PharmaTech scaffold

A complete program, not a fragment: it compiles as written. Copy it, rename the placeholder identifiers to your domain, and run axon check — the compiler will tell you what your renaming broke. An MCP client can also generate it through the axon.compose tool by naming the pharmatech domain.

// AXON PharmaTech scaffold — pharmaceutical R&D / drug-discovery /
// clinical-trial-data-management pattern (GxP + FDA + HIPAA).
//
// Differs from `healthcare.axon` (patient-care pattern): this
// targets R&D + regulated discovery — compound screening, activity
// profiling, clinical-data ingestion, FDA 21 CFR Part 11 audit
// trails, IRB-supervised workflows. The persona is researcher /
// scientific, not clinician.

// ── Regulated data types ──────────────────────────────────────────

type Compound compliance [GxP] {
    compound_id:     Text
    structure:       Text
    molecular_weight: Number
    discovery_phase: Text
}

type ActivityProfile compliance [GxP, HIPAA] {
    compound_id:    Text
    assay_id:       Text
    ic50:           Number
    selectivity:    Text
    safety_signal:  Text
}

type ResearchReport {
    summary:       Text
    citations:     Text
    confidence:    Number
}

type ScreenRequest    { compound: Compound }
type ProfileRequest   { activity: ActivityProfile }

// ── Identity + grounding ──────────────────────────────────────────

persona PharmaResearcher {
    domain: ["medicinal-chemistry", "pharmacology", "drug-discovery", "toxicology"]
    tone: analytical
    confidence_threshold: 0.9
    cite_sources: true
}

context PharmaResearch {
    memory: persistent
    language: "en"
    depth: exhaustive
    max_tokens: 4096
    temperature: 0.15
}

anchor ClinicalEvidenceRequired {
    require: evidence_backed
    confidence_floor: 0.88
    unknown_response: "Evidence insufficient — flagging for senior reviewer."
    on_violation: raise EvidenceInsufficientError
}

// ── Shields — GxP + audit ─────────────────────────────────────────

shield ComplianceShield {
    scan:       [prompt_injection, pii_leak, data_exfil, hallucination]
    on_breach:  quarantine
    severity:   critical
    compliance: [GxP, HIPAA, SOC2]
}

// ── Flows ─────────────────────────────────────────────────────────

flow ScreenCompound(compound: Compound) -> FlowEnvelope<ResearchReport> {
    step Predict {
        given: compound
        ask: "Predict target binding profile + selectivity ranges; cite published assay precedents."
        output: FlowEnvelope<ResearchReport>
    }
    return Predict.output
}

flow ProfileActivity(activity: ActivityProfile) -> FlowEnvelope<ResearchReport> {
    step Analyze {
        given: activity
        ask: "Analyse the activity profile against safety signals; cite the relevant 21 CFR Part 11 clauses for record retention."
        output: FlowEnvelope<ResearchReport>
    }
    return Analyze.output
}

// ── HTTP boundaries ───────────────────────────────────────────────

axonendpoint CompoundScreeningAPI {
    method:      post
    path:        "/v1/discovery/screen"
    body:        ScreenRequest
    execute:     ScreenCompound
    output:      FlowEnvelope<ResearchReport>
    shield:      ComplianceShield
    backend:     auto
    compliance:  [GxP, SOC2]
    retries:     1
    timeout:     30s
    requires:    ["pharmatech.discovery.screen"]
}

axonendpoint ActivityAnalysisAPI {
    method:      post
    path:        "/v1/discovery/activity"
    body:        ProfileRequest
    execute:     ProfileActivity
    output:      FlowEnvelope<ResearchReport>
    shield:      ComplianceShield
    backend:     auto
    compliance:  [GxP, HIPAA, SOC2]
    retries:     1
    timeout:     20s
    requires:    ["pharmatech.discovery.analyze"]
}