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# PRIME Public Health Data Infrastructure (PHDI)
# DIBBs Query Connector

[![codecov](https://codecov.io/gh/CDCgov/phdi/branch/main/graph/badge.svg)](https://codecov.io/gh/CDCgov/phdi)
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- [PRIME Public Health Data Infrastructure (PHDI)](#prime-public-health-data-infrastructure-phdi)
- [Overview](#overview)
- [Problem Scope](#problem-scope)
- [Getting Started](#getting-started)
- [Main Features](#main-features)
- [Where to Get PHDI](#where-to-get-phdi)
- [Documentation](#documentation)
- [Additional Acknowledgments](#additional-acknowledgments)
- [Standard Notices](#standard-notices)
- [Public Domain Standard Notice](#public-domain-standard-notice)
- [License Standard Notice](#license-standard-notice)
- [Privacy Standard Notice](#privacy-standard-notice)
- [Contributing Standard Notice](#contributing-standard-notice)
- [Records Management Standard Notice](#records-management-standard-notice)
- [Related documents](#related-documents)
- [Additional Standard Notices](#additional-standard-notices)

**General disclaimer** This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm). GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.

## Overview

This repository is a part of the CDC/USDS [PHDI project](https://cdcgov.github.io/phdi-site/) and has two components:
1. PHDI Python Package
2. PHDI containerized Building Blocks
This repository is a part of the CDC/USDS [PHDI project](https://cdcgov.github.io/phdi-site/) and seeks to build the DIBBs Query Connector.

The PHDI Python package contains source code for a platform to help public health authorities (PHAs) ingest and report on public health data. This platform is composed of **Building Blocks**, which are modular software tools that, when composed together, can improve data quality and reduce data cleaning workloads by providing analysis-ready data to downstream public health surveillance systems and other analytical and reporting applications.
The DIBBs Query Connector app offers a REST API and comprehensive UI for public health staff to query a wide network of healthcare organizations (HCOs), providing access to more complete and timely data.

PHDI contains:
- Our SDK — the Python library containing Building Block source code
- [Repository](https://github.com/CDCgov/phdi/tree/main/phdi)
- [API documentation](https://cdcgov.github.io/phdi/latest/sdk/phdi.html)
- Containerized web services exposing Building Block functionality as HTTP endpoints
- [Repository](https://github.com/CDCgov/phdi/tree/main/containers)
- [User guide](https://cdcgov.github.io/phdi/) (under Building Blocks)
- Cloud Starter Kit — Repositories that implement a complete cloud-based pipeline composed of Building Blocks
- [Azure](https://github.com/CDCgov/phdi-azure)
- [Google Cloud Platform](https://github.com/CDCgov/phdi-google-cloud)
The Query Connector is a tool for public health practitioners to quickly retrieve patient records and relevant case information from HCOs. The tool works by connecting to Qualified Health Information Networks (QHINs) within the Trusted Exchange Framework and Common Agreement (TEFCA), ensuring immediate access to essential health data and facilitating timely public health decisions and interventions. Public health staff can interact with the Query Connector manually by entering simple patient details — such as name, date of birth, or medical identifiers — into a web-based search form. The tool also allows for automated queries via integration engines like Rhapsody and Mirth.  

### Problem Scope

Current public health systems that digest, analyze, and respond to data are siloed. Lacking access to actionable data, our national, as well as state, local, and territorial infrastructure, isn’t pandemic-ready. Our objective is to help the CDC best support PHAs in moving towards a modern public health data infrastructure. See our [public website](https://cdcgov.github.io/dibbs-site/) for more details.

PHDI is a sibling project to [PRIME ReportStream](https://reportstream.cdc.gov), which focuses on improving the delivery of COVID-19 test data to public health departments, and [PRIME SimpleReport](https://simplereport.gov), which provides a better way for organizations and testing facilities to report COVID-19 rapid tests to public health departments.

## Getting Started

In order to use the PHDI library, you need [Python 3.9 or higher](https://www.python.org/downloads/) and [pip python package manager](https://pip.pypa.io/en/stable/installation/) (or any python package manager).

