1ce4004807
This commit adds the read path (Cortex) to complement the write path (Spine): ## Crates - stemedb-api: HTTP API with axum + utoipa OpenAPI - /v1/assert, /v1/query, /v1/epoch, /v1/skeptic, /v1/trace, /v1/audit - Metered endpoints with quota enforcement - Ed25519 signature verification - stemedb-lens: Truth resolution lenses - RecencyLens, ConsensusLens, ConfidenceLens - VoteAwareConsensusLens (Ballot Box pattern) - TrustAwareAuthorityLens (The Hive pattern) - SkepticLens (conflict analysis) - EpochAwareLens (paradigm-safe queries) - stemedb-query: Query engine with materialized views ## Storage Extensions - VoteStore: Vote aggregation with cached counts - TrustRankStore: Agent reputation with decay - AuditStore: Query audit trail - IndexStore: SP/P/S index structures - SupersessionStore: Epoch supersession chains ## SDKs - sdk/go/steme: Go HTTP client with Ed25519 signing - sdk/go/adk: ADK-Go tools for AI agents ## Documentation - Updated CLAUDE.md, architecture.md, roadmap.md - New ai-lookup entries for all services - Use case docs for consumer health intelligence - Arena roadmap for simulation advancement Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
497 lines
16 KiB
Markdown
497 lines
16 KiB
Markdown
# StemeDB Data Structures
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> **Last Updated:** 2026-01-31
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> **Source:** `crates/stemedb-core/src/types.rs`
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This document describes the core data structures in StemeDB (Episteme). These types form the foundation of the "Git for Truth" knowledge graph.
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---
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## Design Principles
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1. **Append-Only**: Data is never mutated. New assertions create new records.
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2. **Content-Addressed**: Every assertion's ID is a BLAKE3 hash of its content.
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3. **Zero-Copy**: Uses `rkyv` for serialization - data can be read directly from disk without parsing.
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4. **Provenance-First**: Every fact carries its source, signers, and confidence.
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---
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## Primitive Types
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```rust
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pub type Hash = [u8; 32]; // BLAKE3 256-bit hash
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pub type PHash = [u8; 8]; // Perceptual hash for images (8 bytes)
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pub type EntityId = String; // Subject or object identifier
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pub type RelationId = String; // Predicate identifier
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pub type EpochId = Hash; // Paradigm/era identifier
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pub type QueryId = Hash; // Query audit record identifier
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```
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---
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## The Assertion (Atomic Unit of Knowledge)
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The `Assertion` is the fundamental unit. It represents a single claim about the world.
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```rust
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pub struct Assertion {
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// ═══════════════════════════════════════════════════════════
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// 1. THE FACT (What is being claimed)
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// ═══════════════════════════════════════════════════════════
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/// The entity this assertion is about (e.g., "Semaglutide", "Tesla_Inc")
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pub subject: EntityId,
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/// The relationship or property (e.g., "has_side_effect", "annual_revenue")
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pub predicate: RelationId,
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/// The claimed value
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pub object: ObjectValue,
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// ═══════════════════════════════════════════════════════════
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// 2. THE LINEAGE (Why we believe it)
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// ═══════════════════════════════════════════════════════════
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/// If this modifies/forks another assertion, its hash
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pub parent_hash: Option<Hash>,
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/// Hash of the source evidence (PDF, URL, database export)
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pub source_hash: Hash,
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/// Authority tier of the source (enables indexing and decay rates)
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pub source_class: SourceClass,
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/// Perceptual hash of a visual anchor (e.g., screenshot of table)
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pub visual_hash: Option<PHash>,
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/// Which paradigm/era this belongs to (for paradigm shifts)
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pub epoch: Option<EpochId>,
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/// Lifecycle stage (Proposed → Approved → Deprecated)
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pub lifecycle: LifecycleStage,
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// ═══════════════════════════════════════════════════════════
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// 3. META-COGNITION (Who said it, how sure are they)
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// ═══════════════════════════════════════════════════════════
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/// Cryptographic signatures from agents vouching for this
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pub signatures: Vec<SignatureEntry>,
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/// Subjective confidence score (0.0 to 1.0)
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pub confidence: f32,
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/// Unix timestamp when created
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pub timestamp: u64,
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/// Semantic embedding vector for similarity search
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pub vector: Option<Vec<f32>>,
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}
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```
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### ObjectValue
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The value in a subject-predicate-object triple:
