Open Targets Platform 22.02 has been released!
The latest release of the Platform — 22.02 — is now available at platform.opentargets.org.
Key points
- Gene2Phenotype terminology updated
- Data updates: Open Targets Genetics, ChEMBL
- A note on data availability
- COVID tool deprecation
Key stats
| Metric | Count |
|---|---|
| Targets | 61,524, of which 29,186 are associated with at least one disease |
| Diseases | 18,468, of which 13,768 are associated with at least one target |
| Drugs | 12,594 |
| Evidence strings | 10,880,832 (see the Community for a breakdown by datasource) |
| Associations | 7,980,448, of which 2,230,103 are direct associations |
New terminology for Gene2Phenotype
Gene2Phenotype has updated their confidence value terms, in line with the new terminology established by the Gene Curation Coalition (GenCC).
The GenCC provides information pertaining to the validity of gene-disease relationships. They have harmonised the terms and definitions describing the level of evidence for a gene’s role in disease. This work is described in their recent preprint.
In the Platform, the following terms have been updated:
| Previous G2P term | New G2P term |
|---|---|
| Confirmed | Definitive |
| Possible | Limited |
| Probable | Strong |
More details on the updated terminology, as well as the confidence value term definitions, is available from Gene2Phenotype.
We have also updated our scoring to reflect the changes.
Data updates
This release integrates new data from almost all of our providers. In particular, Chemical Probes has been updated from Probes&Drugs v04.2021, and data from the International Mouse Phenotypes Consortium has been updated, affecting both Phenodigm and the mouse phenotypes datasets.
Of note, EPMC evidence has not been updated since our last release, but the number of evidence strings has increased because the co-occurrences have been grounded to the newer drug, target, and disease indexes.
Open Targets Genetics
Version 7 of the Open Targets Genetics portal was released last week. It included new GWAS and pQTL associations.
We have integrated the updated data into the Open Targets Platform, revealing some novel associations (e.g. TET2 and primary biliary cirrhosis), and strengthening some known ones (e.g. SNCA and Parkinson's disease).
ChEMBL
This release features more than 7,600 target-disease evidence strings, aggregating data from more than 1,450 new clinical trials.
This has allowed us to feature some new associations, such as the association between TLR9 and Graves ophthalmopathy. This association was not previously reported in the Platform but was established by a new study from the National Taiwan University Hospital (NCT05126147).
A note on data availability
Did you know? As part of our work to make the Open Targets Platform data more widely accessible, we have also made it available through Amazon Web Services: https://registry.opendata.aws/opentargets/
Deprecation of the Open Targets Covid-19 Target Prioritisation Tool
The Open Targets Covid-19 tool — previously available at covid19.opentargets.org — has now been deprecated.
We have made the decision to deprecate the tool, as we have now integrated the information it contains directly into the Open Targets Platform. You can explore targets associated with COVID-19, and explore available information on COVID-19 such as drugs approved or under investigation to treat the disease.
The tool was created to bring together key sources of information and to enable users to explore host and viral targets, and potential treatments for Covid-19. We integrated a number of key public datasets and publications, but designed the tool to be complementary to other resources, such as the Open Targets Platform, Uniprot, or EuropePMC. Read more about how and why we developed the tool in our release post.
The archived codebases are available in our GitHub archive.
What do you think of our updates? Let us know on the Open Targets Community or on Twitter.