The quality of AI-generated clinical documentation depends entirely on the prompt. In psychedelic-assisted therapy, where the clinical phenomena are unlike anything in conventional practice, generic prompts produce generic output — and generic output is worse than useless. It misrepresents the work, creates audit risk, and fails the client. This guide introduces the MycenAI Clinical Prompt Library and explains how structured, PAT-specific prompt templates produce documentation that actually reflects the complexity of what happens in the room.

Why Prompts Matter More in PAT Than Anywhere Else

If you have used a general-purpose AI tool to draft a clinical note, you already know what happens. You get something plausible but flat. The language is correct but not clinically precise. The structure is recognisable but generic. It reads like documentation written by someone who has never sat with a client — because it was.

In conventional therapy, this is a nuisance. You spend ten minutes editing a draft that should have been right the first time. In psychedelic-assisted therapy, it is a genuine problem. PAT documentation must capture phenomena that most clinical frameworks were never designed to describe: non-ordinary states of consciousness, somatic release patterns, ego dissolution, mystical-type experiences, challenging psychological content that unfolds in real time, and integration processes that span weeks or months after a single dosing session.

A standard SOAP or DAP note template does not have fields for these experiences. A generic AI prompt will not generate them. The result is documentation that either omits the most clinically significant material or shoehorns it into categories where it does not belong.

The fix is not better AI models. It is better prompts. A well-structured prompt tells the AI exactly what clinical territory to cover, what terminology to use, what structure the output should follow, and what therapeutic orientation to write from. The prompt is the clinical framework. The AI is just the engine.

The PAT Treatment Arc: Where Templates Fit

Psychedelic-assisted therapy follows a distinctive treatment arc that differs from conventional weekly-session psychotherapy. Each phase has its own documentation requirements, and each document in the chain depends on what came before. Understanding this arc is essential to understanding why PAT-specific prompt templates exist and where they fit in the clinical workflow.

Phase 1: Intake and Assessment

The intake phase in PAT is more extensive than in most conventional modalities. It includes standard clinical assessment — presenting problems, psychiatric history, psychosocial history, risk factors — but also PAT-specific screening: contraindication assessment (cardiovascular conditions, psychotic spectrum disorders, certain medication interactions), informed consent that covers the unique risks and nature of non-ordinary states, and readiness evaluation that goes beyond symptom severity to consider psychological preparedness, relational stability, and the client’s capacity for surrender and self-regulation.

The prompt templates for this phase generate structured intake documents that include all of these PAT-specific domains alongside the standard clinical intake fields. The AI does not guess what to include. The prompt tells it.

Phase 2: Preparation

Preparation sessions are a defining feature of PAT. They are where the therapeutic alliance deepens, intentions are explored and documented, psychological preparation occurs (including psychoeducation about the medicine experience and emotional safety planning), and set and setting considerations are assessed. This phase typically involves two to four sessions before the first dosing experience.

Documentation templates for preparation cover intention setting, psychological readiness assessment, safety planning, and set and setting evaluation. Each template captures both the content of the preparation work and the clinician’s assessment of the client’s readiness to proceed.

Phase 3: Dosing and Ceremony

The dosing session is where PAT documentation departs most radically from conventional clinical writing. The clinician needs to document observations in real time or shortly after: the client’s progression through non-ordinary states, somatic experiences (tremoring, postural changes, autonomic shifts), emotional content as it arises, any challenging material and how it was navigated, the quality and timing of the experience arc, and any interventions (verbal, somatic, musical, environmental) used during the session.

Standard clinical note formats cannot capture this. The dosing observation templates provide structured fields for phenomenological documentation — what the experience looked like from the outside and, based on the client’s verbal and non-verbal communication, what it appeared to involve from the inside. These templates also include fields for documenting the physical setting, substances administered, dose and timing, vital sign monitoring, and any adverse events.

