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Maintain agent-authored investigation memory over Genomi evidence links, reviewed source findings, decisions, contradictions, and unresolved questions.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
| name | journal |
| description | Maintain agent-authored investigation memory over Genomi evidence links, reviewed source findings, decisions, contradictions, and unresolved questions. |
| tools | ["journal.append_entry","journal.search_entries","journal.summarize","journal.export_memory","research.list_sources","research.build_target_packet","gnomad.fetch_population_frequency","research.record","research.query","research.search"] |
| mutating | true |
Use journal when an investigation spans multiple Genomi tools and the host agent needs to record reasoning, evidence links, or reviewed source findings.
Record the host agent's observations, hypotheses, decisions, contradictions, plans, summaries, and unresolved questions while preserving traceability to Genomi operations and evidence identifiers.
Journal entries are the append-only notebook. Reviewed research records are source-memory entries in the evidence DB. They live in the same capability because both preserve investigation memory, but they have different roles: journal entries explain what the host agent concluded or still needs to check; reviewed research records store source-backed findings for reuse.
Neither journal entries nor reviewed research records rank candidates by themselves. Candidate ranking still belongs to the relevant evidence tools, with reviewed source records passed only when a tool explicitly accepts them.
session: current chat/session notebook. It may link private/sample evidence
only after scoped Active Genome Index access is approved for this session.project: current workspace notebook. It is public/target-scoped and
rejects private/sample evidence links.A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.
Append a new journal entry, or append evidence links and/or an amendment to an existing entry.
Use when: Record an observation, hypothesis, decision, contradiction, plan, summary, unresolved question, or append evidence/amendment to an existing entry.
Why necessary: Multi-tool investigations need one append-only write path for notes, evidence links, and corrections so agents do not sequence separate journal mutations.
Not for: Not source evidence and not a candidate-ranking input by itself.
Example prompts: Record this supported Genomi finding with evidence links.
Result semantics: With no entry_id, creates a new entry. With entry_id, adds evidence_links and/or stores content as an append-only amendment; original entry text is preserved.
Return a MemOS-shaped JSON memory artifact from journal entries without requiring or writing to MemOS.
Use when: The user or host agent explicitly wants the journal exported for ingestion by another memory system.
Why necessary: External memory systems need a shaped export without requiring Genomi to write to that system.
Result semantics: Exports journal memory records only; private evidence links are omitted unless explicitly requested and approved.
Token-search session and project journal entries by scope, target, tag, entry type, and text.
Use when: The host agent needs to recover recorded investigation state before continuing a multi-tool Genomi analysis.
Why necessary: Agents need to recover prior investigation state without treating chat memory as authoritative evidence.
Result semantics: Returns agent-authored notes and traceability links; journal entries are not source evidence.
Summarize journal state into observations, decisions, contradictions, unresolved questions, and commonly linked evidence sources.
Use when: The host agent needs a compact state of an ongoing Genomi investigation before deciding next evidence steps.
Why necessary: Long investigations need compact journal state before the agent chooses the next evidence step.
Result semantics: Summarizes journaled reasoning only; evidence authority remains in the linked Genomi outputs and public sources.
source_records, provide reviewed research or
tool-returned source records that satisfy that tool's verified source-record
input contract.journal.append_entry with entry_id for corrections; do not silently
overwrite entries.Use this skill for genetics, genome source, variant, gene, phenotype, disease, screen, pharmacogenomics, and Genomi install/setup maintenance questions.
Build and inspect ClinVar exact-match evidence and candidate inventories. Use for clinical labels, VUS/conflict, carrier context, and drug-response rows.
Activate this skill for "/genomi decode", "decode my genome", "decode my DNA", "show me the dashboard", "the Genomi dashboard", "one-shot rundown", or any all-at-once request that asks Genomi to compose every capability's findings into a single artifact. This is the whole-genome dashboard kicker — it sweeps every relevant Genomi capability in one shot, not a per-target lookup. Composes evidence from every relevant Genomi capability into a single self-contained Genomi Dashboard.html and returns localhost serve metadata. Active genome required.
Answer drug-response, medication, PharmGKB-style, PGxDB, ATC, DrugBank, gene-drug, and variant-drug questions using public PGx evidence plus local sample genotype support when an Active Genome Index is selected.
Plan rare disease, hereditary disease, cancer risk, carrier-relevance, and observed-condition source investigation from public targets or selected active genome evidence.
Answer specific rsID, allele, gene, region, genotype, and absence/callability questions using explicit session context or public evidence.