Metadata-Version: 2.4
Name: meds-biobank
Version: 0.0.37
Summary: Unofficial, lightweight Python re-implementation of parts of the **MEDS** software ecosystem, built to operate on in-memory tables loaded via PySpark rather than directly on disk. Designed for small-to-medium biobanks queried through cloud services in interactive Python notebooks.
Author-email: Andrew Zolensky <andrewlzolensky@gmail.com>
License-Expression: Apache-2.0
Project-URL: Homepage, https://github.com/Verma-Lab/meds-biobank
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pyspark>=3.0
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Dynamic: license-file

![](./docs/meds_biobank_logo.png)

# meds-biobank

> Unofficial, lightweight Python re-implementation of parts of the **MEDS** software ecosystem, built to operate on in-memory tables loaded via PySpark rather than directly on disk. Designed for small-to-medium biobanks queried through cloud services in interactive Python notebooks.

**Primary target:** Penn Medicine Biobank

---

## Table of Contents

- [Diagram](#diagram)
- [Features](#features)
  - [Standardizers](#standardizers)
  - [ETL_Pipelines](#etl_pipelines)
  - [Ontologies](#ontologies)
  - [Tokenizers](#tokenizers)

---

## Diagram

![Diagram](./docs/meds_biobank.png)

---

## Features

### Standardizers

Docs: [docs](docs/standardizers.md)

---

### ETL_Pipelines 

Docs: [docs](docs/etl_pipelines.md)

---

### Ontologies

Docs: [docs](docs/ontologies.md)

---

### Tokenizers

Docs: [docs](docs/tokenizers.md)

---
