notebooks.qmd

# Introduction

Tufts CTSI Informatics uses interactive "RDR notebooks" to provide cohort discoveries and data deliveries to its clients.

RDR notebooks are hosted within a section of our Tufts Research Data Warehouse (TRDW) called the **[Research Data Request Portal](https://trdw-rdr.tuftsmedicine.org/)**.

# Notebook Anatomy

## Purpose
While RDR notebooks are used to deliver data, they also contain code, text, hyperlinks, HTML snippets and more. This can all be overwhelming when receiving aviewing a notebook for the first time. The purpose of this guide is to introduce the sections and features of a typical RDR notebook. Once you've become familiar with the general RDR notebook structure, you'll be better able to understand the factors that went into developing your cohort and trace the provenance of your data extraction.

## Overview
Concept sets representing an array of clinical events can be combined with logic statements to create cohort definitions. Developing concept sets to accurately represent clinical events of interest and then piecing them together to correctly define a cohort are the first two steps to every data extraction.

Besides just delivering data, one goal of our RDR notebooks is to provide a transparent and collaborative way to build concept sets and cohort definitions. 

## Section: *Cohort Overview*
The Cohort Overview section contains information about your cohort: patient and event counts, demographic breakdowns, and the cohort definition itself.

### Subsection: *Cohort Demographics*

### Subsection: *Cohort Definition*

## Section: *Clinical Events and Concept Sets*
The Clinical Events and Concept Sets section is structured around the key tables in the [OMOP CDM v5.4](https://ohdsi.github.io/CommonDataModel/cdm54.html), which is the data model used by our TRDW. Clinical events represent all things that are recorded within the clinical setting, such as lab tests, diagnoses, administration of medication, and more. To model a single one of these "concepts", we create "concept sets": one or more terms from a medical terminology.