DOI: 10.5281/zenodo.18400991
title: Methods2AOP Extended Data: Supplementary Table of Structured Method Metadata and Ontology Terms

description: This record contains the extended data referenced in Section 2.3 of the manuscript “Methods2AOP: A Collaboration to Strengthen the Integration of Test Methods into the Adverse Outcome Pathway Framework”. It provides Supplementary Table 1, which lists the structured metadata fields and corresponding ontology terms (including four real-life examples) proposed by the Methods2AOP collaboration as a foundation for consistent and FAIR methods annotation within the Adverse Outcome Pathway (AOP) framework.

About Methods2AOP

Methods2AOP is an international collaboration established to enhance how New Approach Methodologies (NAMs) and other experimental methods are represented within the AOP-Wiki and the broader AOP-Knowledge Base (AOP-KB).While AOPs organize mechanistic biological knowledge and provide a transparent chain linking molecular events to regulatory-relevant adverse outcomes, the methods used to generate evidence for Key Events (KEs) have historically been documented only in free text. This limits interoperability, reduces comparability across AOPs, and weakens the visibility of NAMs for regulatory uptake.

Methods2AOP proposes a harmonized, ontology-supported structure for documenting methods information in a way that is FAIR (Findable, Accessible, Interoperable, Reusable), more transparent, and more directly useful for regulators, AOP developers, and method developers.

What this table contains

The file Methods2AOP_SUPPLEMENTAL v2.xlsx corresponds directly to Supplementary Table 1 cited in Chapter 2.3.It includes:

In the tab Ontology Sources Defined:



A list of ontolgies the Methods2AOP team have considered during their work, including URs leadign to the ontology's home page.


In the tab Suggested Ontologies and Fields:





The hierarchically organized metadata fields identified by the Methods2AOP collaboration for describing test methods and study designs in a structured, machine-readable format.




Grouping of fields into study-type tiers (e.g., in vitro, in silico, in vivo, human, ecological), reflecting the tiered data model shown in Figures 3 and 4 of the manuscript.




For each field, the recommended ontology term (where available) from the OBO Foundry or related controlled vocabularies.




IRIs and ontology identifiers enabling unambiguous annotation.




Definitions, examples, and where relevant, controlled vocabulary suggestions.




Mapping of each field to its role within the proposed conceptual framework (e.g., test system description, assay endpoint, stressor information, documentation fields).



In the tabs “EXAMPLE_in vitro_hCLAT”, “EXAMPLE_in chemico_ADRA”, “EXAMPLE_in vitro_EpiSensA” and “EXAMPLE_in vivo_electrocardiograph”:



Columns A-C: Repetition of the “Supplementary File” tab for reference

Colums D and beyond: Real life examples for the four specific methods


Rows that make no sense in the specific example are greyed out.

 

In essence, the table is a curated set of metadata fields that elevates method descriptions from free text to structured, searchable, and interoperable information.

How this dataset supports the manuscript

Supplementary Table 1 underpins the manuscript’s discussion in Section 2.3 by:





Demonstrating how structured metadata and ontologies can standardize methods descriptions in the AOP context.




Providing concrete examples of fields needed to document study design, assay characteristics, test system properties, stressor information, and applicability domain.




Showing how ontology-backed descriptors can increase transparency, comparability, and regulatory confidence in NAM-based evidence supporting Key Events.


Showing real life examples for data that would describe specific test methods


This extended dataset is intended to provide detailed data fields which could assist researchers and method developers in aligning their documentation practices with the Methods2AOP recommendations.