Open PHACTS now offers patent information and interactions from Pathways
Creators: name: Evelo, Chris
name: Willighagen, Egon
name: Lynch, Nick
name: Jones, Bryn Williams
name: Loizou, Antonis
name: Soiland­Reyes, Stian
name: Miller, Ryan
name: Gaulton, Anna
name: Papadatos, George
name: Harland, Lee
name: Goble, Carole
name: Woollard, Peter
name: Ecker, Gerhard
name: Digles, Daniela
name: Senger, Stefan
Publisher: name: F1000Research
Year: 2016

description: Open PHACTS background and History<br>Open PHACTS started as an Innovative Medicines Initiative (IMI) project in 2011. The objective was to integrate a wide range of pharmacologically related data into a central resource that is described according to standards of the semantic web community. Central to this unification was the development of an API to allow the project partners to build their own custom applications and work streams. Over the course of the IMI project, the number of data resources grew. Open PHACTS 2.1 includes data from ChEMBL, SureChEMBL, DisGeNET, AERS­LD, WikiPathways (with Reactome content), DrugBank, ChEBI,OPDDR, PDB, MeSH,UniProt, and the Gene Ontology. Also central to the Open PHACTS Discovery Platform is the development of an identity resolution and identity mapping service and a chemistry resolution service. Over the last year the Open PHACTS Discovery Platform has matured with many exciting improvements and greater sustainability of the platform, improved code, data updates and new data sources.<br><br>Major content and feature release 2.1<br>At time of writing, the current release for Open PHACTS API is version 2.1, published in May 2016. This release introduced new data (SureChEMBL prominently), changes to the mapping service, as well as API and Swagger updates. The new data includes an update to include the November 2015 release of Uniprot. A November 2015 update of WikiPathways came with additional pathways as well as improvement to current pathway information. Since release 2.0, there was also a complete chemistry refresh to include: ChEMBL 20, refresh of chemistry resources (PDB ligands, WikiPathways, ChEBI, and DrugBank), updated linksets for chemistry, and inclusion of calculated properties for the molecules added since the initial release of version 1.4. OPDDR Phenotypic data was introduced in this release, available in the form of an AssayAPI call and using the BioAssay Ontology (BAO).<br><br>SureChEMBL and updated WikiPathways<br>The latest release includes a new dataset, SureChEMBL, as well as improvements to API calls for pathway information. The association between patent documents and annotated chemical and biological entities for 3.6 million life­ science relevant patents are now available via a set of API calls. A series of web services calls have been developed to allow users to query the data and to integrate it with the other data resources:the newAPI calls include Patent Information, Patent Entities, Patents for Compound, Patents for Target, and Patents for Disease. The combination of such calls within workflow environments, allow for the development of novel use cases, which can be applied to the target validation or lead generation stages of drug discovery. Biological pathways are a key resource in understanding data from omics platforms, and even just knowing which pathways are enriched helps. WikiPathways increasingly tracks the interactions semantically by connecting data nodes in the pathway diagram to one another. The humanReactome pathways in WikiPathways are also incorporated in the Open PHACTS knowledge base. In the latest update for theAPI,three methods were added for pathway information, and specifically around interactions:Interactions by Entity andAllInteractions. The first allows to query specifically for only up­ or downstream interactions.<br><br>Project Future<br>Since the version 2.0 was released, the IMI funding has concluded and in February 2016 the project officially moved into the hands of the Open PHACTS Foundation, a UK registered charity. The foundation is committed to sustainably support and further develop the API and data content, and is currently receiving income from membership payments by industry partners in addition to being involved in the EUH2020 projects EUToxRisk and BigDataEurope. The 2.1 release was the first new version of theAPI released since the transition from the IMI project to the Foundation.