openbel-api

The OpenBEL API provides RESTful API access to your BEL content. It is part of OpenBEL Platform.

Features

Nanopub Store
- Storage of nanopub including creation, retrieval, modification, and deletion actions.
- Flexible filtering of stored, nanopub based on user's custom data requirements.
- Upload a document (e.g. BEL script, XBEL, or nanopub JSON), to the Nanopub Store, as a dataset. These can later be retrieved or deleted from the nanopub Store.
- Flexible filtering of nanopub contained within a dataset.
- Download a document (e.g. BEL script, XBEL, or Nanopub JSON) from a dataset.
BEL Expressions
- Autocomplete a BEL term expression.
- Retrieve the structural components of a BEL expression.
Annotations and Namespaces
- Retrieve annotation (e.g. Disease Ontology) and namespace (e.g. GO) data.
- Retrieve equivalent namespace values from the individual.
- Retrieve orthologous namespace values from the individual.

Vocabulary

Annotation A name/value property that describes an aspect of a nanopub. For example Ncbi Taxonomy:Homo sapiens is an annotation for the Human species.

Namespace A biological identifier that is curated and maintained by an organization. For example the Gene Ontology (i.e. GO) or HGNC (i.e. HUGO Gene Nomenclature Committee) database.

nanopub A biological interaction curated from scientific literature. It is comprised of five parts.

Citation: The identification for the scientific literature where the interaction was stated.
BEL Statement: The biological interaction curated from the Citation.
Support: The text (i.e. quotation) within the Citation that supports the BEL Statement.
Experiment Context: The biological context within the experiment where the BEL Statement was observed. For example if the experiment sample was a biopsy on Human, Lung tissue then you might provide Ncbi Taxonomy: Homo sapiens and Uberon: lung epithelium.
Metadata: Additional data about this nanopub that is not part of the experiment (i.e. in Experiment Context). For example the nanopub's Reviewer, Create Date, or Reviewed Date would be considered metadata.
References: The annotation and namespace sources used in the BEL Statement, Experiment Context, and Metadata. For example Ncbi Taxonomy may refer to an annotation identified by the URI http://www.openbel.org/bel/namespace/ncbi-taxonomy.

Document: A file containing a collection of nanopub with document metadata like Name, Description, and Version. The supported document formats are BEL script, XBEL, and JSON Nanopub.

Dataset: The representation of a BEL Document within the OpenBEL API. This provides access to document metadata as well as the collection of nanopub stored in the OpenBEL API that originate from the BEL Document.

Expression: A string encoded in BEL that may represent a parameter (e.g. AKT1, GO:"apoptotic process"), term (e.g. bp(GO:"apoptotic process")), or statement (e.g. p(HGNC:AKT1) increases bp(GO:"apoptotic process")).

Nanopub Store: A database used for BEL nanopubs. It facilitates storage, filtering, and transformation of nanopubs.

Technical requirements

The OpenBEL API is built to run with JRuby and Java 8.

System Requirements

Java 8
JRuby, 9.x series (9.0.x.0 is recommended)
- The 9.x series is required due to a Ruby language 2.0 requirement.
- See "Installation" below for configuring JRuby and isolating the openbel-api application.
MongoDB, version 3.2 or greater
- Follow MongoDB download page for download and installation instructions.
SQLite, version 3.8.0 or greater
- Follow SQLite download page for download and installation instructions.

Getting up and Running

See the DOCKER.md file instructions for using Docker (recommended).

Installation

The OpenBEL API is packaged and installed as a Ruby gem. A Ruby gem is packed library or application that runs on the Ruby virtual machine. In this case OpenBEL API runs only on JRuby.

JRuby Configuration

Unpack JRuby archive.
Export the JRUBY_HOME environment variable to the unpacked JRuby archive directory.
Add "$JRUBY_HOME/bin" to your PATH environment variable.
Export the GEM_HOME and GEM_PATH environment variable to any directory accessible to the current user. This is where JRuby gems will be installed. The OpenBEL API and dependencies will be installed into this directory for isolation from other Ruby applications running on the system.

Example JRuby Configuration

Assume that we have unpacked JRuby to /opt/jruby. We should then:

Export JRUBY_HOME to /opt/jruby.
Add $JRUBY_HOME/bin to our PATH environment variable.
Export both GEM_HOME and GEM_PATH to /opt/jruby/gems.
Add $GEM_HOME/bin to our PATH environment variable.
Proceed with Installation of OpenBEL API.

Installation of OpenBEL API

Installation uses the RubyGems site to download and install the gem from. To install the OpenBEL API gem run the gem install command available within your JRuby installation.

gem install openbel-api

All of the application dependencies needed by openbel-api will be installed during this process.

