Release notes

Release 3.13 (2019-06-27)

Status

In this release, we integrate 3,306,780 target-disease associations covering 10,473 diseases and 27,021 targets from the following public resources:

New features include:

  • More Target Enabling Packages (TEPs) and chemical probes

  • More target safety information

  • More download options for the drug information table

For more details, check our blog.

Release 3.12 (2019-05-02)

Status

In this release, we integrate over 3.3 million target-disease associations covering 10,419 diseases and 28,501 targets from the following public resources:

New features include:

  • CRISPR data on evidence page

  • Safety data on target profile page

  • New TEP data

  • Bug fixes throughout the platform

For more details, check our blog.

Release 3.11 (2019-02-25)

Status

In this release, we integrate over 3.1 million target-disease associations covering 10,183 diseases and 28,426 targets from the following public resources:

New Open Targets Platform features include:

  • New data: We have 11% more evidence in release 19.02 when compared to 18.12

  • Bug fixes throughout the platform

For more details on the Open Targets Platform releases, check our blog.

Release 3.10 (2018-12-14)

Status

In this release of the Open Targets Platform we integrate over 3.0 million target-disease associations covering 10,050 diseases and 28,275 targets from the following public resources:

New Open Targets Platform features include:

  • Improved prioritisation view on disease associations page

  • Systems biology data: added datasource to associations facets

  • Systems biology data: added display to evidence page

  • Bug fixes, UI and data improvements throughout the website

For more details on the Open Targets Platform releases, check our blog.

Release 3.9 (2018-10-29)

Status

In this release of the Open Targets Platform we integrate over 3.0 million target-disease associations covering 10,074 diseases and 21,730 targets from the following public resources:

New Open Targets Platform features include:

  • Target tractability information on target profile page

  • Prioritisation view on disease associations page

  • Bug fixes, UI and data improvements throughout the website

For more details on the Open Targets Platform releases, check our blog.

Release 3.8 (2018-08-28)

Status

In this release of the Open Targets Platform we integrate over 2.9 million target-disease associations covering 10,101 diseases and 21,149 targets from the following public resources:

New Open Targets Platform features include:

  • Probe Miner information featured on relevant target profile pages

  • Odds ratio and confidence information for common diseases evidence

  • Bug fixes, UI and data improvements throughout the website

For more details on the Open Targets Platform releases, check our blog.

Release 3.7 (2018-06-25)

Status

In this release of the Open Targets Platform we integrate over 2.4 million target-disease associations covering 10,086 diseases and 21,060 targets from the following public resources:

New Open Targets Platform features include:

  • Chemical Probes data featured on relevant target profile pages

  • Updated Cancer Biomarkers data table with disease information details

  • Updated associations heatmaps visualisation

  • Bug fixes, UI and data improvements throughout the website

For more details on the Open Targets Platform releases, check our blog.

Release 3.6 (2018-05-11)

Status

In this release of the Open Targets Platform we integrate over 2.3 million target-disease associations covering 9,700 diseases and 21,016 targets from the following public resources:

New Open Targets Platform features include:

  • Drugs table summary visualisations for quicker overview of drugs data

  • Cancer Biomarkers data table

  • New data source: PROGENy

API new features and fixes include:

  • Fixed batch search issues

  • Batch search: added HGNC id lookup

  • Search: improved search functionality ngram token length, type and weights

For more details on the Open Targets Platform releases, check our blog

Release 3.5 (2018-03-12)

Status

This release of the Open Targets Platform data includes:

  • Targets: 20,974

  • Diseases: 9,728

  • Evidence: 5,905,247

  • Associations: 2,306,670

New features of this release include:

  • Cancer Hallmarks data and visualisations

  • Bibliography section with 'chips' visualisation and improved sorting

  • Association studies with targeted arrays, where only specific sets of variants (e.g. SNPs) are genotyped

For more details on the Open Targets Platform releases, check our blog

Release 3.4 (2017-12-06)

Status

In this release of the Open Targets Platform we integrate over 2.2 million target-disease associations covering 9,294 diseases and 20,633 targets from the following public resources:

This release also includes several new features in the Open Targets Platform website:

  • New data and visualisation for mouse phenotypes in the target profile page.

