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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)
  1. 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

  1. 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.

  1. rapid__match_notes_sample_patients.sql
  • disease_alias
  • subject_ref
  1. rapid__match_icd10_sample_patients.sql
  • disease_alias
  • subject_ref
  1. 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

  1. 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