Tip If the openbel-api executable is not available make sure $GEM_HOME/bin is included on your PATH. See JRuby Configuration above.

Configuration

The OpenBEL API requires a configuration file to set up a few things. You can create an initial configuration file using the openbel-config command.

openbel-config --file openbel-api-config.yml

[Configuring the Nanopub Store][https://github.com/OpenBEL/openbel-api/wiki/Configuring-the-Nanopub-Store]

Resource RDF data Annotations, namespaces, and dataset storage are represented as RDF data. The data is stored in an on-disk database using Apache Jena (Java library included with openbel-api).

You will need to configure the location of the Apache Jena TDB database that holds this data.

The default configuration is:

resource_rdf:
  jena:
    tdb_directory: 'biological-concepts-rdf'

Tip You can obtain the latest Resource RDF database (20150611) from the OpenBEL build server.

Resource search Annotations and namespaces can be full-text searched using a SQLite database. The data is stored in an on-disk file.

The default configuration is:

resource_search:
  sqlite:
    database_file: 'biological-concepts-rdf.db'

Tip You can obtain the latest Resource Search database (20150611) from the OpenBEL build server.

Enabling Authentication

The OpenBEL API uses Token-based authentication supported by Keycloak. The OpenBEL API is equipped to require authentication for specific API paths (e.g. nanopub, Datasets). The implementation uses Keycloak for a single sign-on service.

By default, authentication is disabled. The default configuration is:

# Set a secret used during session creation....
session_secret: 'changeme'

auth:
  # Controls whether the API requires authentication
  enabled: false
  # Used by the auth middleware to decode and verify the JWT
  #secret:   'JWT secret here'

# API Authentication is provided via JWTs from Keycloak
#    see http://jwt.io/ and https://keycloak.org
# auth:
#   # Controls whether the API requires authentication
#   enabled: true
#   # Used by the auth middleware to decode and verify the JWT
#   secret: |
#     -----BEGIN PUBLIC KEY-----
#     <keycloak_pub_key>
#     -----END PUBLIC KEY-----

An example The keycloak Pub Key can be found in the Admin console for Keycloak:

Realm Settings
Keys tab
Public Key -> View

Running the OpenBEL API

The OpenBEL API can be run using the openbel-api command and passing a configuration file.

The configuration file can be provided in two ways:

Command option (--file)
Environment variable named OPENBEL_API_CONFIG_FILE

Command option

openbel-api --file "/path/to/openbel-api-config.yml"

Environment variable

export OPENBEL_API_CONFIG_FILE="/path/to/openbel-api-config.yml"

openbel-api

To configure server options such as port, background execution, or number of threads you will need to provide an extra set of arguments to the openbel-api command. These options help configure the Puma HTTP server that is included with OpenBEL API.

Example running on port 9000 with up to 16 threads.

openbel-api --file openbel-api-config.yml -- --port 9000 --threads 1:16

Note Run openbel-api --help for more information and options.

Running behind Nginx (or another reverse proxy)

The OpenBEL API beings at the /api path. If you plan OpenBEL API behing a reverse proxy then you will want to setup a route to /api.

For example the following Nginx configuration will proxy from http://$hostname/api to http://localhost:9000/api.

server {
    listen        0.0.0.0:80;
    server_name   $hostname;
    access_log    /var/log/nginx/access.log main;
    error_log     /var/log/nginx/error.log info;

    location /api {
        proxy_pass               http://localhost:9000;
        proxy_set_header         Host $host;
        proxy_set_header         X-Real-IP $remote_addr;
        proxy_set_header         X-Real-Base-URL $scheme://$host;
        proxy_set_header         X-Real-URL $scheme://$host$request_uri;
        proxy_buffer_size        128k;
        proxy_buffers            4 256k;
        proxy_busy_buffers_size  256k;
        client_max_body_size     50M;
    }
}

Upgrading

Upgrading instructions

API Documentation

API documentation with Try it functionality is available here OpenBEL API documentation. You can download the RAML 0.8 or Swagger specification files, try it on the webpage or generate curl, httpie, and various language templates for using the API.

Development

Branches

master branch
- Contains stable code. Releases are created from this branch using a tag (e.g. MAJOR.MINOR.PATCH).
next branch
- Contains unstable code. Commits should be merged into master after it stabilizes.

Releases

Releases of openbel-api should follow these steps:

Add changes for this version to the CHANGELOG file. This file is modelled after http://keepachangelog.com/.
Push the changes for CHANGELOG on the master branch.
Ensure the master branch has all of the required changes.
Run make deploy-{major|minor|patch} in order to bump the version, tag and push tag
Create a release on GitHub for this version and attach the gem file (openbel-api-VERSION-java.gem)

Built with collaboration and a lot of ❤️ by the OpenBEL community.