  • New table filters in the evidence and profile pages.

  • New sections in the drug profile page showing the targets and diseases associated with the drug.

  • New section in the drug profile page showing the adverse events of a drug.

  • Some bug fixes and small UI improvements throughout the website.

For more details on the Open Targets Platform releases, check our blog

Release 3.3 (2017-11-03)

Status

In this release of the Open Targets Platform we have included two new data sources: somatic mutations from UniProt and affected pathway evidence from SLAPenrich. In total we integrate over 2.6 million target-disease associations covering 9,341 diseases and 19,803 targets from the following public resources:

This release also includes several new features in the Open Targets Platform website:

  • New facet in the disease associations page to filter by tissue expression.

  • New tissue expression summary in the target profile page.

  • New visualisation of target to target relationships based on common associated diseases in the target profile page.

  • New visualisation of disease to disease relationships based on common associated targets in the disease profile page.

  • New table to display GO terms enrichment in the batch search results.

  • Several bug fixes and small improvements throughout the website to improve the usability of the whole website.

For more details on this new release, check our blog

Release 3.2 (2017-07-27)

Status

In this release of the Open Targets Platform we integrate over 2.8 million target-disease associations covering 9,150 diseases and 26,122 targets from the following public resources:

Apart from several bug fixes, this release also includes a new table showing the homology relationships for targets in the "Gene tree" section of the target profile page

For more details on this new release, check our blog

Release 3.1 (2017-05-15)

Status

In this release of the Open Targets Platform we integrate over 2.6 million target-disease associations covering 8,891 diseases and 31,380 targets from the following public resources:

This release also includes several bug fixes

For more details on this new release, check our blog

Release 3.0 (2017-03-30)

Status

This release includes several new features in the Open Targets Platform website:

  • New tool to search for multiple targets at once

  • New web display for protein interactors based on OmnipathDB data

  • New summary page for Pathways

  • New summary page for Drugs

  • New FAQs and improvements to the documentation

  • More information of the best hit of a search

  • Several bug fixes

Release 2.1 (2017-03-27)

Status

In this release of the Open Targets Platform we integrate over 2.6 million target-disease associations covering 8,718 diseases and 31,352 targets from the following public resources:

This release also includes several bug fixes

For more details on this new release, check our blog

Release 2.0 (2016-12-09)

Status

In this release of the Open Targets Platform we integrate over 2.5 million target-disease associations covering 8,659 diseases and 31,071 targets from the following public resources:

Some other highlights include:

  • A new redesigned home page

  • A new option to filter by target class the targets associated with a disease

  • A new feature to filter the targets associated with a given disease based on a user-provided target list

  • A new visualisation for GTEx data in the target profile page

  • An improved search including drug and phenotype information to retrieve targets and diseases

  • A new Python client to interface our REST API

  • A new page to find our outreach activities

  • Improved data retrieval for text mining results

  • Many bug fixes and small improvements based on feedback from our users.

  • A survey to get feedback from our users

For more details on this new release, check our blog

Release 1.2.1 (2016-09-21)

Status

In this minor release we have incorporated some data and bug fixes

Release 1.2 (2016-08-17)

Status

In this third release of the Open Targets Platform, we have new web displays and plenty of new data to assist you in drug discovery and validation:

  • 30,591 targets

  • 9,425 diseases

  • 4.8 million evidence

  • 2.4 million target-disease associations

Some highlights:

  • New widgets for 'RNA baseline expression' and 'Protein Structure' of a target. In the latter, you can now rotate the protein structure, change its colour, zoom in and out, and highlight any amino acid residue

  • Fly and worm are two of the new species in our phylogenetic trees, which have a new name, 'Gene tree'

  • You can now find targets in human by searching for their orthologues in fly (D. melanogaster) and worm (C. elegans), as well as other 12 model organism.

