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:
|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|
||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|
|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:
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.|
Statements that compose of the scientific assertion
Contextual information can be added
(e.g. species, method)
|Provenance||Authorship or origin of the assertion.|