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```rust
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pub enum ObjectValue {
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Text(String), // "muscle loss"
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Number(f64), // 96.7
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Boolean(bool), // true
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Reference(EntityId), // Points to another entity (graph edge)
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}
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```
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### LifecycleStage
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Assertions progress through stages (as new assertions, not mutations):
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```
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Proposed → UnderReview → Approved
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↘ Rejected
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↘ Deprecated
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```
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```rust
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pub enum LifecycleStage {
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Proposed, // Initial idea, not for production use
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UnderReview, // Gathering votes and feedback
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Approved, // Accepted as current truth
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Deprecated, // Was true, now superseded
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Rejected, // Explicitly declined
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}
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```
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### SourceClass
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Authority tier classification for sources. Enables indexing by tier and tier-based decay rates:
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| Tier | Class | Example | Default Decay |
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|------|-------|---------|---------------|
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| 0 | Regulatory | FDA, EMA, WHO | Never |
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| 1 | Clinical | Phase III trials, peer-reviewed RCTs | 2 years |
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| 2 | Observational | Real-world evidence, cohort studies | 1 year |
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| 3 | Expert | Medical professional opinions, guidelines | 6 months |
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| 4 | Community | Curated forums, patient advocacy groups | 3 months |
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| 5 | Anecdotal | Reddit posts, individual testimonials | 1 month |
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```rust
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pub enum SourceClass {
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Regulatory, // Tier 0: Highest authority, never decays
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Clinical, // Tier 1: Peer-reviewed research
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Observational, // Tier 2: Real-world evidence
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Expert, // Tier 3: Professional opinions (default)
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Community, // Tier 4: Curated community knowledge
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Anecdotal, // Tier 5: Individual reports, fast decay
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}
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impl SourceClass {
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pub fn tier(&self) -> u8; // Returns 0-5
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pub fn default_decay_days(&self) -> Option<u32>;
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pub fn authority_weight(&self) -> f32; // 1.0 for Regulatory, 0.1 for Anecdotal
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}
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```
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**Key Benefits:**
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- **Indexing**: `SC:{source_class}` index enables "show me only regulatory sources"
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- **Decay rates**: Anecdotal claims decay faster than clinical evidence
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- **Trust weighting**: Lenses can weight sources by authority tier in conflict resolution
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### SignatureEntry
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Cryptographic proof that an agent vouches for an assertion:
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```rust
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pub struct SignatureEntry {
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pub agent_id: [u8; 32], // Ed25519 public key
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pub signature: [u8; 64], // Ed25519 signature over assertion content
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pub timestamp: u64, // When the agent signed
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}
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```
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---
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## The Vote (High-Velocity Consensus)
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Votes are separated from assertions to enable thousands of agents to vote simultaneously without lock contention (the "Ballot Box" pattern).
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```rust
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pub struct Vote {
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/// Hash of the assertion being voted on
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pub assertion_hash: Hash,
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/// Ed25519 public key of the voter
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pub agent_id: [u8; 32],
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/// Weight of the vote (0.0 = reject, 1.0 = full endorsement)
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pub weight: f32,
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/// Signature over the assertion_hash
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pub signature: [u8; 64],
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/// When the vote was cast
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pub timestamp: u64,
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}
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```
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**Key Insight**: Votes are append-only. An agent can change their vote by submitting a new one with a later timestamp.
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---
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## The Epoch (Paradigm Shifts)
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Epochs represent distinct periods of truth. When knowledge paradigms shift, old epochs can be superseded.
