Agent skill

trioexplorer

Search clinical notes using the Trioexplorer CLI. Use when the user wants to search patient notes, list cohorts, view search history, or explore the clinical notes database.

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Install this agent skill to your Project

npx add-skill https://github.com/majiayu000/claude-skill-registry/tree/main/skills/data/trioexplorer

SKILL.md

Trioexplorer CLI

Search clinical notes using the trioexplorer CLI. The CLI requires TRIOEXPLORER_API_KEY to be set.

Commands

Search clinical notes

bash
trioexplorer search "query" [options]

Options:

  • -k N — Number of results (default: 10)
  • -d MODE — Dedupe mode: patient, encounter, note, or none (default: encounter)
  • --type TYPE — Search type: keyword, semantic, or hybrid (default)
  • --cohort-ids IDS — Comma-separated cohort IDs to search
  • --format FORMAT — Output: table (default), json, or csv
  • --full-text — Show full note text
  • --entity-filters JSON — Filter by extracted entities (see Filters section)
  • --filters JSON — Turbopuffer metadata filters
  • --rerank false — Disable semantic reranking
  • --vector-weight N — Weight for vector vs keyword (0.0-1.0)

List resources

bash
trioexplorer list cohorts [--limit N]
trioexplorer list notetypes [--search TEXT]
trioexplorer list history [--page N] [--user-id ID]
trioexplorer list entities
trioexplorer list filters [--namespace NS] [--field NAME]

Statistics

bash
trioexplorer stats history [--date-from DATE] [--date-to DATE]

Global options

  • --debug — Enable request/response logging
  • --help — Show help for any command

Basic Examples

Search for diabetes-related notes:

bash
trioexplorer search "diabetes management" -k 20

Semantic search with JSON output:

bash
trioexplorer search "patient having trouble with blood sugar" --type semantic --format json

Search within specific cohorts, dedupe by patient:

bash
trioexplorer search "chest pain" --cohort-ids abc123 -d patient -k 10

Entity Filters

Filter search results by extracted medical entities. Use --entity-filters with JSON.

Available filter fields

Category Fields
Entities medications, diagnoses, symptoms, procedures, lab_tests, vitals, allergies
Assertions present, negated, historical, hypothetical, family
Combined medications_present, diagnoses_negated, lab_tests_present, etc.

Medications filters

bash
# Notes where metformin is currently prescribed
trioexplorer search "diabetes control" \
  --entity-filters '{"medications_present": ["metformin"]}'

# Multiple medications (OR within field)
trioexplorer search "pain management" \
  --entity-filters '{"medications_present": ["oxycodone", "hydrocodone", "tramadol"]}'

# Biologics for asthma
trioexplorer search "asthma exacerbation" \
  --entity-filters '{"medications_present": ["Dupixent", "Nucala", "Fasenra"]}'

Lab tests filters

bash
# Notes mentioning A1C
trioexplorer search "glycemic control" \
  --entity-filters '{"lab_tests": ["A1C", "hemoglobin A1c"]}'

# Kidney function labs
trioexplorer search "renal function" \
  --entity-filters '{"lab_tests_present": ["creatinine", "BUN", "GFR"]}'

# Liver function panel
trioexplorer search "hepatotoxicity" \
  --entity-filters '{"lab_tests": ["AST", "ALT", "bilirubin"]}'

Vitals filters

bash
# Blood pressure mentions
trioexplorer search "hypertension management" \
  --entity-filters '{"vitals": ["blood pressure", "BP", "systolic"]}'

# Respiratory vitals
trioexplorer search "respiratory distress" \
  --entity-filters '{"vitals_present": ["oxygen saturation", "SpO2", "respiratory rate"]}'

Combining filters (AND logic between fields)

bash
# Medication AND diagnosis
trioexplorer search "treatment efficacy" \
  --entity-filters '{"medications_present": ["metformin"], "diagnoses_present": ["diabetes"]}'

# Medication AND lab monitoring
trioexplorer search "drug monitoring" \
  --entity-filters '{"medications_present": ["warfarin"], "lab_tests": ["INR"]}'

Discovering Filter Values

Check what entities are indexed before filtering:

bash
# List available filter fields for a cohort
trioexplorer list filters --namespace "v2-cohort-COHORT_ID-arctic"

# List medication values
trioexplorer list filters --namespace "v2-cohort-COHORT_ID-arctic" --field medications --limit 100

# Search for specific medication
trioexplorer list filters --namespace "v2-cohort-COHORT_ID-arctic" --field medications -o csv | grep -i "metformin"

Fallback: Query-based filtering

If an entity isn't indexed, include it in the search query:

bash
# Instead of entity filter, include medication in query
trioexplorer search "dupixent lack of efficacy" --cohort-ids COHORT_ID -d patient -k 10

Task: $ARGUMENTS

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