glebis 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(usesGENOME_VAULT_ROOTenv 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.