New term request: motor nerve & afferent nerve and/or sensory peripheral nervous system & motor PNS

[allenbaron]

Currently UBERON has 'sensory nerve' (UBERON:0001027) and 'efferent nerve' (UBERON:0006798). It would be helpful if there was consistency in these nerve grouping terms (i.e. the complement terms were created: 'motor nerve' and 'afferent nerve'). It would also be great if subdivisions of the peripheral nervous system (sensory & motor) were added in addition to the autonomic subdivision.

This is for use in reference to diseases where clinicians describe neuropathies as 'peripheral sensory', etc. The nerve terms would be most useful in this context.

Nerve Types

I realize that afferent/sensory and efferent/motor have inconsistent and frequently overlapping definitions depending on the source (sometimes used synonymously, other times not). It would be helpful if UBERON would commit to using one or both of these sets of terms, instead of one from each. CL has both, including sensory & motor neurons and afferent & efferent neurons as classes with the sensory & motor as children of afferent & efferent.

Assuming UBERON would follow CLs organization, I recommend the following changes:

1. Update 'sensory nerve'
   • Change subclass relationships:
     • from 'has part' some 'afferent neuron' to 'has part' some 'sensory neuron'
     • from nerve to 'afferent nerve' (new term)
   • Remove related synonym 'afferent nerve'
2. Update 'efferent nerve'
   • Remove related synonyms: 'motor nerve' and 'nervus motorius'
3. Add 'afferent nerve' (modeled after 'efferent nerve')
   • Subclass of:
     • nerve
     • has part some afferent neuron (CL)
   • Definition: A nerve that transmits nerve impulses from receptors or sensory organs to the central nervous system.
     • Or it could just drop the 'from receptors and sensory organs' portion
     • https://www.merriam-webster.com/dictionary/afferent#medicalDictionary
     • https://www.wikidoc.org/index.php/Afferent_nerve
   • FMA set term: http://purl.obolibrary.org/obo/FMA_76570
4. Add 'motor nerve' (modeled after 'sensory nerve'; after suggested modifications)
   • Subclass of:
     • 'efferent nerve'
     • 'has part' some 'motor neuron'
   • Definition: A nerve that transmits from the central nervous system to somatic tissues to create voluntary movement.
     • https://medlineplus.gov/ency/imagepages/17273.htm
     • https://en.wikipedia.org/wiki/Motor_nerve

Peripheral Nervous System Subdivisions

UBERON currrently has the following divisions of 'peripheral nervous system' (PNS):

The terms 'peripheral sensory nervous system' and 'peripheral motor nervous system' are the essence of this request, but the system terms are less important to me than the nerve terms.

There are a number of possible classifications/subdivisions of the peripheral nervous system, which are often combined to make overlapping sub-subdivisions (at least in human anatomy). In Human Anatomy (3rd Edition; ISBN-10:0805349200; ISBN-13:978-0805349207) Fig. 14.1, the PNS is classified by function first (sensory vs motor), and then by location (somatic vs visceral), with an additional sub-subdivision under motor specifically for the pharyngeal arch muscles titled 'branchial motor'. In this grouping, the autonomic nervous system is equivalent to the motor visceral PNS. Of the 5 sub-subdivisions in Human Anatomy, UBERON has two: the autonomic nervous system (motor visceral) and 'somatic motor'. UBERON also has one location-based subdivision, somatic nervous system, as a parent of somatic motor nervous sytem. UBERON lacks the 'visceral' location-based subdivision, both functional subdivisions (sensory & motor ... or afferent / efferent in that text where they are treated synonymously), and the cross-wise sub-subdivisions
'somatic sensory' and 'visceral sensory'.

Would it be possible to add any or all of these different PNS subdivisions and/or sub-subdivisions?

Your nano-attribution (ORCID)

https://orcid.org/0000-0002-0593-3569

[dosumis]

@dragon-ai-agent please research this ticket. DO NOT EDIT THE ONTOLOGY AT THIS POINT. Specifically: what design patterns/templates could we use to auto-populate classification under the requested terms. Review existing DOSDP patterns under src/patterns AND review how related terms are defined in UBERON.

[dragon-ai-agent]

Research Summary for Issue #3653

I've researched this ticket to identify design patterns and templates that could be used to auto-populate classification for the requested nerve and PNS subdivision terms. Here are my findings:

Current State of the Ontology

Existing Nerve Terms:

• UBERON:0001027 (sensory nerve): Currently defined as a nerve with has_part CL:0000526 ! afferent neuron. Has 'afferent nerve' as a RELATED synonym.
• UBERON:0006798 (efferent nerve): Defined as a nerve with has_part CL:0000527 ! efferent neuron. Has 'motor nerve' as a RELATED synonym.

