Awesome

GOGOApi

Express RESTFul interface for providing information about GO and Taxonomy for supporting functional annotation efforts.

Installation and usage

In a local computer install node.js (you can use Node Version Manager).

Adapt config.json to suit your needs and point to suitable database locations. Data can be provided from generated or existing datasets, as explained in Datasets section below.

Install dependendencies with: npm install and start the application with node index.js /path/to/config.json

This will start a service under 0.0.0.0:4242/api (if defined as such in basepath and port configuration parameters).

NOTE: Neo4j options can be ignored for now and will be removed in upcoming releases.

Docker

A Dockerfile and an already generated Docker image are available as well. Care must be taken to adapt Docker networks so it can find pointed databases in config.json file.

Adapt your config.json file and execute as follows:

docker run --name mygogoapi -v /path/to/your/config.json:/data/config/config.json toniher/gogoapi

Datasets

• Data used by the application can be filled in a MySQL database using the following scripts: https://github.com/toniher/biomirror/tree/master/mysql

• Database dumps are also provided for convenience

  • 202010 (22G)

Import MySQL dump into an existing database (e.g., biosql):

# First uncompress the file
gunzip biosql-202010.sql.gz
# Import dump into a database
mysql -umyuser -pmypasswd biosql < biosql-202010.sql

• byosql: Name of the database, which it must be created in advance (e.g., with CREATE DATABASE `biosql` ;)
• myuser and mypasswd are a MySQL user and password, which must have read-write permissions to the database above

More information: How To Import and Export Databases in MySQL or MariaDB

Options

• Once the webservice is set up, check 0.0.0.0:4242/api for different REST examples.