rapid-elastic

Disease Synonyms Curation

• Disease names and synonyms were HUMAN expert curated and assisted via ChatGPT with additional checks within NLM GeneReviews, OrphaNet, and Google searches.
• disease_names_expanded.json is pre-built and recommended for use without modification.
• disease_names.py assists curation if changes need to be made: read spreadsheet CSV, write disease names JSON, recommend GPT4 prompts, find duplicates, and merges curated JSON.

Quickstart

1. configure ENV variables query your Elasticsearch server (within your VPN/firewall)

   1. ELASTIC_HOST : default http://localhost:9200
   2. ELASTIC_USER : basic auth
   3. ELASTIC_PASS : basic auth

2. pipx install rapid-elastic

3. rapid-elastic

Elasticsearch server

Read the server setup docs.

KQL (Kibana Query Language)

• By default, synonyms used to match any "exact phrase" in the note.
• see kql_syntax.py for alternate methods of building Elasticsearch queries.

Each Elasticsearch hit is saved to "output" folder

• subject_ref (FHIR Patient.id)
• encounter_ref (FHIR Encounter.id)
• document_ref (FHIR DocumentReference.id)
• group_name (optional)
• document_title (optional)

SQL Tables

SQL files are loaded in order 1-6 to produce the result table rapid__match_compare

ICD10 diagnosis

1. rapid__codeset.sql

• disease_name (human label)
• disease_alias (machine label)
• orpha_code (Orphanet code)
• icd10_code (ICD10 code)

2. rapid__match_icd10.sql

• disease_name (human label)
• disease_alias (machine label)
• orpha_code (Orphanet code)
• icd10_code (ICD10 code)
• subject_ref (FHIR Patient.id)
• encounter_ref (FHIR Encounter.id)
• FHIR condition (optional metadata)

NOTES search results

3. rapid__match_notes.sql

• disease_alias (machine label)
• subject_ref (FHIR Patient.id)
• document_ref (FHIR DocumentReference.id)
• encounter_ref (FHIR Encounter.id)
• document_title (optional)
• group_name (optional)

SAMPLE tables

Select up to 100 patients per disease into these tables.

4. rapid__match_notes_sample_patients.sql

• disease_alias
• subject_ref

5. rapid__match_icd10_sample_patients.sql

• disease_alias
• subject_ref

6. rapid__match_both_sample_notes.sql

• disease_alias
• subject_ref
• document_ref
• encounter_ref
• document_title (optional)
• group_name (optional)

X. rapid__match_notes_sample_notes.sql (deprecated)

COMPARE results tables

6. rapid__match_compare.sql

• disease_alias
• hit_icd10 (matched ICD10-10)
• hit_notes (matched note search)
• hit_sample_patients (in sample of selected patients)
• hit_sample_notes (in sample of selected patient notes)
• icd10_code (match result if hit_icd10=True)
• document_ref
• subject_ref