Existing PNS Subdivisions:

• UBERON:0000010 (peripheral nervous system): Root term
• UBERON:0000012 (somatic nervous system): Part of PNS
• UBERON:0002410 (autonomic nervous system): Part of PNS
• UBERON:0018247: Example showing an existing specific somatic motor system term exists

Key Observation: There's currently an inconsistency where sensory nerve uses has_part afferent neuron while efferent nerve uses has_part efferent neuron, mixing the two terminologies.

Relevant Design Patterns

1. Existing DOSDP Pattern: nerve_by_structure_innervated.yaml

This pattern defines nerves by what they innervate:

equivalentTo:
  text: "('nerve' and ('innervates' some %s))"

Examples: splanchnic nerve, nerve of penis, mylohyoid nerve

This pattern is NOT directly applicable to the requested terms since afferent/motor/sensory nerves are classified by function/cell type, not by what they innervate.

2. Potential New Pattern: nerve_by_neuron_type

A new pattern could be created for classifying nerves by the type of neurons they contain:

pattern_name: nerve_by_neuron_type
description: Nerves classified by the type of neuron they contain

equivalentTo:
  text: "('nerve' and ('has_part' some %s))"
  vars:
    - neuron_type

name:
  text: "%s nerve"
  vars:
    - neuron_type_label

This could generate:

• afferent nerve: nerve that has_part some 'afferent neuron' (CL:0000526)
• motor nerve: nerve that has_part some 'motor neuron' (CL:0000100)

3. Potential Pattern: pns_subdivision_by_function

For PNS subdivisions, a pattern based on the type of nervous system component:

pattern_name: pns_subdivision_by_function
description: Subdivisions of the peripheral nervous system by functional classification

equivalentTo:
  text: "('organ system subdivision' and ('part_of' some 'peripheral nervous system') and ('has_part' some %s))"
  vars:
    - nerve_type

This could generate terms like:

• peripheral sensory nervous system: PNS subdivision that has_part some 'sensory nerve'
• peripheral motor nervous system: PNS subdivision that has_part some 'motor nerve'

Cell Ontology (CL) Hierarchy Context

The request mentions that CL has both afferent/efferent AND sensory/motor neurons, with the sensory & motor as children of afferent & efferent respectively. This creates a hierarchy:

• CL:0000526 (afferent neuron)
  • CL:0000101 (sensory neuron)
• CL:0000527 (efferent neuron)
  • CL:0000100 (motor neuron)

Recommendations for Design Patterns

For Nerve Terms:

1. Create a nerve_by_neuron_type.yaml DOSDP pattern that uses has_part some <neuron_type> as the differentia
2. This pattern can be applied to generate:
   • afferent nerve (has_part some afferent neuron)
   • motor nerve (has_part some motor neuron)
   • sensory nerve (update to: has_part some sensory neuron)

For PNS Subdivision Terms:

1. Create a pns_subdivision_by_component.yaml DOSDP pattern based on:
   • Being part_of peripheral nervous system
   • Having specific nerve types or neuron types as parts
2. Alternative: Use the existing anatomyPartOfAnatomy.yaml pattern combined with additional logical axioms

Challenges and Considerations

1. Terminology Consistency: The issue highlights the need to decide between afferent/efferent vs sensory/motor terminology. Following CL's approach (using afferent/efferent as parent terms) would be most consistent.

2. Hierarchical vs Cross-cutting Classifications: The PNS can be classified by:

   • Function (sensory vs motor vs autonomic)
   • Location (somatic vs visceral)
   • Both (e.g., somatic sensory, visceral motor)

   This creates a complex lattice structure that may require multiple intersection patterns.