Phase 4: Integration

Integration is where meaning-making happens. It is often the most therapeutically rich phase of PAT, and the documentation needs to reflect that richness. Integration session notes must capture the client’s evolving understanding of their dosing experience, emergent insights and how they connect to presenting problems, somatic and emotional processing that continues after the session, behavioural changes (or resistance to change), and the relationship between the experience and the client’s broader life narrative.

The integration templates generate SOAP-structured notes that include PAT-specific fields: experience processing, insight tracking, meaning-making progress, and connection to the original treatment intentions documented during the preparation phase.

Phase 5: Treatment Planning

Treatment planning in PAT is inherently multi-phase. A SMART-goal treatment plan for a PAT client needs to account for preparation goals, dosing session parameters, integration objectives, and longer-term maintenance. The treatment plan templates generate modality-specific plans that reference the client’s intake data, preparation work, and — if treatment is already underway — dosing session outcomes and integration progress.

Phase 6: Progress Notes

Session-to-session documentation across the full treatment arc. The progress note templates adapt to the current phase: preparation-phase notes emphasise readiness indicators, dosing-phase notes capture phenomenological observations, and integration-phase notes track meaning-making and behavioural change. Outcome measures relevant to PAT (such as the Mystical Experience Questionnaire, Challenging Experience Questionnaire, or standard measures like the PHQ-9 and GAD-7) can be incorporated directly.

Phase 7: Discharge and Follow-Up

The final documentation phase ties together the entire treatment arc. Discharge summaries and completion reports synthesise the client’s journey from intake through integration, documenting outcomes against the original presenting problems and treatment goals. Aftercare plans address ongoing integration support, relapse prevention, and any referrals. Referrer feedback letters communicate treatment outcomes in language appropriate for the referring clinician, who may or may not be familiar with PAT.

Example: How the Intention Setting Template Works

To make this concrete, let us walk through a single template in detail. The Intention Setting Documentation template is used during the preparation phase, typically across one or two sessions before a dosing experience. It generates a structured clinical document that captures the client’s therapeutic intentions and the clinician’s assessment of them.

The Prompt Structure

The template begins with a context block that tells the AI what kind of document it is writing, what clinical framework to use, and what information the clinician is providing. This is not a vague instruction like “write an intention-setting note.” It is a structured specification:

Document type: Intention Setting Documentation for psychedelic-assisted therapy preparation phase.
Therapeutic context: The client’s presenting problems, relevant history, and the specific medicine and protocol being used.
Session content: The clinician’s notes from the preparation session — what the client expressed about their intentions, how those intentions connect to presenting problems, any ambivalence or concerns, and the clinician’s observations.
Therapeutic orientation: The modality or modalities the clinician works from (more on this below).

What the AI Generates

Given this structured input, the template directs the AI to generate a document with specific sections:

Client-stated intentions: What the client articulated as their hopes, goals, or questions for the upcoming experience, documented in language that stays close to the client’s own words.
Connection to presenting problems: How the stated intentions relate to the clinical issues identified at intake.
Depth and specificity assessment: The clinician’s evaluation of whether the intentions are sufficiently explored, overly intellectualised, or still emerging.
Somatic and emotional readiness: Observations about the client’s embodied relationship to their intentions — are they speaking from the head or from a place of genuine felt sense?
Potential challenging territory: Areas where the dosing experience may bring difficult material, based on the intentions and the clinical picture.
Safety considerations: Any concerns about psychological safety related to the stated intentions, and how these have been addressed in preparation.
Clinician assessment: An overall assessment of the intention-setting process, including readiness to proceed and any recommended further preparation.

How the Clinician Reviews and Endorses

The AI-generated document is a draft. It is never a finished clinical record. The clinician reviews every section, corrects any inaccuracies, adds nuance the AI could not capture, removes anything that does not reflect the actual clinical picture, and endorses the final document. This review-and-endorse step is not optional — it is the entire point. The AI saves the clinician the labour of structuring the document from scratch. The clinician provides the clinical judgement that makes it a good clinical note.

In practice, this process typically takes five to eight minutes of clinician review time, compared to twenty to thirty minutes of writing from scratch. The result is a more structured, more thorough document than most clinicians would produce under time pressure — because the template ensures nothing is omitted.

