Journal and Research Memory
How Genomi records investigation notes, evidence links, reviewed source findings, and reusable research context.
The journal is agent-authored investigation memory. It records what the agent observed, decided, contradicted, or still needs to check while preserving links back to Genomi evidence.
Reviewed research findings are different: they are source-backed records stored in evidence storage for reuse by later evidence gathering.
Two memory types
| Type | Purpose | Authority |
|---|---|---|
| Journal entries | Notes, hypotheses, decisions, contradictions, plans, summaries, unresolved questions | Not source evidence by themselves |
| Reviewed research findings | Short source-backed findings tied to a target such as gene, drug, condition, topic, or variant | Reusable source context, still subject to freshness and source quality |
Downstream candidate ranking should use the relevant evidence tools. Journal entries are traceability and reasoning memory, not ranking inputs.
Journal scopes
| Scope | Use |
|---|---|
session | Current chat/session notebook; can link private sample evidence after AGI access is approved |
project | Workspace notebook; public or target-scoped and rejects private sample links |
Journal operations
| Operation | Use |
|---|---|
journal.append_entry | Create an entry or append evidence links/amendments |
journal.search_entries | Search entries by text, target, tag, type, or scope |
journal.summarize | Summarize observations, decisions, contradictions, unresolved questions, and common evidence links |
journal.export_memory | Export a MemOS-shaped JSON artifact without writing to MemOS |
Entry types include observation, hypothesis, decision,
contradiction, unresolved_question, protocol_note, plan, and
summary.
Reviewed research operations
| Operation | Use |
|---|---|
research.list_sources | List source families relevant to a target type |
research.build_target_packet | Build a target-centric evidence packet |
research.record | Store reviewed source findings with explicit shared/private scope |
research.query | Retrieve reviewed findings for an exact target |
research.search | Token and semantic search over reviewed findings |
Reviewed findings can be shared or private. Private reviewed research
requires a selected Active Genome Index or explicit private evidence database.
Good journal hygiene
- Link operation names and evidence IDs when recording a material finding.
- Use amendments for corrections; do not silently overwrite prior notes.
- Keep private evidence out of project-scope journal entries.
- Export private evidence links only when the user explicitly asks and AGI access is approved.
- Treat source dates and
source_accessed_atas part of the freshness story.