Summary

This release of Open PHACTS covers a range of changes and updates plus setting the scene for releases of SureChEMBL and other updates.

The mains changes are:

  • Complete Refresh of the Chemistry Data sets including Chemistry Database (OCRS), including coverage for ChEMBL 20
  • Reload and refresh of IMS and the linksets
  • Swagger refresh with a new Swagger version
  • We also be introducing a version independent URL to our API to support transitions

New Data

  • Uniprot

Uniprot has been updated to version: Nov 2015

  • WikiPathways

In this release there are now 1737 pathways compared to 1448 in release 1.5

  • Chemistry refresh
    • ChEMBL 20 chemistry has been processed to include in the chemistry registry
    • All other chemistry sources have been refreshed including (PDB ligands, WikiPathways, Chebi, HMDB, Drugbank)
    • Updated Linksets for all these data sources
    • Calculated properties for all new molecules introduced since 1.4
  • OPPDR Phenotypic data
    • OPDDR Phenotypic Assays are now available through the Assay API call.
    • This is using BAO ontology that has also been introduced
    • In our next release we are adding further access to the substances and activities

IMS Changes

There have been significant efforts to reload the IMS to improve the quality of the linksets and also consistency in searching.

All the linksets have been reloaded from scratch and we have been going through making decisions on what to reload or not


API Changes

  • Assay API calls in preview
    • Includes OPDDR phenotypic assays
    • Assay Information
    • Assay Class Members Count/List (based on BAO classes)
  • The BAO ontology is now supported by the Concept Class Hierarchies API calls
  • ChEMBL data validation parameters are now returned by all Pharmacology API calls, and can also be used to filter the data returned.
  • Refactored and better performing Chemical Structure Search API calls.
  • Deprecated 3 Pharmacology Filter API calls and introduced new ones that are more consistent in terms of the URI structure to the other APIs.

API Response Change

  • targetOrganismName now available again in Target pharmacology API call after being omitted in API 1.5
  • targetOrganismName now available again in Target and compound class pharmacology API calls after being omitted in API 1.5
  • A ConceptWiki label is no longer a required for API calls: Compound Classification and Compound Classification for Targets
    • Also see 1.5 changes as a refresher for those moving directly from 1.4 API

Swagger Changes

We have upgraded our API documentation to use Swagger 2.0. We did this to allow our Knime nodes to be created more easily in the future.

We hope you like you new look and can find all the calls.

We have not changed the API URL but there are changes in the order of API calls and call name (see docs)