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```rust
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pub struct Epoch {
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pub id: EpochId,
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pub name: String, // "Pre-2024", "Newtonian"
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pub supersedes: Option<EpochId>, // What this replaces
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pub supersession_type: Option<SupersessionType>,
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pub start_timestamp: u64,
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pub end_timestamp: Option<u64>,
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}
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pub enum SupersessionType {
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Invalidation, // Old epoch was factually wrong (e.g., "Earth is flat")
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Temporal, // Old epoch was correct but outdated (e.g., "President is Obama")
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Refinement, // Old epoch was a simplification (e.g., Newtonian → Relativity)
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}
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```
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---
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## Query Results
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### MaterializedView (O(1) Winner Lookup)
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Pre-computed resolution stored at `MV:{subject}:{predicate}`:
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```rust
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pub struct MaterializedView {
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/// The winning assertion from lens resolution
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pub winner: Assertion,
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/// Which lens produced this (e.g., "VoteAwareConsensus")
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pub lens_name: String,
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/// Confidence in the resolution (0.0 to 1.0)
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pub resolution_confidence: f32,
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/// How many candidates were considered
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pub candidates_count: usize,
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/// When this view was computed
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pub materialized_at: u64,
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}
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```
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### ConflictAnalysis (Trust but Verify)
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For the SkepticLens - surfaces all competing claims instead of picking a winner:
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```rust
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pub struct ConflictAnalysis {
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/// Overall status: Unanimous, Agreed, or Contested
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pub status: ResolutionStatus,
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/// Conflict score (0.0 = unanimous, 1.0 = maximum chaos)
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/// Calculated using normalized Shannon entropy
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pub conflict_score: f32,
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/// All distinct claims, ranked by weight_share descending
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pub claims: Vec<ClaimSummary>,
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/// Total candidates considered
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pub candidates_count: usize,
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}
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pub enum ResolutionStatus {
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Unanimous, // All agree (entropy < 0.1)
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Agreed, // Strong majority (entropy < 0.4)
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Contested, // Significant disagreement (entropy >= 0.4)
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}
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```
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### ClaimSummary
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A single competing claim within a ConflictAnalysis:
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```rust
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pub struct ClaimSummary {
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/// The claimed value
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pub value: ObjectValue,
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/// This claim's share of total support (0.0 to 1.0)
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pub weight_share: f32,
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/// Number of assertions making this claim
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pub assertion_count: u32,
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/// Hash of the highest-confidence assertion (for drill-down)
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pub representative_hash: Hash,
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/// Source provenance
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pub source: SourceSummary,
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/// Agents who signed assertions for this claim
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pub supporting_agents: Vec<AgentSummary>,
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}
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```
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### SourceSummary & AgentSummary
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Provenance types for "show me the proof" UX:
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```rust
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pub struct SourceSummary {
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pub source_hash: Hash, // Hash of source document
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pub visual_hash: Option<PHash>, // Visual anchor (screenshot)
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}
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pub struct AgentSummary {
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pub agent_id: [u8; 32], // Agent's public key
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pub trust_score: f32, // Trust score at query time
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}
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```
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---
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## Query Audit Trail
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Every query is logged for "Why did you think that?" debugging:
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```rust
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pub struct QueryAudit {
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pub query_id: QueryId,
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pub agent_id: Option<[u8; 32]>, // Who queried (from X-Agent-Id header)
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pub timestamp: u64,
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pub params: QueryParams,
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pub result_hash: Option<Hash>, // Winning assertion hash
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pub result_confidence: f32,
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pub contributing_assertions: Vec<ContributingAssertion>,
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}
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pub struct QueryParams {
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pub subject: Option<EntityId>,
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pub predicate: Option<RelationId>,
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pub lifecycle: Option<LifecycleStage>,
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pub epoch: Option<EpochId>,
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pub lens: Option<String>,
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}
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pub struct ContributingAssertion {
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pub assertion_hash: Hash,
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pub weight: f32, // How much this influenced the result
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pub source_hash: Hash,
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pub lifecycle: LifecycleStage,
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}
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```
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---
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## Storage Layout
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Key patterns in the KV store:
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| Key Pattern | Value | Purpose |
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|-------------|-------|---------|
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| `H:{hash}` | Serialized Assertion | Primary assertion storage |
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| `S:{subject}` | `Vec<Hash>` | Subject index |
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| `SP:{subject}:{predicate}` | `Vec<Hash>` | Compound index (O(1) lookup) |
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| `MV:{subject}:{predicate}` | MaterializedView | Pre-computed winner |
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| `V:{assertion_hash}:{vote_hash}` | Vote | Individual votes |
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| `VC:{assertion_hash}` | u64 | Vote count cache |
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| `VW:{assertion_hash}` | f32 | Aggregate vote weight cache |
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| `TR:{agent_id}` | TrustRank | Agent reputation |
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| `TP:{pack_id}` | TrustPack | Curated agent lists |
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| `AUD:{query_id}` | QueryAudit | Query audit record |
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| `E:{epoch_id}` | Epoch | Epoch definitions |
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---
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## The Trust Pack (Curator Economy)
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Trust Packs are the "App Store for Trust" - curated lists of trusted agents that filter consensus through domain expertise.
