Add definitions to electrophysiology terms based on Petilla Convention

[Copilot]

Added definitions to 14 electrophysiology spiking phenotype terms (PATO:0070045-0070059) that were previously undefined in the ontology. All definitions cite PMID:20445542 (Petilla Convention, Ascoli et al. 2008).

Changes

• General phenotypes: Added definitions for spiking phenotype, fast spiking phenotype, regular spiking non pyramidal phenotype, accommodating spiking phenotype, and non-accommodating spiking phenotype

• Initial response phenotypes (first 100-300ms of stimulus): Defined initial spiking phenotype and its three subtypes:

  • initial burst spiking phenotype (b) - burst of ≥2 spikes at short intervals at onset
  • initial classical spiking phenotype (c) - single spike at onset
  • initial delayed spiking phenotype (d) - delayed first spike

• Sustained response phenotypes (after initial phase): Defined sustained spiking phenotype and its four subtypes:

  • sustained accommodating phenotype (ac) - progressive increase in interspike intervals
  • sustained non accommodating phenotype (nac) - constant interspike intervals
  • sustained irregular phenotype (ir) - variable, unpredictable intervals
  • sustained stuttering phenotype (stut) - alternating bursts and silence

All definitions follow existing PATO ontology conventions and maintain proper parent-child relationships in the class hierarchy.

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Original prompt

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This section details on the original issue you should resolve

<issue_title>Add NLX electrophys terms to PATO</issue_title>
<issue_description>@tgbugs creating this ticket to keep track of this.
Happy to add them myself if you can point me to the terms, if not happy for you to create tickets and I'll add them too.
Thanks</issue_description>

<agent_instructions>Please add definitions to terms added in response to this ticket on this branch / PR https://github.com/pato-ontology/pato/tree/Electrophys-Properties #463 . Definitions must be based on the text of https://pmc.ncbi.nlm.nih.gov/articles/PMC2868386/ - please check any supplementary material for additional relevant info.

</agent_instructions>

Comments on the Issue (you are @copilot in this section)

@tgbugs https://github.com/SciCrunch/NIF-Ontology/blob/78f17596d18bd3f1139ea33bbb6b112c97f8162f/ttl/phenotypes.ttl#L303

I think you want the subclasses of ilxtr:ElectrophysiologicalPhenotype. They mostly cover the petilla nomenclature or a blue brain nomenclature that is quite similar.</comment_new>
<comment_new>@shawntanzk
thanks @tgbugs :)</comment_new>
<comment_new>@dosumis
Instruction to @copilot - please add definitions based on text (plus supp matt of) https://pmc.ncbi.nlm.nih.gov/articles/PMC2868386/. Please edit this branch https://github.com/pato-ontology/pato/tree/Electrophys-Properties DO NOT make a new branch/PR</comment_new>

• Fixes Add NLX electrophys terms to PATO #462

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