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

Cruz-Castillo, C.; Fumis, L.; Mehta, C.; Martinez-Osorio, R. E.; Roldan-Romero, J. M.; Cornu, H.; Uniyal, P.; Solano-Roman, A.; Carmona, M.; Ochoa, D.; McDonagh, E. M.; Buniello, A.

doi:10.1101/2024.09.10.612089

bioRxiv · 10.1101/2024.09.10.612089

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

Cruz-Castillo, C.·Fumis, L.·Mehta, C.·Martinez-Osorio, R. E.·Roldan-Romero, J. M.·Cornu, H.·Uniyal, P.·Solano-Roman, A.·Carmona, M.·Ochoa, D.·McDonagh, E. M.·Buniello, A.

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Abstract

MotivationThe 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, harmonises 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 previous 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. ResultsHere, we describe "Associations on the Fly" (AOTF), a new Platform feature - developed as part of a wider product refactoring project - to enable formulation of more flexible and impactful therapeutic hypotheses through dynamic adjustment of the weight of contributing evidence from each source, altering the prioritisation of targets. Availability and implementationAll Open Targets code is available as open source: [https://github.com/opentargets]. This tool was implemented using React v18 and its code is accessible here: [https://github.com/opentargets/ot-ui-apps]. The tools described in the paper 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/]. Supplementary informationAdditional information on this tool can be found on the Platform documentation pages [https://platform-docs.opentargets.org/web-interface, https://platform-docs.opentargets.org/web-interface/associations-on-the-fly, https://platform-docs.opentargets.org/target-prioritisation] and training video [https://youtu.be/2A9bksboAag]. ContactAnnalisa Buniello, EMBL-EBI, buniello@ebi.ac.uk

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Cruz-Castillo, C., Fumis, L., Mehta, C., Martinez-Osorio, R. E., Roldan-Romero, J. M., Cornu, H., Uniyal, P., Solano-Roman, A., Carmona, M., Ochoa, D., McDonagh, E. M., Buniello, A.. 2024-09-14. Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence. https://doi.org/10.1101/2024.09.10.612089

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