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```rust
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pub struct TrustPack {
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/// Content-addressed pack ID (BLAKE3 hash)
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pub id: PackId,
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/// Human-readable name (e.g., "Mayo_Clinic_Experts")
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pub name: String,
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/// Ed25519 public key of the pack maintainer
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pub maintainer: [u8; 32],
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/// Agent public keys in this pack
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/// Future: Replace with RoaringBitmap for O(1) membership
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pub agents: Vec<[u8; 32]>,
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/// Unix timestamp when pack was created
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pub created_at: u64,
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/// Unix timestamp of last modification
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pub updated_at: u64,
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}
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```
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**Key Methods:**
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- `add_agent(agent_id)` - Idempotent agent addition
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- `remove_agent(agent_id)` - Safe removal
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- `contains_agent(agent_id) -> bool` - Membership check
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**Use Case:** Users subscribe to packs like "Skeptical Cardio Pack" to filter GLP-1 side effect claims through vetted cardiologists.
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---
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## Serialization
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All types use `rkyv` for zero-copy deserialization:
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```rust
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use stemedb_core::serde::{serialize, deserialize};
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// Serialize
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let bytes: Vec<u8> = serialize(&assertion)?;
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// Deserialize (zero-copy when possible)
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let assertion: Assertion = deserialize(&bytes)?;
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```
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**Critical Rule**: Never use raw `AllocSerializer` in production code. Always use `stemedb_core::serde::{serialize, deserialize}`.
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---
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## Relationship Diagram
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```
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┌─────────────────────────────────────────────┐
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│ ASSERTION │
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│ ┌─────────┐ ┌───────────┐ ┌─────────────┐ │
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│ │ subject │ │ predicate │ │ object │ │
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│ └─────────┘ └───────────┘ └─────────────┘ │
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│ │
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│ ┌─────────────────┐ ┌──────────────────┐ │
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│ │ source_hash │ │ signatures[] │ │
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│ └────────┬────────┘ └────────┬─────────┘ │
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│ │ │ │
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└───────────┼────────────────────┼────────────┘
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│ │
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┌───────────▼───────┐ ┌────────▼────────┐
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│ SOURCE DOCUMENT │ │ AGENTS │
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│ (PDF, URL...) │ │ (Ed25519 keys) │
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└───────────────────┘ └────────┬────────┘
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│
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┌────────▼────────┐
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│ TRUST RANK │
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│ (reputation) │
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└─────────────────┘
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┌─────────────────┐ ┌─────────────────┐
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│ VOTE │◄────────│ ASSERTION │
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│ (Ballot Box) │ votes │ (target) │
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│ weight: 0.0-1.0│ on │ │
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└─────────────────┘ └─────────────────┘
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┌─────────────────┐ ┌─────────────────┐
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│ EPOCH B │◄────────│ EPOCH A │
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│ supersedes: A │ older │ │
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│ type: Temporal │ epoch │ │
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└─────────────────┘ └─────────────────┘
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```
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---
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## API Representation
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All binary data (hashes, signatures, agent IDs) is hex-encoded in JSON APIs:
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```json
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{
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"subject": "Semaglutide",
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"predicate": "muscle_effect",
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"object": { "type": "Text", "value": "Significant loss" },
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"source_hash": "a1b2c3d4e5f6...",
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"signatures": [
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{
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"agent_id": "deadbeef...",
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"signature": "cafebabe...",
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"timestamp": 1706745600
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}
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],
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"confidence": 0.85,
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"timestamp": 1706745600
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}
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```
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---
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## See Also
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- [Architecture Overview](../architecture.md)
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- [Lens Documentation](../ai-lookup/services/lens.md)
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- [API Endpoints Guide](../.claude/guides/backend/api-endpoints.md)
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