PheKB ⬇️ Exporter & 🔬 Viewer

Utility that extracts PheKB phenotypes into a semi-structured JSON format, a simple API that serves them up, and a UI that can be used to view them and make notes.

Requirements

1. NodeJS 10+

Setup

1. Install dependencies

npm install -g yarn && yarn install

2. Setup Credentials

Create a file called .env in the workspace root that looks like:

[email protected]
PHEKB_PASS=s3cretp4ss

Run

Scraper

yarn run update-data

By default, this will only scrape the phenotypes with IDs that are listed in phekb-phenotypes-calculated.json. To crawl PheKB, set the PHEKB_CRAWL environment variable to true. This can be done by adding to the .env file, or running:

PHEKB_CRAWL=true yarn run update-data

Crawling will try all the nodes on the Drupal site between 0 and 2000. To change the start and end point, set the PHEKB_CRAWL_START and PHEKB_CRAWL_END environment variables:

PHEKB_CRAWL=true PHEKB_CRAWL_START=1990 PHEKB_CRAWL_END=2000 yarn run update-data

💡 This will delete your local data and generate a fresh copy by scraping PheKB.

Viewer

yarn run viewer

This will spin up the express api at http://localhost:3000/phenotype and serve up the web app at http://localhost:1234.

Usage

View the UI at http://localhost:1234.

Columns will be created containing phenotype data from PheKB. Click on files and datasets to view them in a resizable side panel. Add columns for taking notes, and right click on column headers to move them or delete them.

The Download button will export a CSV file containing your notes.

ℹ Data is saved in localStorage, so exporting isn't required unless you want to share your notes.