Fungal Electrophysiology Data Structure Specification (Core)

Scope

This version of the standard addresses only the atomic unit of fungal electrophysiology recordings:

Time-indexed electrical potential measured at a defined electrode pair.

Each channel represents a difference of electrical potential imposed by electrode geometry, not a discrete biological component.

The core specification defines only the physics of measurement. Biological interpretation is explicitly excluded.

Directory Structure (Normative)

dataset_root/
├── dataset_description.json
├── samples.tsv
└── sub-01/
    └── signal/
        ├── sub-01_task-recording_electrodes.tsv
        ├── sub-01_task-recording_signal.json
        └── sub-01_task-recording_signal.tsv.gz

• samples.tsv — Identifies physical recording units (e.g., block, culture, substrate-associated colony).
• sub-* — Neutral sample identifiers.
• signal/ — Directory and file names describe what is measured, not biological context. "Fungal" is already encoded at the standard level (FEDS).

signal.json Metadata Requirements (v0.1)

To ensure the standard survives long-term technical shifts, only metadata required to reconstruct the physical signal from the digital recording is considered Required. All other information is Optional or belongs in Extensions.

Required Fields (Hard-Fail)

Missing any Required field results in validator failure.

Strongly Recommended Fields (Warning)

• RecordingStartTime — ISO 8601 timestamp. Absolute time anchoring is encouraged for alignment with external processes, but legacy datasets using relative time remain valid.

Missing these triggers a validator warning, not failure.

Recommended Fields (Warning)

• PowerLineFrequency — Relevant for environments affected by mains interference; not required for all recording setups
• DeviceSerialNumber
• LowPassFilterCutoff
• HighPassFilterCutoff
• ADCResolution

Missing these triggers a validator warning, not failure.

Optional Fields (Ignorable)

• ElectrodeMaterial
• ElectrodeImpedance
• SoftwareVersion
• RecordingNotes

These fields may be safely ignored by downstream tools.

Validator Logic (Normative)

Required (Error)

If a physicist cannot reconstruct voltage vs time, the field is required.

Optional (Ignore)

If removing the field does not change the waveform shape, it is optional.

Minimal Example (signal.json)

{
  "SamplingFrequency": 1000.0,
  "VoltageUnit": "mV",
  "ChannelCount": 4,
  "RecordingStartTime": "2025-01-15T13:45:00Z",
  "PowerLineFrequency": 60,
  "DeviceSerialNumber": "FUNG-AMP-001"
}

What Is NOT in the Core Specification

• Biological state labels
• Stimulus intent
• Species-specific traits
• Signal interpretation or meaning

These belong exclusively in Extensions.