REST Web Service API

REST API Design

The general format of the REST API web services is:

https://HOST_URL/APPLICATION/webservices/rest/{apiVersion}/{resource}/{endpoint}?{options}

where HOST_URL is the URL pointing to the host server and APPLICATION is the name of Java war file deployed in web server (e.g. Tomcat), for example, http://localhost:8080/bionetdb

Entities inside the curly braces { } are the web service parameters:

• apiVersion: indicates BioNetDB version to retrieve information from, data models and API may change between versions.

• resource: specifies the data type of what the user wants to query by, e.g.: node, newtork, path...

• endpoint: these parameters must be specified depending on the resource.

• option : variables in key-value pair form, passed as query parameters.

Exmaple of BioNetDB web service URL:

http://localhost:8080/bionetdb/webservices/rest/v1/node/query?label=GENE&limit=25

Resources and Endpoints

Table below shows the different endpoint for running BioNetDB analysis.

Category	Path (/resource)	Description	Endpoints
Node Analysis	/node	Operations over nodes to facilitate complete analysis with different tools.	query, stats, add, update, delete, cypher
Path Analysis	/path	Operations over network paths to facilitate complete analysis with different tools.	query, cypher
Network Analysis	/network	Operations over subnetworks facilitate complete analysis with different tools.	stats
Functional Analysis	/functional	Complete functional analysis, e.g., to identify the most relevant genetic variants underlying a patient’s phenotypes and symptoms.	iterpretation, diseasome

Swagger

BioNetDB has been documented using Swagger project.

Client Libraries

Currently BioNetDB implements the following four client libraries:

1. Java

2. Python

3. JavaScript