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General consideration

First, deploy the BioNetDB WAR file (bionetdb.war) following the intructions from Deploy WAR file.

Understanding the URL

The general format of the REST API web services is: 

Code Block
titleOpenCGA RESTful URL Structure

where HOST_URL is the name of the host machine and the name of Java war file deployed in web server (e.g. tomcat) over that server for example localhost:8080/bionetdb

Entities inside the curly braces { } are the web service parameters, and they are treated as variables. For example the following URL:

Code Block
titleQuick Example
http://localhost:8080/bionetdb/webservices/rest/v1/table/cypher?query="match (n:VARIANT) return count(n)"

As is explained later in this documentation, this RESTful web service will execute a Cypher query returning results as a table:

  • apiVersion (v1) : indicates BioNetDB version to retrieve information from, data models and API may change between versions. 
  • resource (table) : specifies the data type of what the user wants to retrieve. This can be one of resources listed below. 
  • endpoint (cypher) : these parameters must be specified depending on the nature of your input data; in our example, cypher indicates we are going to execute a Cypher query. 
  • options (query) : variables in key value pair form, passed as query parameters; in our example, it is the Cypher query itself: "match (n:VARIANT) return count(n)"

URL parameters


apiVersions are numbered as v1v2, etc. At this moment we are heading to first stable apiVersion which is v1.


There are several resources implemented: 

ResourcePathDescriptionMain endpoints
Network/networkMethods to work with networkscyper, info, model
Node/nodeMethods to work with nodescyper, info
Path/pathMethods to work with paths between nodescypher
Table/tableMethods to get output results as tabelscypher


These query parameters can modify the behaviour of the query (excludeincludelimitskip and count) or add some filters to some specific endpoints to add useful functionality. The following image shows the options for the previous webservice.


BioNetDB has been documented using Swagger project. Detailed information about resourcesendpoints and options is available at your own installation:


Image Added

Table of Contents:

Table of Contents