Add `*_scattering` ExperimentalMethodEnum

[dsclassen]

X-ray (or neutron) diffraction and X-ray (or neutron) scattering are related techniques, but they probe structure at different levels of order. X-ray diffraction refers specifically to the coherent, constructive interference of X-rays scattered by a highly ordered, periodic structure, such as a crystal, producing sharp Bragg peaks that report atomic positions and long-range order. In contrast, X-ray scattering is a broader term that includes both ordered and disordered systems and typically measures how X-rays are deflected over a range of angles to provide information about size, shape, and structural organization. For example, small-angle X-ray scattering (SAXS) is used to study macromolecules, nanoparticles, and other non-crystalline materials in solution, yielding low-resolution structural information without requiring crystallization. Obviously, this all applied to Neutron Diffraction and Neutron scattering too.

Current:

  ExperimentalMethodEnum:
    description: "Experimental methods for structure determination"
    permissible_values:
      x_ray_diffraction:
        description: "X-ray diffraction"
        meaning: CHMO:0000156
      neutron_diffraction:
        description: "Neutron diffraction"
      electron_diffraction:
        description: "Electron diffraction (e.g., microED)"
      fiber_diffraction:
        description: "Fiber diffraction"

Desired:

  ExperimentalMethodEnum:
    description: "Experimental methods for structure determination"
    permissible_values:
      x_ray_diffraction:
        description: "X-ray diffraction"
      x_ray_scattering:
        description: "X-ray scattering"
        meaning: CHMO:0000156
      neutron_diffraction:
        description: "Neutron diffraction"
      neutron_scattering:
        description: "Neutron scattering"
      electron_diffraction:
        description: "Electron diffraction (e.g., microED)"
      fiber_diffraction:
        description: "Fiber diffraction"

I would fix this myself and submit a PR, but I'm not exactly sure which file to edit.

[github-actions]

Summary & Analysis

This is a well-motivated schema enhancement request from @dsclassen. The core distinction is scientifically sound:

• Diffraction = coherent, constructive interference in ordered/periodic structures (crystals) → produces sharp Bragg peaks → atomic-resolution structure
• Scattering = broader term covering both ordered and disordered systems; measures angular deflection to infer size/shape/organization at lower resolution (SAXS/WAXS/SANS)

X-ray diffraction is technically a subclass of X-ray scattering — this relationship has recently been formalized in the PaNET ontology (see PMC12416419, which documents 117 newly inferred subclass relationships including <x-ray diffraction technique> as a subclass of <x-ray scattering technique>).

---

File to Edit

The file to edit is:

src/lambda_ber_schema/schema/lambda_ber_schema.yaml

The ExperimentalMethodEnum is around line 3866.

---

Ontology Mapping Clarification

The proposed desired state in the issue moves CHMO:0000156 from x_ray_diffraction to x_ray_scattering — this appears to be a mistake. According to Ontobee:

CHMO:0000156 label = "X-ray diffraction" (with "X-ray crystallography" as an exact synonym)

So CHMO:0000156 should stay on x_ray_diffraction. The new x_ray_scattering and neutron_scattering values will need their own CHMO mappings — or can be left without meaning: annotations initially.

---

Relationship to TechniqueEnum

This schema already has a TechniqueEnum with fine-grained scattering techniques (added in #50):

Technique	CHMO	PaNET
saxs	CHMO:0000204	PaNET:01188
waxs	CHMO:0000207	PaNET:01191
sans	CHMO:0000184	PaNET:01189

The ExperimentalMethodEnum appears to serve as a higher-level categorization on ExperimentRun.experimental_method, distinct from ExperimentRun.technique. Adding x_ray_scattering and neutron_scattering as coarse-grained method categories here makes sense to complement the existing x_ray_diffraction / neutron_diffraction entries.

---

Suggested Change

  ExperimentalMethodEnum:
    description: "Experimental methods for structure determination"
    permissible_values:
      x_ray_diffraction:
        description: "X-ray diffraction"
        meaning: CHMO:0000156  # keep here - this IS x-ray diffraction
      x_ray_scattering:
        description: "X-ray scattering (e.g., SAXS, WAXS)"
        # CHMO parent term for x-ray scattering TBD; PaNET has no single top-level term
      neutron_diffraction:
        description: "Neutron diffraction"
      neutron_scattering:
        description: "Neutron scattering (e.g., SANS)"
        # CHMO:0000184 is SANS specifically; a parent CHMO term for neutron scattering TBD
      electron_diffraction:
        description: "Electron diffraction (e.g., microED)"
      fiber_diffraction:
        description: "Fiber diffraction"

It may also be worth considering adding electron_scattering for completeness (e.g., for electron energy loss spectroscopy or similar disordered-system electron-based methods), though this is lower priority for the structural biology context here.

---

Related Issues

• Align TechniqueEnum with PaNET ontology for photon/neutron techniques #50 (closed): Added PaNET mappings to TechniqueEnum for SAXS, WAXS, SANS, XAS variants — provides the precedent for ontology term annotation in this schema
• Technique or instrument as higher level? Same instrument can do SPA, Tomography, microED with different metadata/workflows #34 (open): Technique vs. instrument as higher-level organizer — relevant to how ExperimentalMethodEnum vs TechniqueEnum should relate

@dragon-ai-agent please implement the suggested change above (keeping CHMO:0000156 on x_ray_diffraction, adding x_ray_scattering and neutron_scattering without CHMO meanings for now), update any relevant test examples, and submit a PR.

[dsclassen]

What black magic is all that 👆 ? Crazy agentic GitHub bot thingee... I guess it will just apply the suggested fix automagically? and create PR?