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PubMed · 39936578

Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence.

Carlos Cruz-Castillo·Luca Fumis·Chintan Mehta·Ricardo Esteban Martinez-Osorio·Juan Maria Roldan-Romero·Helena Cornu·Prashant Uniyal·Antonio Solano-Roman·Miguel Carmona·David Ochoa·Ellen Mary McDonagh·Annalisa Buniello
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Abstract

MOTIVATION: The Open Targets Platform (https://platform.opentargets.org) is a unique, comprehensive, open-source resource supporting systematic identification and prioritisation of targets for drug discovery. The Platform combines, harmonizes and integrates data from >20 diverse sources to provide target-disease associations, covering evidence derived from genetic associations, somatic mutations, known drugs, differential expression, animal models, pathways and systems biology. An in-house target identification scoring framework weighs the evidence from each data source and type, contributing to an overall score for each of the 7.8M target-disease associations. However, the old infrastructure did not allow user-led dynamic adjustments in the contribution of different evidence types for target prioritisation, a limitation frequently raised by our user community. Furthermore, the previous Platform user interface did not support navigation and exploration of the underlying target-disease evidence on the same page, occasionally making the user journey counterintuitive. RESULTS: Here, we describe 'Associations on the Fly' (AOTF), a new Platform feature-developed with a user-centred vision-that enables the user to formulate more flexible therapeutic hypotheses through dynamic adjustment of the weight of contributing evidence from each source, altering the prioritisation of targets. AVAILABILITY AND IMPLEMENTATION: The codebases that power the Platform-including our pipelines, GraphQL API, and React UI-are all open source and licensed under the APACHE LICENSE, VERSION 2.0. You can find all of our code repositories on GitHub at https://github.com/opentargets and on Zenodo at https://zenodo.org/records/14392214. This tool was implemented using React v18 and its code is accessible here: (https://github.com/opentargets/ot-ui-apps). The tools are accessible through the Open Targets Platform web interface (https://platform.opentargets.org/) and GraphQL API (https://platform-docs.opentargets.org/data-access/graphql-api). Data is available for download here: (https://platform.opentargets.org/downloads) and from the EMBL-EBI FTP: (https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/).

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Carlos Cruz-Castillo, Luca Fumis, Chintan Mehta, Ricardo Esteban Martinez-Osorio, Juan Maria Roldan-Romero, Helena Cornu, Prashant Uniyal, Antonio Solano-Roman, Miguel Carmona, David Ochoa, Ellen Mary McDonagh, Annalisa Buniello. 2025-03-29. Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence.. https://doi.org/10.1093/bioinformatics%2Fbtaf070

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