Refreshing the OPS Platform

Producing a new version of the Open PHACTS platform requires both updating the software components and populating the software services with updated versions of datasets and linksets.

Core OPS software components

  • Data Querying Service (i.e., Virtuoso + SPARQL)
  • Identity Mapping Service
  • Linked Data API Service

Steps to build (refresh) Data & Links

blue boxes are goal states
green boxes are actions
lines represent dependencies

Data Querying Service (Software)

Provides a SPARQL Endpoint for querying pharmacological & life sciences data.

Build & Deploy Process:

  • Select Triple-Store product & version (e.g., Virtuoso)
  • Obtain (download)
  • Build and/or install
  • Configure
  • Integrate
  • Run
  • Expose/Shield
  • Dockerize
  • Publish
  • Document
  • Maintain

Data Querying Service (Data)

Obtaining, preparing, and loading RDF data into the Data Service triple-store (i.e., Virtuoso)

  1. Dataset identification, inventory, selection, location

  2. Pre-Download data file preparation

  3. Download of source data files

  4. Unpack archives

  5. Transform non-RDF data into loadable RDF data files.

  6. Assembly of all required files into a staging area.

  7. Add supplementary files.

  8. Load the RDF data into the triple-store (Virtuoso)

  9. Execute post-loading SPARQL Update queries.

  10. SPARQL Data Service final steps

  11. Dump loaded data for future “quick loading”.

Identity Mapping Service (Software)

Obtaining, building, configuring, running IMS - Identity Mapping Service

IMS consists of 4 software components:

  • QueryExpander
  • IdentityMappingService
  • Validator
  • BridgeDb.

Plus 2 database components:

  • MySQL
  • Derby

Build & Deloy Process:

  • Obtain (download/clone from GitHub)
  • Build and/or install
  • Configure
  • Integrate
  • Run
  • Expose/Shield
  • Dockerize
  • Publish
  • Document
  • Maintain

Identity Mapping Service (Data)

Create, obtain, organize, integrate, and load the linkset data to populate the IMS.

Build process:

  1. Linkset identification, inventory, selection, location

  2. Pre-Download linkset preparation

  3. Download Linkset files

  4. Unpack linkset archives

  5. Transform into IMS-ingestible format.

  6. Generate linksets from software.

  7. Assembly of all required Linkset files into a staging area.

  8. Add supplementary files

  9. Load IMS

  10. Post-loading IMS final steps.

  11. Dump loaded data for future “quick loading”.

Linked Data API Service (software)

Obtaining, building, configuring, and running the Linked Data API REST web service.

Optional/Supplementary components

  • Explorer
  • KNIME
  • ops.js
  • ops search
  • Java library to access Linked Data API.