  • We have two additional data sources: somatic mutations from IntOGen and variants curated by clinical geneticists from Gene2Phenotype

  • You can now export our widgets as a .png file, with scale factors ranging from 1x (lower resolution) to 3x (higher resolution)

  • The options of 'Bubbles', 'Table' and 'Tree' views in the Diseases associated with a target pages are now saved in their URLs

  • R client package for Open Targets REST API (ropentargets): if you know R, you can now query our API and download all target-disease associations into convenient data frames. ropentargets is available from our Open Targets GitHub repository.

  • We have changed the display of the EuropePMC text mining results and made exploration of the "matched sentences" more intuitive

  • We have moved to Elasticsearch 2.3.0, which is based on Lucene 5.5.0

  • 'Feedback' and 'Follow us' buttons on the homepage: it's so easy to connect with the team now

  • We have also updated our help pages, a great place to find out more about the Open Targets Platform

For more details on this new release, check our blog

Release 1.1 (2016-04-18)

Status

This is the second public version of the Open Targets Platform

The Open Targets Platform integrates over 2.1M target-disease associations covering 7,954 diseases and 24,774 targets from the following public resources:

  • 9,445 ontology classes from the Experimental Factor Ontology (EFO version 2.69)

  • 10,571 genetic evidence from UniProt, a comprehensive, high-quality and freely accessible resource of protein sequence and functional information

  • 19,857 genetic evidence from European Variation Archive (EVA), an open-access database of all types of genetic variation data from human

  • 25,536 genetic evidence from GWAS Catalog, the NHGRI-EBI Catalog of published genome-wide association studies

  • 29,812 evidence from ChEMBL, a database that contains compound bioactivity data against drug targets

  • 433,809 evidence from Expression Atlas that provides information on gene expression patterns under different biological conditions

  • 9,468 affected pathway evidence from Reactome, a free, open-source, curated and peer reviewed pathway database

  • 9,790 evidence from the COSMIC cancer Gene Census, a catalogue of genes for which mutations have been causally implicated in cancer

  • 457 somatic evidence from European Variation Archive (EVA)

  • 395,407 evidence from PhenoDigm, a database of animal model matches ranked by their phenotypic similarity to human disorder

  • 3,166,744 scientific literature evidence from co-occurence mining in Europe PMC

This release includes the following features described in details in the documentation:

  • REST API: programmatic access to the Open Targets Platform (see documentation)

  • Data dumps: direct access to the data (see downloads)

  • Look and Feel: new 'Open Targets' logo and new color palette

  • Search results: results of a search are presented by order of relevance and indicates the number of diseases associated for any target and the number of targets associated for any disease. Matched terms are highlighted

  • Target Association page: Therapeutic Areas are now presented as individual facets that can be combined. This is consistent with the data types facets

  • Target-Disease Evidence page: somatic mutations from the Cancer Gene Census are presented by mutation type with the number of samples recorded for each mutation type. The cellular mechanism of the mutation (dominant/recessive) is also given based on the Cancer Gene Census annotation

  • Target-Disease Evidence: for known drug evidence, the clinical trial phase status is presented

For more details on this new release, check our blog

Release 1.0 (2015-12-08)

Status

This is the first public version of the CTTV platorm

The CTTV platform integrates over 2M target-disease associations covering 7,359 diseases and 24,309 targets from the following public resources:

  • 9,600 ontology classes from the Experimental Factor Ontology (EFO version 2.66)

  • 9,741 genetic evidence from UniProt, a comprehensive, high-quality and freely accessible resource of protein sequence and functional information

  • 19,084 genetic evidence from European Variation Archive (EVA), an open-access database of all types of genetic variation data from human

  • 25,876 genetic evidence from GWAS Catalog, the NHGRI-EBI Catalog of published genome-wide association studies

  • 20,830 evidence from ChEMBL, a database that contains compound bioactivity data against drug targets

