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 Athena

SQL tables are generated from spreadsheet CSV files

  • disease_name
  • orpha_code
  • icd10_code

FHIR resources are referenced using

  • subject_ref (FHIR Patient.id)
  • encounter_ref (FHIR Encounter.id)
  • documentreference_ref (FHIR DocumentReference.id)

FHIR Condition.code is selected using

  • icd10_code

Project links

Data verified by PyPI on Apr 16, 2025
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

Owner

PyPI data
Data sourced directly from PyPI's database.

GitHub Statistics

Data verified by PyPI on Apr 16, 2025
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

Apache Software License

Requires

Python >=3.10

Provides Extra

tests

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

rapid_elastic-1.0.1.tar.gz (32.5 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

rapid_elastic-1.0.1-py3-none-any.whl (29.5 kB view details)

Uploaded Python 3

File details

Details for the file rapid_elastic-1.0.1.tar.gz.

File metadata

  • Download URL: rapid_elastic-1.0.1.tar.gz
  • Upload date:
  • Size: 32.5 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.12.9

File hashes

Hashes for rapid_elastic-1.0.1.tar.gz
Algorithm Hash digest
SHA256 e37c20bd233c7356c21be72c880fff21cc8d76c7d3265b26de3020b018750ae1
MD5 9a0e8d1c335b9df2d3f0a392129720d0
BLAKE2b-256 f2f89e682f42bd977e1638b68a0d5d11411fc10ddad202b026815b0f1f082155

See more details on using hashes here.

Provenance

The following attestation bundles were made for rapid_elastic-1.0.1.tar.gz:

Publisher: pypi.yaml on smart-on-fhir/rapid-elastic

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file rapid_elastic-1.0.1-py3-none-any.whl.

File metadata

  • Download URL: rapid_elastic-1.0.1-py3-none-any.whl
  • Upload date:
  • Size: 29.5 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.12.9

File hashes

Hashes for rapid_elastic-1.0.1-py3-none-any.whl
Algorithm Hash digest
SHA256 73333c691f1775cb4c6768a972336cff10dcbfc60b48a322e204b2f7ccbf97e6
MD5 3f1206273cc2ec419da0189b370c5d10
BLAKE2b-256 347ece7885f3aa340da2f185f9abd00321b2d9aa34757e53b8d9eb3be8beb5ca

See more details on using hashes here.

Provenance

The following attestation bundles were made for rapid_elastic-1.0.1-py3-none-any.whl:

Publisher: pypi.yaml on smart-on-fhir/rapid-elastic

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Release history Release notifications | RSS feed

This release

1.0.1 This release

2 files

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page