Orientation-Aware Prompting

One of the most significant design features of the MycenAI prompt templates is orientation awareness. PAT practitioners rarely work from a single therapeutic modality. The field draws from Internal Family Systems, somatic experiencing, transpersonal psychology, psychodynamic therapy, Acceptance and Commitment Therapy, Cognitive-Behavioural Therapy, Dialectical Behaviour Therapy, and various contemplative and indigenous traditions. Most practitioners blend several of these approaches, and the blend often shifts across phases of treatment.

This matters for documentation because different modalities use different language, different conceptual frameworks, and different ways of understanding what is happening in therapy. A somatic practitioner documents body sensations, movement impulses, and autonomic regulation. An IFS practitioner documents parts, protectors, exiles, and Self energy. A psychodynamic practitioner documents transference, defences, and unconscious material. A transpersonal practitioner documents spiritual emergence, archetypal imagery, and non-dual awareness.

Generic AI prompts default to a vaguely CBT-inflected clinical language that does not serve practitioners working from other orientations. The MycenAI templates include an orientation parameter that adjusts the AI’s output to match the practitioner’s theoretical framework. When you specify IFS as your primary orientation, the generated documentation uses IFS language and conceptual structure. When you specify somatic experiencing, the documentation centres body-based observations and autonomic regulation frameworks.

This is not cosmetic. The difference between documenting that a client “experienced anxiety” and documenting that a client “noticed a protective part carrying fear about abandonment, which softened when approached with curiosity from Self” is the difference between a note that says nothing and a note that captures the actual clinical work. The same session, documented from different orientations, will produce legitimately different — and equally valid — clinical records. Orientation-aware prompting ensures the documentation matches how the practitioner actually thinks about and practises the work.

Blended Approaches

Many PAT practitioners work from an explicitly integrative framework, drawing on multiple modalities within a single session. The templates accommodate this by allowing practitioners to specify a primary orientation with secondary influences. For example, a practitioner might specify somatic experiencing as their primary framework with IFS and transpersonal psychology as secondary orientations. The AI then generates documentation that leads with somatic language but incorporates parts language and transpersonal frameworks where the session content calls for it.

This reflects the reality of PAT practice, where a dosing session might begin with somatic processing, move into parts work as specific emotional content emerges, and culminate in a transpersonal or mystical experience that requires entirely different clinical language to document accurately.

Document Chaining in PAT

If you have read about document chaining in conventional therapy documentation, the concept will be familiar. In PAT, it is even more critical — and more complex.

Document chaining means that the output from one template becomes the input for the next. The intake assessment feeds into the treatment plan. The treatment plan feeds into the preparation session notes. The preparation notes — including the intention-setting documentation — feed into the dosing observation template. The dosing observations feed into the integration session notes. And the integration notes, together with everything before them, feed into the discharge summary.

Each template in the MycenAI Clinical Prompt Library is designed to accept input from prior templates in the chain. This means:

The treatment plan template references the presenting problems, contraindication screening, and readiness assessment from the intake. You do not re-enter this information. The chain carries it forward.
The preparation session templates reference the treatment goals and the client’s specific clinical picture. The intention-setting documentation is automatically contextualised against the presenting problems documented at intake.
The dosing observation template references the client’s stated intentions from the preparation phase, so the clinician can document whether and how the experience connected to those intentions.
The integration session templates reference both the original intentions and the dosing observations, creating a natural structure for tracking how the experience is being processed and integrated over time.
The discharge summary template draws from the entire chain — intake baseline, treatment goals, preparation work, dosing outcomes, integration progress — to produce a comprehensive end-of-treatment document.

The clinical value of this chaining is significant. In PAT, where treatment arcs can span months and a single dosing session can produce material that takes weeks to integrate, it is easy for the documentation to lose coherence. Earlier themes get forgotten. The connection between a client’s intake presentation and their integration work six months later gets lost in the volume of session notes. Chaining prevents this by ensuring that each document in the record explicitly references the documents that came before it.