  • 377,360 evidence from Expression Atlas that provides information on gene expression patterns under different biological conditions

  • 9,390 affected pathway evidence from Reactome, a free, open-source, curated and peer reviewed pathway database

  • 12,079 evidence from the COSMIC cancer Gene Census, a catalogue of genes for which mutations have been causally implicated in cancer

  • 459 somatic evidence from European Variation Archive (EVA)

  • 440,601 evidence from PhenoDigm, a database of animal model matches ranked by their phenotypic similarity to human disorder

  • 3,327,695 scientific literature evidence from co-occurence mining in Europe PMC

This release includes the following features described in details in the documentation:

  • Search box: you can retrieve targets of interest by entering gene symbols, gene names, gene synonyms, Ensembl identifiers and UniProt accessions

  • Search box: you can also search by disease name provided the disease label and its synonyms are part of the Experimental Factor Ontology (EFO)

  • Search box: you can also search by phenotype provided the phenotype label and its synonyms are included in the Experimental Factor Ontology (EFO)

  • Search results: results of a search are presented by order of relevance based on the matching of symbols, names and synonyms. Matched terms are highlighted

  • Search filters: search results can be filtered by target and/or disease. Number of matching targets and number of matching diseases are shown

  • Auto-completion box: search terms are auto-completed. the auto-completion presents - up to 3 - matched target and disease terms

  • Auto-completion box: EFO disease ontology classification is presented under the disease term and clickable. A disease hyperlink links to the disease association page

  • Auto-completion box: the hyperlink of an auto-completed target links to a Target Association page for this target

  • Target Association page: provides an overview of all diseases associated to a target. 3 views are available: a 'bubble view', a 'tabular view' and a 'tree' view

  • Target Association page bubble view: groups disease by therapeutic area into bubbles. Because of the EFO ontology, a disease can belong to multiple therapeutic area

  • Target Association page bubble view: you can click on any bubble to get the association score between a specific disease and a target. This score is broken down by data types and represented as a flower

  • Target Association page bubble view: you can go to a detailed target-disease Evidence page by following the view details link when clicking on a bubble

  • Target Association page tabular view: lists all diseases associated to a particular gene ordered by association score. This score is broken down by data types

  • Target Association page tree view: represents diseases associated to a specific target at different classification levels of the EFO ontology. Nodes in the tree can be collapsed or expanded

  • Target Association page filters: filter by datatypes and therapeutic areas

  • Disease Association page: provides a tabular view of all potential targets associated to a disease ordered by association score. This score is broken down by data types

  • Target-Disease Evidence page: provides details on the evidence found to associate a particular target to a particular disease (from EFO). The association score flower represents the relative contribution of each data type when scoring a target to disease association

  • Target-Disease Evidence: genetic associations evidence from eVA, UniProt and the GWAS catalog are presented. A genome browser is embedded to display mutations

  • Target-Disease Evidence: somatic mutations evidence from the cancer gene census COSMIC resource and from eVA are presented

  • Target-Disease Evidence: known drug evidence from ChEMBL are presented

  • Target-Disease Evidence: RNA expression evidence from the Expression Atlas are presented

  • Target-Disease Evidence: target-disease co-occurence evidence mined from Europe PMC are presented

  • Target-Disease Evidence: disrupted pathways evidence from Reactome are presented

  • Target-Disease Evidence: mouse models of disease from PhenoDigm are presented

  • Target Profile page: summarises all information known about a particular target including synonyms, UniProt and Ensembl information, GO terms, baseline protein and RNA expression and list of publications from EUROPE PubMed Central

  • Disease Profile page: provides a description of a disease, its synonyms and its classification in the Experimental Factor Ontology

The CTTV platform also integrates third-party visualisations components:

  • The human baseline expression widget from the EMBL-EBI Expression Atlas

  • The protein features widget from UniProt

  • The pathway navigation widget from Reactome

  • The protein structure visualisation is extracted from PDBe