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The Next Generation Open Targets Platform
- 2. KeyPoints Complete refactoring of the codebase Overhaul of the user interface New features and data Allowing for rapid development and deployment strategies Improving user experience and access to information From our latest data release — 21.04
- 3. community.opentargets.org Introducingthe OpenTargets Community We have created a community forum to host discussions and foster collaborations among users. It will feature the latest updates from the Platform, and provide technical support.
- 4. Newdata& approaches Increase in target-disease evidence As part of our project-wide rewrite efforts, we have completely overhauled our evidence data model. We have a new data schema that is flatter and more streamlined, allowing for much more efficient analysis of the evidence across different data sources. platform.opentargets.org
- 6. Binary molecular interactions Our pipeline integrates different pairwise interactions — physical, regulatory, functional — between the selected target and all other human or pathogenic (e.g. SARS-CoV2) proteins and RNA molecules. platform.opentargets.org
- 7. Sourcesofmolecular interactiondata platform.opentargets.org Intact Reactome Signor STRING Genes and proteins which interact typically work together in the same processes, and are therefore more likely to be associated in disease. Molecular interactions can indicate other potentially relevant targets, or increase the confidence in a given target.
- 8. Black box warnings A black box warning, or boxed warning, is the FDA’s most severe warning for drugs on the market, indicating serious side effects such as injury or death. Thanks to work from our colleagues at ChEMBL, this information is now available in the Open Targets Platform. platform.opentargets.org Hunter FMI, Bento AP, Bosc N, et al. Drug Safety Data Curation and Modeling in ChEMBL: Boxed Warnings and Withdrawn Drugs. Chemical Research in Toxicology. 2021 Feb;34(2):385-395.
- 9. Our recent work has classified the type of adverse effect described in boxed warnings on a per drug basis. For medicinal products that contain one active pharmaceutical ingredient, a boxed warning can be directly linked to a drug. Therefore, toxicity class(es) have been assigned to approved drugs with boxed warning information described on medicinal product labels. platform.opentargets.org
- 10. Uniprot Variants With this latest release, we are re- introducing the variant-based target- disease evidence source from Uniprot. It complements the curated associations in the ClinVar evidence set with an additional 7127 unique variants, as well as further curated information. platform.opentargets.org
- 11. A new literature mining strategy Through collaboration with Europe PubMedCentral, we created a new literature- mining strategy using natural language processing, which is noticeably more accurate. Our new pipeline uses a deep learning method for named entity recognition and reports sentence level target-disease co- occurrences as associations. platform.opentargets.org
- 12. New algorithms to explore entities We have implemented new algorithms to explore the universe of entities and their similarities in the literature. This allows us to display significantly more relevant publications, and enables users to explore different entities mentioned similarly in the literature. platform.opentargets.org
- 13. platform.opentargets.org Clinical signs & symptoms Clinical signs and symptoms associated with diseases provide more detailed evidence connecting targets and diseases. Evidence pages Compared to the previous version, the evidence pages have a completely new design. Each data source has its own section for easy navigation. Literature We have made our literature sources easier to navigate, with the full reference displayed. We also indicate whether the full text is available Additional features
- 14. Redesigned infrastructure The technical stack for the next-generation Open Targets Platform has been completely overhauled. This has enabled us to implement an entirely new ETL pipeline, API and web application, using powerful modern technologies. platform.opentargets.org
- 15. platform.opentargets.org The user interface has been both redesigned and completely reimplemented in order to maximise the impact of casual findings. The underlying algorithms provide flexible, on-the- fly calculations of association scores, and as such, unblock more user-driven queries. This also enables much faster development and deployment strategies, facilitating the implementation of custom instances of the Platform.
- 16. Dataaccess options Depending on the complexity of the query and the user’s programmatic skills, we have a range of ways to access our data. platform.opentargets.org
- 17. platform.opentargets.org Users can use the search function on our web interface, and navigate to entity pages, associations pages, or evidence pages. Data tables and visualisations can be downloaded in multiple formats. Web application The GraphQL API provides a friendly, language-agnostic access point to the information displayed in the web application. The GraphQL playground contains a schema to help you construct tailored queries. GraphQL API Single entities or associations
- 18. platform.opentargets.org Google BigQuery allows you to run asynchronous SQL queries using Google Cloud’s infrastructure, and export the results or copy them into Google Cloud buckets. Google BigQuery We also provide downloads for all data files generated by our ETL pipelines, with more than 20 datasets available. These data downloads contain information on all targets, diseases/phenotypes, and drugs, allowing users to explore specific datasets and integrate them into their own pipelines. Data downloads Complex queries