Practical Example: From Intake to Discharge

Consider a client who presents at intake with treatment-resistant depression, early relational trauma, and chronic somatic tension. The intake template captures all of this in structured form. When the clinician generates a treatment plan, the template automatically pulls forward the presenting problems and formulation, structuring the plan around preparation goals (building somatic awareness, exploring relational patterns), dosing session parameters (substance, dose, setting, support team), and integration objectives (processing trauma material, developing new relational patterns, sustained symptom reduction).

During preparation, the intention-setting template contextualises the client’s stated intentions against the clinical picture: the client’s intention to “understand why I feel so disconnected” is documented in relation to the early relational trauma and the somatic holding patterns identified at intake. After the dosing session, the observation template links what happened in the room to those intentions and that clinical context. And when integration begins, the session notes track meaning-making against the entire chain: the original presenting problems, the treatment goals, the stated intentions, and the actual experience.

When it is time to write the discharge summary, the clinician does not need to re-read fifty pages of notes. The chain has maintained the narrative thread throughout. The AI can generate a comprehensive summary that traces the client’s journey from intake to completion, with the clinician reviewing and endorsing the final document.

Common Mistakes With Clinical AI Prompts

Before discussing how to get started, it is worth naming the most common errors practitioners make when using AI for PAT documentation — even with good templates.

Using the AI as a scribe instead of a structuring tool. The templates are not designed to transcribe what happened in session. They are designed to structure the clinician’s input into well-organised clinical documentation. The clinician still needs to provide the substance — what the client said, what the clinician observed, what clinical judgements were made. The AI organises and formats this material. If you give it nothing, you get nothing useful back.

Skipping the review step. AI-generated documentation always requires clinician review. In PAT, where the clinical phenomena are unfamiliar to the AI’s training data, this is especially important. The AI may use language that is close but not quite right. It may overemphasise one aspect of the session and underrepresent another. The review step is where clinical expertise enters the document. Skipping it creates records that are technically fluent but clinically hollow.

Not specifying the therapeutic orientation. If you do not tell the template what orientation you work from, the AI will default to generic clinical language. This is particularly costly in PAT, where the practitioner’s orientation shapes not just the language of documentation but the conceptual framework for understanding the client’s experience. Always specify your orientation. If you work from a blended approach, specify the blend.

Treating each document as standalone. The templates are designed to chain. If you use the dosing observation template without feeding in the preparation notes, you lose the contextual thread that makes the documentation coherent. Take the extra thirty seconds to include the prior document in the chain. The output quality improves dramatically.

Getting Started

The MycenAI Clinical Prompt Library is a downloadable collection of structured prompt templates covering every phase of the PAT treatment arc. Each template is designed to work as a standalone tool or as part of a chained workflow. The library includes templates for intake and assessment, preparation (including intention setting, psychological preparation, and safety planning), dosing observation, integration sessions, treatment planning, progress notes, and discharge documentation.

Every template includes clear instructions for what input to provide, what output to expect, and how to review and endorse the generated document. The orientation parameter is built into each template, so you can specify your therapeutic framework from the outset.

If you are already using AI for clinical documentation, the templates will immediately improve the specificity and clinical relevance of your output. If you are new to AI-assisted documentation, the templates provide a structured starting point that avoids the most common pitfalls of generic prompting.

For practitioners looking for a fully integrated platform — where the templates, document chaining, and clinical workflow are built into a secure, privacy-first environment — visit confideai.ai. Confide AI provides the infrastructure for using these templates with clinical-grade security, so you can focus on the work that matters: helping your clients navigate some of the most profound therapeutic experiences available.

Psychedelic-assisted therapy is reshaping mental health treatment. The documentation practices that support this work need to keep pace. PAT practitioners deserve tools that understand the unique structure of their clinical workflow — not generic templates borrowed from conventional therapy and stretched to fit. Structured, PAT-specific prompt templates are how we close that gap: better prompts, better documentation, better clinical records, better care.

Clinical Prompt Templates for PAT Practitioners: A Practical Guide