/ncbi2postgresql

Load NCBI data into PostgreSQL database

Primary LanguageShellApache License 2.0Apache-2.0

ncbi2postgresql

Import NCBI data into a PostgreSQL database. Data included:

  • PMC-id
  • gene2pubmed
  • gene2pubtator and organism2pubtator

The sections below detail the steps taken to generate files and run scripts for this project.

Install Dependencies

With direnv, you will enter the Nix shell environment when you cd into this directory. If you don't want to use direnv, you'll have to explicitly call:

nix-shell

Load Data into Database

Get the data:

bash download.sh

Create and load the database:

bash create_db.sh

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