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Enhancing the FAIRness (Findability, Accessibility, Interoperability, and Reusability) of the AOP-Wiki
Citation:
Hench, V., S. Edwards, T. Karschnik, D. Villeneuve, J. O'Brien, AND C. Wittwehr. Enhancing the FAIRness (Findability, Accessibility, Interoperability, and Reusability) of the AOP-Wiki. Society of Toxicology 62nd Annual Meeting, Nashville, TN, March 19 - 23, 2023. https://doi.org/10.23645/epacomptox.24749379
Impact/Purpose:
The AOP-Wiki is a central repository of biological/toxicological knowledge and evidence organized according to the adverse outcome pathway framework. The knowledge contained therein is intended to help support the application of new approach methodologies (NAMs) in regulatory decision-making, but laying out the scientific support for causal connections between bioactivity and pathway-perturbations and resulting apical adverse outcomes. A goal of many computational systems that provide access to data or knowledge is to make the information contained therein findable, accessible, interoperable with other platforms and reusable (FAIR). This poster outlines both recent and planned upgrades to the AOP-Wiki that are intended to enhance the overall "FAIRness" of the knowledgebase. These upgrades can improve the overall utility of the information for a wide range of applications.
Description:
The AOP-Wiki provides a central repository for development of adverse outcome pathways (AOPs) and dissemination of AOP information without restrictions. Each AOP is described in narrative form with interconnected pages that house information on the key events (KEs) and key event relationships (KERs) that make up the AOP. The AOP-Wiki currently houses over 400 AOPs containing over 1,500 KEs and 2,000 KERs. KE pages contain information regarding the measurement of biological phenotypes indicative of toxicity progression from perturbation of the molecular initiating event to manifestation of an adverse outcome. KER pages document the evidence supporting a causal relationship between the related key events and can include quantitative considerations when available. In addition to the browsing and search capabilities offered by the AOP-Wiki web interface, the content is also available for download (XML formatted files) or via an application programming interface (JSON or XML formats) to support the development of third-party tools or provide real-time data for computational analyses. While some fields within the AOP, KE, and KER pages are populated with tabulated content from controlled vocabularies, which aligns with FAIR standards, there are still a number of areas for improvement where free text fields can be made more structured. This poster will highlight recent and upcoming updates to the AOP-Wiki data model and user interface, designed to make the content more accessible and interoperable both interactively and programmatically. This includes more accurate representation of information regarding prototypical stressors and modulating factors. We have also developed a prototype web user interface to aid in developing an intuitive and useful evidence mapping submission workflow. The evidence mapping prototype supports evidence submission to KERs in a manner that maintains a linkage between the evidence details and the referenced source publication. The KER-centric evidence submission process includes creation of linkages between the evidence and the KEs that are part of each KER. These enhancements also allow better documentation of the AOP development strategy to make the provenance of the knowledge more visible, which has been identified as a key requirement for engendering trust. A preview of upcoming features will include improvements to the underlying data model to promote crowdsourcing of AOP development and further improve transparency regarding the knowledge provenance. Finally, an overview of the reuse of information from the AOP-Wiki by third-party tools will demonstrate the added value that results from making the information freely available in a computable form. In some cases, the third-party tools have further improved the FAIRness of the wiki data. [The contents of this abstract neither constitute nor necessarily reflect official policies of the authors’ organizations.]
URLs/Downloads:
DOI: Enhancing the FAIRness (Findability, Accessibility, Interoperability, and Reusability) of the AOP-Wiki
POSTER.PDF (PDF, NA pp, 1014.971 KB, about PDF)