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Open PHACTS is based upon the assimilation of data already stored as triples, in the form subject-predicate-object, present in - currently - various stable, publicly-available databases:

Database Download      Version             
ChEBI 04 Mar 2015 release 125
ChEMBL 18 Feb 2015  ChEMBL 20
Open PHACTS Chemical Registration Service (OCRS) 11 Nov 2013  
ConceptWiki 12 Dec 2013  
DIsGeNET
31 Mar 2015 v2.1.0
DrugBank 19 Feb 2015 version 4.1
Enzyme 02 Feb 2015  release 2015_1
FDA Adverse Events (FAERS) 09 Jul 2012  
Gene Ontology 04 Mar 2015  
Gene Ontology Annotations 17 Feb 2015  
neXtProt
Feb 2014 v1.0
UniProt (manually curated entries only) 28 Jan 2015 release 2015_1 
WikiPathways 20 Mar 2015 v20150312

To integrate this data, extensive cross-referencing of scientific concepts is needed across all databases. Data generated by Open PHACTS will be released under an open license. To link the databases featured in the Open PHACTS Discovery Platform, a community specification known as Vocabulary of Interlinked Datasets (VoID) is used. This records versions, author and derivation of data, and allows all data provenance to be easily tracked.

The Open PHACTS Discovery Platform uses databases of physicochemical and pharmacological properties, with chemistry normalised by ChemSpider, to create a main data cache (Virtuoso Triple Store). The Large Knowledge Collider (LarKC) links data via the Identity Mapping Service and ConceptWiki, to create a central Linked Data Application Programming Interface (API) composed of interoperable data.

This data can be queried by use of:

  • The Open PHACTS Explorer.
  • Example applications developed to showcase the possibilities of the Open PHACTS Discovery Platform (PharmaTrek, ChemBioNavigator, GARField, Target Dossier, Utopia Documents).
  • Partner applications exploiting the Open PHACTS API. The JSON REST-style API supports XML, Turtle etc.

Architecture graphic 500pxwide

Nanopublications

A nanopublication is the smallest unit of publishable information. Nanopublications are used by the Open PHACTS Discovery Platform to provide support for data provenance, to allow credit to be given to data providers and to permit user-annotations to be incorporated into the live system. The nanopublication model is intended to be extensible; as new features are required, new elements can be created within the model. Compatibility of older nanopublications will be retained.

 

 Nanopublication ID Each nanopublication is unique and requires an identifier.
 Integrity key To ensure authenticity on behalf of the author.
 The assertion
Statements that compose of the scientific assertion
 being made.
 Supporting information
Contextual information can be added
(e.g. species, method)
 Provenance Authorship or origin of the assertion.