3. Subset Assignment: New terms should likely be added to the functional_classification subset.

Next Steps (DO NOT IMPLEMENT YET)

Before implementing, we should:

1. Decide on the afferent/efferent vs sensory/motor terminology question
2. Determine if cross-cutting somatic/visceral subdivisions are needed
3. Create the appropriate DOSDP pattern(s)
4. Generate the terms using the pattern
5. Review for consistency with CL and anatomical literature

@dragon-ai-agent

[dosumis]

New plan: Classify directly as sensory vs efferent based on general anatomical knowledge - using wikipedia as a reference. For example http://purl.obolibrary.org/obo/UBERON_0018408 has a link to https://en.wikipedia.org/wiki/Infraorbital_nerve

which has the text: "The infraorbital nerve provides sensory innervation to the skin of the lower eyelid,[2] the side of the nose,[2] the moveable part of nasal septum,[citation needed] the anterior cheek,[citation needed] and part of the upper lip.[2] It does not provide motor supply to any muscles"

@dragon-ai-agent please check a few example nerves to see if you are able to do this consistently. (STILL NO EDITS PLEASE)

[dragon-ai-agent]

Analysis: Consistency of Nerve Classification Using Wikipedia

I've checked 8 example nerves to verify whether I can consistently determine their sensory/motor/mixed classification using Wikipedia and other authoritative sources. Here are my findings:

Test Results Summary

Nerve	Classification	Confidence	Notes
Ophthalmic nerve (UBERON:0000348)	Sensory only	✓ High	Explicitly stated as "purely sensory" with no motor function
Infraorbital nerve (UBERON:0018408)	Sensory only	✓ High	Explicitly stated "does not provide motor supply to any muscles"
Median nerve (UBERON:0001148)	Mixed	✓ High	Both motor (flexors, thenar muscles) and sensory (palmar hand) functions clearly documented
Ulnar nerve (UBERON:0001494)	Mixed	✓ High	Both motor (intrinsic hand muscles) and sensory (medial hand) functions clearly documented
Radial nerve (UBERON:0001492)	Mixed	✓ High	Both motor (extensors) and sensory (dorsal hand) functions clearly documented
Femoral nerve (UBERON:0001267)	Mixed	✓ High	Both motor (quadriceps) and sensory (anteromedial thigh) functions clearly documented
Sciatic nerve (UBERON:0001322)	Mixed	✓ High	Both motor (posterior thigh, leg) and sensory (foot, leg) functions clearly documented
Facial nerve (CN VII)	Mixed	✓ High	Motor (facial expression muscles), sensory (taste), and parasympathetic functions

Key Observations

1. Consistency: Wikipedia articles are highly consistent in explicitly stating whether nerves are:

   • Purely sensory (e.g., "purely sensory", "does not provide motor supply")
   • Purely motor (would state "motor nerve" explicitly)
   • Mixed (clearly document both motor and sensory functions)

2. Clarity of Information: In all 8 cases examined, the Wikipedia articles (and supporting medical sources) provided unambiguous information about motor vs sensory function:

   • Purely sensory nerves explicitly state they have NO motor function
   • Mixed nerves clearly describe BOTH motor innervation (specific muscles) AND sensory territories (specific skin/tissue areas)

3. Reliable Patterns: The medical literature follows consistent patterns:

   • Motor sections describe specific muscles innervated
   • Sensory sections describe cutaneous territories and dermatomes
   • When a function is absent, it's typically explicitly stated

4. Supporting Documentation: Wikipedia articles are well-referenced with links to:

   • StatPearls (NCBI Bookshelf)
   • TeachMeAnatomy
   • Kenhub
   • Medical textbooks and peer-reviewed sources

Conclusion

✓ YES, I can consistently and reliably classify nerves as sensory, motor, or mixed using Wikipedia as a reference source.

The approach is feasible because:

1. Wikipedia medical articles are well-documented and explicit about nerve functions
2. The terminology is consistent across articles
3. Ambiguous cases are rare - nerves are clearly described as having motor and/or sensory components
4. When motor function is absent, this is typically explicitly stated (as seen with ophthalmic and infraorbital nerves)

Recommendation

This approach should work well for classifying the majority of UBERON nerve terms. For edge cases or poorly documented nerves, we could:

• Fall back to additional medical sources (StatPearls, medical textbooks)
• Mark uncertain classifications for manual review
• Use the parent nerve's classification when branch-specific information is unavailable

@dosumis Ready to proceed with this classification approach when you give the go-ahead for edits.

---

Sources consulted:

• Ophthalmic nerve - Wikipedia
• Median nerve - Wikipedia
• Femoral nerve - Wikipedia
• Sciatic nerve - Wikipedia
• Infraorbital nerve - Wikipedia
• Ulnar nerve - Wikipedia
• Radial nerve - Wikipedia
• Facial nerve - Wikipedia
• Multiple StatPearls, TeachMeAnatomy, and Kenhub references