genome-query

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".

Genome Query

SQL-like queries over Obsidian vault frontmatter from the command line.

Vault Configuration

• Script: scripts/vault_query.py
• Parser: scripts/lib/vault_parser.py (shared with other toolkit scripts)
• Config: scripts/lib/config.py (uses GENOME_VAULT_ROOT env var)

Quick Start

# 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

Query Syntax

Conditions

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.

Logic

• AND: type=gene AND sensitivity — both conditions must match
• OR: type=gene OR type=system — either condition matches
• NOT: NOT sensitivity — negates a condition
• Combined: type=gene AND NOT sensitivity — AND/OR/NOT compose freely

OR binds loosely, AND binds tightly: A AND B OR C AND D means (A AND B) OR (C AND D).

Special Fields

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

CLI Flags

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

Common Queries for Genome Vault

Gene notes

# 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

Systems and phenotypes

# 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

Research and protocols

# 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

Vault health

# 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

Biomarkers

# 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

Output Formats

• Table (default): Aligned columns with headers
• JSON (--json): Full frontmatter as JSON array
• Count (--count): Single integer
• Group (--group): Field value + count pairs
• Stats (--stats): Vault-wide summary (types, tiers, folders, word counts)
• Schema (--schema): All frontmatter keys with frequency, types, examples

Integration

The 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.