菜单
Query Obsidian vault frontmatter with SQL-like syntax. Filter, sort, group, and aggregate notes by any frontmatter field. Replaces Dataview for CLI use. Triggers on: /genome-query, "query vault", "find notes", "list genes", "show protocols", "vault stats", "vault schema", "filter by".
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
Universal genome data import supporting 23andMe v4/v5, AncestryDNA, MyHeritage, Nebula, and generic VCF. Also handles imputation prep and post-imputation import. Triggers on: /genome-import, "import my DNA data", "add raw file", "prepare for imputation", "import imputed data".
Goal-driven onboarding for new genome vault users. Triggers on: /genome-onboard, "set up my vault", "I just imported my data", "help me get started with my genome". Two modes: --quick (4 questions, fast vault bootstrap) or --full (22-question interview with validated psychological instruments, generates Profile Card + Action Plan).
Daily health tracking with genetic context: supplements, medications, symptoms, interventions, metrics. Use this skill whenever the user mentions taking supplements, logging symptoms, tracking health, reporting how they feel, or asks about their daily routine. Also triggers on: /genome-log, /log, "daily check-in", "track today", "I took my supplements", "feeling anxious", "my stomach hurts", "forgot my B12", "log symptoms", "how am I doing", "what did I take today". Even casual health mentions like "my nose is stuffed" or "had a rough night" should trigger this skill to offer logging.
Multi-agent validation pipeline for fact-checking claims, verifying evidence tiers, and ensuring prescriber document accuracy. Uses Codex CLI, NotebookLM, PubMed subagents, and Tavily search. Supports: audit (full vault), gene SYMBOL (single gene fact-check), protocol NAME (protocol/report fact-check). Triggers on: /genome-validate, "validate this note", "fact-check", "cross-check claims", "verify evidence", "audit this report", "fact-check gene X", "check protocol X".
Run analysis scripts: PRS, enrichment, vault audit, PubMed monitoring, consistency checks. Triggers on: /genome-analytics, "run PRS", "audit vault", "check PubMed", "run enrichment", "check consistency", "analyze pathway".
Create gene, system, or phenotype notes from SQLite genotype data and templates. Triggers on: /new-gene SYMBOL, /new-system NAME, "add gene X", "create system note", "create phenotype note for X".
| name | genome-query |
| description | Query Obsidian vault frontmatter with SQL-like syntax. Filter, sort, group, and aggregate notes by any frontmatter field. Replaces Dataview for CLI use. Triggers on: /genome-query, "query vault", "find notes", "list genes", "show protocols", "vault stats", "vault schema", "filter by". |
SQL-like queries over Obsidian vault frontmatter from the command line.
scripts/vault_query.pyscripts/lib/vault_parser.py (shared with other toolkit scripts)scripts/lib/config.py (uses GENOME_VAULT_ROOT env var)# Set vault location (or rely on CWD)
export GENOME_VAULT_ROOT=~/my-genome-vault
# Basic query
python3 scripts/vault_query.py "type=gene"
# With field selection and sorting
python3 scripts/vault_query.py "type=gene" --fields gene_symbol,evidence_tier --sort evidence_tier
# Vault overview
python3 scripts/vault_query.py --stats
| Operator | Meaning | Example |
|---|---|---|
= | Equals (or in list) | type=gene |
!= | Not equals | type!=gene |
~ | Contains / substring | evidence_tier~E1 |
> | Greater than | _words>500 |
< | Less than | _words<100 |
>= | Greater or equal | coverage>=80 |
<= | Less or equal | coverage<=50 |
Bare field names test for existence/truthiness: sensitivity matches notes where the field is present and non-empty.
type=gene AND sensitivity — both conditions must matchtype=gene OR type=system — either condition matchesNOT sensitivity — negates a conditiontype=gene AND NOT sensitivity — AND/OR/NOT compose freelyOR binds loosely, AND binds tightly: A AND B OR C AND D means (A AND B) OR (C AND D).
| Field | Alias for | Description |
|---|---|---|
file | _file | Relative path from vault root |
name | _name | Filename without .md extension |
folder | _folder | Parent directory relative to root |
words | _words | Word count of note body |
links | _links_out | Count of outgoing wikilinks |
| Flag | Short | Description |
|---|---|---|
--fields F1,F2 | -f | Comma-separated fields to display |
--sort FIELD | -s | Sort results by field |
--desc | Sort descending | |
--limit N | -l | Limit to N results |
--count | -c | Print count only |
--json | -j | Output as JSON |
--group FIELD | -g | Group by field and count |
--stats | Print vault-wide statistics | |
--schema | Print all frontmatter keys and frequency |
# All gene notes
python3 scripts/vault_query.py "type=gene" --fields gene_symbol,evidence_tier,relevance
# High-evidence genes only
python3 scripts/vault_query.py "type=gene AND evidence_tier=E1" --fields gene_symbol,full_name
# Genes with sensitivity flags
python3 scripts/vault_query.py "type=gene AND sensitivity" --fields gene_symbol,sensitivity
# Genes by system
python3 scripts/vault_query.py "type=gene AND systems~Dopamine" --fields gene_symbol,systems
# All systems with coverage
python3 scripts/vault_query.py "type=system" --fields system_name,coverage --sort coverage --desc
# Phenotypes by heritability
python3 scripts/vault_query.py "type=phenotype" --fields trait,heritability_estimate --sort heritability_estimate --desc
# Low-coverage systems (gaps)
python3 scripts/vault_query.py "type=system AND coverage<50" --fields system_name,coverage
# Actionable research findings
python3 scripts/vault_query.py "type=research AND actionable_findings=true" --fields name,genes
# All protocols
python3 scripts/vault_query.py "type=protocol" --fields name,evidence_tier
# Research in a folder
python3 scripts/vault_query.py "folder=Research" --fields name,actionable_findings --sort name
# Notes by type
python3 scripts/vault_query.py --stats
# All frontmatter keys
python3 scripts/vault_query.py --schema
# Group by evidence tier
python3 scripts/vault_query.py "type=gene" --group evidence_tier
# Longest notes
python3 scripts/vault_query.py "_words>1000" --fields name,_words --sort _words --desc --limit 10
# Notes with most outgoing links
python3 scripts/vault_query.py "_links_out>20" --fields name,_links_out --sort _links_out --desc
# All lab results
python3 scripts/vault_query.py "type=biomarker" --fields name,test_date,lab --sort test_date --desc
# JSON export for scripting
python3 scripts/vault_query.py "type=gene AND evidence_tier=E1" --json
--json): Full frontmatter as JSON array--count): Single integer--group): Field value + count pairs--stats): Vault-wide summary (types, tiers, folders, word counts)--schema): All frontmatter keys with frequency, types, examplesThe script uses scripts/lib/vault_parser.py for parsing (shared across all toolkit scripts) and scripts/lib/config.py for vault root resolution. Set GENOME_VAULT_ROOT to point at any Obsidian vault.