via OLS.

On Bioportal, NASA's SLSO lists the Spatial Orientations of Pitch, Roll, and Yaw (e.g. A Spatial Orientation of an Object relative to its Pitch Axis) as well as their three rotational axes. Assuming SLSO is not an importable ontology for OBO, it is still worth noting that their rotational axis definitions reference the center of mass, and I have brought those forward below from the first and second iterations attempted previously.

I don't know which relation would be most appropriate for PATO and have left question marks for someone else to suggest. Maybe they are not even needed? They are also specifically anatomical and might not be generic enough for more engineering-type uses, such as aircraft or boats, if our objective is to be maximally generic. If SLSO (above) is suitable, it would provide more generic axes.

1 Label: pitch

• Parent: movement quality PATO:0001906
• Definition: Rotation about the transverse axis through the center of mass.
• Property: ?? BSPO:0000017 left-right axis

NB: NCIT:C48442 Pitch (The degree of deviation from a horizontal plane) may be a broad synonym rather than equivalent, since it appears that it could include roll too. (I think it should say The degree of vertical deviation from a horizontal plane to be equivalent: rolling would then be The degree of lateral deviation from a horizontal plane.)

2 Label: roll

• Parent: movement quality PATO:0001906
• Definition: Rotation about the longitudinal axis through the center of mass.
• Property: ?? BSPO:0000013 anterior-posterior axis

3 Label: yaw

• Parent: movement quality PATO:0001906
• Definition: Rotation about the vertical axis through the center of mass.
• Property: ?? BSPO:0000016 dorsal-ventral axis

4 Label: heave

• Parent: movement quality PATO:0001906
• Definition: Translation along the vertical axis.
• Property: ?? BSPO:0000016 dorsal-ventral axis

5 Label: slip

• Parent: movement quality PATO:0001906
• Definition: Translation along the transverse axis.
• Property: ?? BSPO:0000017 left-right axis

6 Label: surge

• Parent: movement quality PATO:0001906
• Definition: Translation along the longitudinal axis.
• Property: ?? BSPO:0000013 anterior-posterior axis

[Clare72]

I do not have a strong opinion about 'movement behavioral quality' vs 'movement quality', but I agree that these should be broadly applicable and not tied to a particular organism/environment - looking better now.
I still think these names are not specific enough and would personally prefer things like 'slip translational movement quality' to just 'slip'. Others may disagree.

[matentzn]

I still think these names are not specific enough and would personally prefer things like 'slip translational movement quality' to just 'slip'. Others may disagree.

@DitchingIt I have to agree with Clare on this one. PATO is not just a terminology, and as an ontology precise names beat "nice" ones. So you would:

1. Add a precise name
2. Add the "nice" name as an exact synonym

Two things to consider:

1. We are widely moving away from the notion of "quality" to "characteristic". Not sure what that means for naming yet. (slip (movement characteristic) or simply slip movement characteristic?) - inputs welcome
2. Your definitions do not follow the genus differentia patterns, which is very important.

[DitchingIt]

Thanks @Clare72 @matentzn for the further input. Iteration 4 offered below.

I am guessing, because it has not been addressed, that there are no strong opinions about relations, so I have removed them (check above if you want to see what the question was).

1 Label: pitching rotational movement characteristic

• Parent: movement quality PATO:0001906
• Synonym: pitch
• Definition: A movement characteristic that involves rotation about the transverse axis, through the center of mass.
• Broad match: NCIT:C48442 Pitch

2 Label: rolling rotational movement characteristic

• Parent: movement quality PATO:0001906
• Synonym: roll
• Definition: A movement characteristic that involves rotation about the longitudinal axis, through the center of mass.

3 Label: yawing rotational movement characteristic

• Parent: movement quality PATO:0001906
• Synonym: yaw
• Definition: A movement characteristic that involves rotation about the vertical axis, through the center of mass.

4 Label: heaving translational movement characteristic

• Parent: movement quality PATO:0001906
• Synonym: heave
• Definition: A movement characteristic that involves translation along the vertical axis.

5 Label: slipping translational movement characteristic

• Parent: movement quality PATO:0001906
• Synonym: slip
• Definition: A movement characteristic that involves translation along the transverse axis.

6 Label: surging translational movement characteristic

• Parent: movement quality PATO:0001906
• Synonym: surge
• Definition: A movement characteristic that involves translation along the longitudinal axis.