AgentSkillsCN

trioexplorer

使用 Trioexplorer CLI 搜索临床病历。当用户需要搜索患者病历、列出队列、查看搜索历史，或探索临床病历数据库时，可选用此工具。

SKILL.md
--- frontmatter
name: trioexplorer
description: 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.
allowed-tools: Bash

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
  • •--patient-id UUID — Filter to specific patient
  • •--encounter-id UUID — Filter to specific encounter
  • •--note-types TYPES — Comma-separated note types (e.g., "Progress Note,Discharge Summary")
  • •--date-from DATE — Filter notes from date (YYYY-MM-DD)
  • •--date-to DATE — Filter notes to date (YYYY-MM-DD)
  • •--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 — Advanced metadata filters (JSON format)
  • •--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

Deduplication Modes

Use -d / --distinct to control how results are deduplicated. Each mode returns the highest-scoring result per entity.

ModeDescriptionUse Case
patientOne result per patientFind unique patients matching criteria
encounterOne result per encounter (default)See different visits for same condition
noteOne result per noteMultiple chunks from same note consolidated
noneNo deduplicationSee all matching chunks

Examples

bash
# Find unique patients with Dupixent side effects
trioexplorer search "Dupixent side effects" -d patient -k 20

# See all encounters mentioning chest pain (default behavior)
trioexplorer search "chest pain" -d encounter -k 15

# Get all matching chunks without deduplication
trioexplorer search "metformin dosing" -d none -k 50

# Dedupe by note (useful when searching for specific documentation)
trioexplorer search "discharge instructions" -d note -k 10

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

Patient & Encounter Filtering

Filter to a specific patient:

bash
trioexplorer search "medication history" --patient-id "001EFCDE-62D9-42A0-B184-3E3C732EBDA5"

Filter to a specific encounter:

bash
trioexplorer search "vital signs" --encounter-id "ABC12345-6789-0DEF-GHIJ"

Combine patient with date range and note types:

bash
trioexplorer search "diabetes management" \
  --patient-id "001EFCDE-62D9-42A0-B184-3E3C732EBDA5" \
  --date-from 2025-01-01 \
  --note-types "Progress Note,Discharge Summary"

Filter by note type only:

bash
trioexplorer search "discharge planning" --note-types "Discharge Summary"

Filter by date range:

bash
trioexplorer search "recent visits" --date-from 2025-01-01 --date-to 2025-06-30

Entity Filters

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

Available filter fields

CategoryFields
Entitiesmedications, diagnoses, symptoms, procedures, lab_tests, vitals, allergies
Assertionspresent, negated, historical, hypothetical, family
Combinedmedications_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