To install using pip:
```
pip install phdi
```

## Main Features

Here are the current tools that PHDI offers:
- **Containerized Building Blocks**
- **[Alerts](https://cdcgov.github.io/phdi/latest/containers/alerts.html)** - Provides the ability to send alerts via SMS, Slack, or Microsoft Teams
- **[FHIR Converter](https://cdcgov.github.io/phdi/latest/containers/fhir-converter.html)** - Enables conversion of health data from legacy formats (e.g., HL7 version 2, CCDA) to [FHIR](https://hl7.org/FHIR/), a standard for health care data exchange
- **[Data Ingestion](https://cdcgov.github.io/phdi/latest/containers/ingestion.html)** - Includes the entire pipeline of Building Blocks below
- **[Harmonization](https://cdcgov.github.io/phdi/latest/containers/ingestion.html#tag/fhirharmonization)** - Standardizes input data (e.g., patient names and phone numbers) to streamline the process of cleaning data and improve data quality
- **[Geospatial](https://cdcgov.github.io/phdi/latest/containers/ingestion.html#tag/fhirgeospatial)** - Provides a common interface for obtaining precise geographic locations based on street addresses from input data
- **[Linkage](https://cdcgov.github.io/phdi/latest/containers/ingestion.html#tag/fhirlinkage)** - Assigns a common identifier to patient records in order to link and deduplicate patient records seen across data contributors
- **[Transport](https://cdcgov.github.io/phdi/latest/containers/ingestion.html#tag/fhirtransport)** - Offers functionality for reading and writing data from storage resources (e.g,. FHIR servers)
- **[Message Parser](https://cdcgov.github.io/phdi/latest/containers/message-parser.html)** - Extracts desired fields from a given message
- **[Tabulation](https://cdcgov.github.io/phdi/latest/containers/tabulation.html)** - Extracts data from a FHIR server, converts it to a tabular representation, and stores it to a user-defined tabular storage file type (e.g., Parquet or CSV)
- **[Record Linkage](https://cdcgov.github.io/phdi/latest/containers/record-linkage.html)** - Links new health care messages to existing records if a connection exists
- **[Validation](https://cdcgov.github.io/phdi/latest/containers/validation.html)** - Checks whether health care messages are in the proper format and contain user-defined fields of interest
- **Implementation Support** - Resources to help users implement PHDI tools to manage their data and analysis workflows
- **[Examples](https://github.com/CDCgov/phdi/tree/main/examples)** - Sample data that simulates how a Building Block could be used
- **[Tutorials](https://github.com/CDCgov/phdi/tree/main/tutorials)** - Step-by-step instructions to implement Building Blocks source code
The current methods that public health jurisdictions use to collect data from HCOs can be time-consuming and cumbersome, often involving manual interventions like phone calls and faxes. The Query Connector aims to streamline the collection of health data using an intuitive querying process that can leverage QHINs within TEFCA or direct connections, thereby enabling data exchange from multiple HCOs for a variety of public health use cases such as newborn screening or STI case investigation. 

## Where to Get PHDI
DIBBs Query Connector is a sibling project to

The source code is hosted on GitHub at: https://github.com/CDCgov/phdi.
* [PHDI](https://github.com/CDCgov/phdi) to further help display, access, and interpret publich health data;
* [PRIME ReportStream](https://reportstream.cdc.gov), which focuses on improving the delivery of COVID-19 test data to public health departments; and
* [PRIME SimpleReport](https://simplereport.gov), which provides a better way for organizations and testing facilities to report COVID-19 rapid tests to public health departments.

The latest released version is available at the [Python Package Index (PyPI)](https://pypi.org/project/phdi/).
## Implementation

**Python modules**
```
pip install phdi
```
**Implementation Support** - Resources to help users implement DIBBs Query Connector tools to manage their data.

**Containerized services**
```
build from source
build Docker locally
pull down Docker images from GitHub
```
- **Examples** - Forthcoming!
- **Tutorials** - Forthcoming!

## Documentation

PHDI documentation is currently hosted on GitHub Pages: https://cdcgov.github.io/phdi/
DIBBs Query Connector documentation, including instructions on how to install dependencies and run locally, is currently hosted within the repository, [here](https://github.com/CDCgov/dibbs-query-connector/blob/main/query-connector/README.md).

There, you can find our:
- SDK API reference documentation
- User guide for containerized Building Blocks
Access to the demo instance of the DIBBs Query Connector is available at [dibbs.cloud/tefca-viewer]().

## Additional Acknowledgments
## Additional Acknowledgments

We mapped the rootnames of the PHDI database to nicknames produced by the aggregation and synthesis of open source work from a number of projects. While we do not employ the packages and wrappers used by the various projects (merely their open source data), we wish to give credit to their various works building collections of nickname mappings. These projects are:

Expand Down Expand Up @@ -165,13 +104,13 @@ published through the [CDC web site](http://www.cdc.gov).

- [Open Practices](docs/open_practices.md)
- [Rules of Behavior](docs/rules_of_behavior.md)
- [Disclaimer](docs/DISCLAIMER.md)
- [Disclaimer](docs/DISCLAIMER.md)g
- [Contribution Notice](docs/CONTRIBUTING.md)
- [Code of Conduct](docs/code-of-conduct.md)

### Additional Standard Notices

Please refer to [CDC's Template Repository](https://github.com/CDCgov/template)
Please refer to [CDC&#39;s Template Repository](https://github.com/CDCgov/template)
for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md),
[public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md),
and [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).

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