openphacts github Repositories

Building and Deploying the OPS Platform

ops-docker

A Docker Compose configuration to bring to life the Open PHACTS platform on Docker.

Most of the docker images are in https://hub.docker.com/u/openphacts/ from other GitHub repositores (See below) - while others are specialized within this repository (e.g. mysql).

Slides: http://slides.com/soilandreyes/2016-07-06-openphacts#/
Webinar and Video
has Dockerfile - Uses Docker Compose
Does not include 3-scale (https + api key authentication)
includes stack from virtuoso up to explorer2
not included: CRS (runs on Windows), ConceptWiki (shared instance)

Q: What does ops-docker depend on?

ops-platform-setup

This is a “meta” repository that contains notes and a few bits-and-bobs scripts and config files. It can’t be “run” by itself.

has 2.0.0 branch, no 2.1.

platform w/o data

Core OPS Components

OPS_LinkedDataApi

PHP implemenation of the Open PHACTS API.

Directory api-config-files contains Puelia templates.

PHP Dependencies:

Puelia
Moriarity
ARC

Web Service Dependencies:

queryExpander
IMS

queryExpander

Java. Last edited 2016/04.

The Standalone Query Expander.

Depends on repos:

Query Expander Demo Page

IdentityMappingService

Java application and web service to obtain URI mappings.

Last commit: 2016/04

explorer2

The Open PHACTS Explorer is an HTML5 & CSS3 application for chemical information discovery and browsing. It is used to search for chemical compound and target information using a web search interface.

Last updated: 2015/11

Has Dockerfile. Has Docker image openphacts/explorer2.

Uses / depends-on:

Ruby on Rails
Ember JS
ops.js repo
OPS_LinkedDataApi repo (Linked Data API)

ops-crs

The sources of the Royal Society of Chemistry’s (RSC) Chemical Registration Service (CRS).

The CRS is a top-level component of the Open PHACTS platform. However, it is not part of the Open PHACTS distribution. Rather, it’s functionality is provided via web apps running at http://www.rsc.org.

The /structure commands of the Open PHACTS API are forwarded to the CRS web app. Thus those commands will fail if you are not connected to the internet.

The CRS is a Microsoft .NET and C# web application.

Chemical Structure Search

Last updated: 2016/07

Currently “broken” (2016/10).

Projects using Open PHACTS

ops-search

ElasticSearch-based search service for Open PHACTS, previously called “IRS2”. Under development.

has Dockerfile

ops.js

Javascript based API with methods used to access the Open PHACTS Discovery Platform and parse the responses

JavaScript, last edited 2016/01.

has Dockerfile for testing

Used by explorer2 and ops-html-widgets and http://www.biojs.io/d/openphacts-vis-compoundinfo
Published on https://www.npmjs.com/package/ops.js
Can be executed standalone as it includes comprehensive tests of API (using node.js)

Available as an npm package (for 1.5): https://www.npmjs.com/package/ops.js