bofuld / phenotype_data_acquisition

The repository for code and documentation produced by the N3C Phenotype and Data Acquisition workstream

Welcome to the N3C Phenotype & Data Acquisition Workstream

Our work. In collaboration with other N3C workstreams, we are working to establish a common COVID-19 phenotype that will define the data pull for the limited data set. We are working to write cohort identification and data extraction scripts against four common data models (OMOP, PCORnet, ACT, and TriNetX) in order to aid sites in submitting data to the N3C central repository.

You’ll find the most recent phenotype here.

If you’re a new N3C site: Please start by reviewing the documentation we’ve written for running our scripts, customized for each data model.

Want to work with us? How to get involved. We encourage participation from the community! If you have a bug or an idea, browse the open issues before opening a new one. Please use the GitHub issue tracker to submit any comments or suggestions.

Where to find known issues

We are using Github issues for our public bugs. We will keep a close eye on this and try to make it clear when we have a fix. Before you file a new issue please check to make sure your problem doesn’t already exist.

Reporting new issues

The best way for your bug to get fixed is to open a GitHub Issue and provide enough information for us to try and replicate what you’re seeing. Useful information includes the database management system you’re using, the data model you’re running, the database client you’re using, your operating system, etc.

Taking it to Slack

It’s important to us that we are able to do our best work and be good members in the community. If we need to understand more about your issue, we will share a quick message with you on the CD2H Slack. That way we will never clog your inbox over this!

Documentation

We will use the Wiki on this repo to share all documentation. Please take a look!

Code of Conduct

It’s important to us to keep our community awesome, growing and collaborative and ask for your help in keeping it that way. Please refer to our Code of Conduct for some guidelines.

How to connect with us. Want to ask a question or just say hi? We’d love to hear from you. If you have already onboarded you can find us on the #n3c-phenotype channel on Slack. To learn more about the N3C and onboard, please visit us here.

We can’t do this without you. Big thanks to all our contributors!