coreason-protocol 0.2.1

Design and Governance Engine for high-stakes research.

coreason-protocol

The Design and Governance Engine for high-stakes research.

Description

coreason-protocol transforms natural language intent into a Rigorous, Audited, and Executable Search Protocol. It acts as the "Study Director" or Design Plane, ensuring that research protocols are designed with rigor, validated with logic (PRESS guidelines), and approved with authority before execution.

Unlike simple RAG retrieval, this package enforces a scientific workflow:

1. AI Draft: Generates PICO blocks and expands terms using ontologies (via coreason-codex).
2. Human Governance: Allows experts to override or inject terms.
3. Strict Validation: Checks structural integrity and PRESS guidelines.
4. Immutable Registration: Locks and registers approved protocols (via coreason-veritas).

Installation

pip install coreason-protocol

Or using poetry:

poetry add coreason-protocol

Features

• PICO Architecture: Structuring of research intent into Population, Intervention, Comparator, and Outcome.
• Ontology Expansion: Integration with coreason-codex for term hydration (Concept IDs).
• Strategy Compilation: Translation of PICO models into executable queries for:
  • PubMed/Ovid (Boolean strings with MeSH/TiAb mapping).
  • LanceDB (Vector embeddings + metadata filters).
  • Graph (Cypher queries).
• HITL Governance: Support for human review with override_term and inject_term capabilities.
• Audit Fidelity: Soft-deletion of terms to maintain a complete history of design decisions.
• Multi-Format Rendering: Export to HTML (visual diff), PRISMA-S text, and JSON-LD.

Usage

from coreason_protocol import ProtocolDefinition, PicoBlock, TermOrigin, OntologyTerm

# Initialize a new Protocol Definition
protocol = ProtocolDefinition(
    id="prot-123",
    title="Statins for CVD Prevention",
    research_question="Do statins reduce CVD risk in elderly patients?",
    pico_structure={},
    status="DRAFT"
)

# Example: Adding a PICO block (programmatically or via AI expansion)
term = OntologyTerm(
    id="term-001",
    label="Statins",
    vocab_source="MeSH",
    code="D019821",
    origin=TermOrigin.USER_INPUT
)

protocol.pico_structure["I"] = PicoBlock(
    block_type="I",
    description="Intervention",
    terms=[term]
)

# Render the protocol for review
html_output = protocol.render(format="html")
print(html_output)

Documentation

For detailed product requirements and architectural philosophy, see docs/product_requirements.md.