Package: phdi
PRIME Public Health Data Infrastructure (PHDI)PRIME Public Health Data InfrastructureOverviewProblem ScopeGetting StartedMain FeaturesWhere to Get PHDIDocumentationStandard NoticesPublic Domain Standard NoticeLicense Standard NoticePrivacy Standard NoticeContributing Standard NoticeRecords Management Standard NoticeRelated documentsAdditional Standard NoticesGeneral disclaimerThis repository was created for use by CDC programs to collaborate on public health related projects in support of theCDC mission. 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.OverviewThis repository is a part of the CDC/USDSPHDI projectand has two components:PHDI Python PackagePHDI containerized Building BlocksThe 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 ofBuilding 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.PHDI contains:Our SDK — the Python library containing Building Block source codeRepositoryAPI documentationContainerized web services exposing Building Block functionality as HTTP endpointsRepositoryUser guide(under Building Blocks)Cloud Starter Kit — Repositories that implement a complete cloud-based pipeline composed of Building BlocksAzureGoogle Cloud PlatformProblem ScopeCurrent 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 ourpublic websitefor more details.PHDI is a sibling project toPRIME ReportStream, which focuses on improving the delivery of COVID-19 test data to public health departments, andPRIME SimpleReport, which provides a better way for organizations and testing facilities to report COVID-19 rapid tests to public health departments.Getting StartedIn order to use the PHDI library, you needPython 3.9 or higherandpip python package manager(or any python package manager).To install using pip:pip install phdiMain FeaturesHere are the current tools that PHDI offers:Containerized Building BlocksAlerts- Provides the ability to send alerts via SMS, Slack, or Microsoft TeamsFHIR Converter- Enables conversion of health data from legacy formats (e.g., HL7 version 2, CCDA) toFHIR, a standard for health care data exchangeData Ingestion- Includes the entire pipeline of Building Blocks belowHarmonization- Standardizes input data (e.g., patient names and phone numbers) to streamline the process of cleaning data and improve data qualityGeospatial- Provides a common interface for obtaining precise geographic locations based on street addresses from input dataLinkage- Assigns a common identifier to patient records in order to link and deduplicate patient records seen across data contributorsTransport- Offers functionality for reading and writing data from storage resources (e.g,. FHIR servers)Message Parser- Extracts desired fields from a given messageTabulation- 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- Links new health care messages to existing records if a connection existsValidation- Checks whether health care messages are in the proper format and contain user-defined fields of interestImplementation Support- Resources to help users implement PHDI tools to manage their data and analysis workflowsExamples- Sample data that simulates how a Building Block could be usedTutorials- Step-by-step instructions to implement Building Blocks source codeWhere to Get PHDIThe source code is hosted on GitHub at:https://github.com/CDCgov/phdi.The latest released version is available at thePython Package Index (PyPI).Python modulespip install phdiContainerized servicesbuild from source
build Docker locally
pull down Docker images from GitHubDocumentationPHDI documentation is currently hosted on GitHub Pages:https://cdcgov.github.io/phdi/There, you can find our:SDK API reference documentationUser guide for containerized Building BlocksAdditional AcknowledgmentsWe 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:Secure Enterprise Master Patient Index, based on OpenEMPI, conducted by Vanderbilt UniversityCurated Nicknames, scraped from genealogy webpages and run by Old Dominion University Web Science and Digital Libraries Research GroupSimple Public Domain Nickname Mappings, hand collected using various sourcesLingua En Nickname, collected from a series of GenWeb projectsdiminutives.db, compiled via a nickname extract using Wikipedia and WiktionaryStandard NoticesPublic Domain Standard NoticeThis repository constitutes a work of the United States Government and is not
subject to domestic copyright protection under 17 USC § 105. This repository is in
the public domain within the United States, and copyright and related rights in
the work worldwide are waived through theCC0 1.0 Universal public domain dedication.
All contributions to this repository will be released under the CC0 dedication. By
submitting a pull request you are agreeing to comply with this waiver of
copyright interest.License Standard NoticeThis project is in the public domain within the United States, and copyright and
related rights in the work worldwide are waived through theCC0 1.0 Universal public domain dedication.
All contributions to this project will be released under the CC0 dedication. By
submitting a pull request or issue, you are agreeing to comply with this waiver
of copyright interest and acknowledge that you have no expectation of payment,
unless pursuant to an existing contract or agreement.Privacy Standard NoticeThis repository contains only non-sensitive, publicly available data and
information. All material and community participation is covered by theDisclaimerandCode of Conduct.
For more information about CDC's privacy policy, please visithttp://www.cdc.gov/other/privacy.html.Contributing Standard NoticeAnyone is encouraged to contribute to the repository byforkingand submitting a pull request. (If you are new to GitHub, you might start with abasic tutorial.) By contributing
to this project, you grant a world-wide, royalty-free, perpetual, irrevocable,
non-exclusive, transferable license to all users under the terms of theApache Software License v2or
later.All comments, messages, pull requests, and other submissions received through
CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more athttp://www.cdc.gov/other/privacy.html.SeeCONTRIBUTING.mdfor more information.Records Management Standard NoticeThis repository is not a source of government records, but is a copy to increase
collaboration and collaborative potential. All government records will be
published through theCDC web site.Related documentsOpen PracticesRules of BehaviorDisclaimerContribution NoticeCode of ConductAdditional Standard NoticesPlease refer toCDC's Template Repositoryfor more information aboutcontributing to this repository,public domain notices and disclaimers,
andcode of conduct.