Table 3.

Description of files provided as part of the data set.

Data type	Description	File structure	File name
KE to gene set annotation	KE to gene set annotations. Annotations provided by specific KE (AOP-KE pairs).	A spreadsheet file with two sheets, one with annotation provided as the gene set names, one with identifiers. Both sheets contain columns AOP, KE, Specific_KE, Description (KE name), and Match_1 through Match_5.	Gene_set_annotations.xlsx
KE to gene annotation	Direct KE to gene associations. KE associated genes are expressed as the union of all the genes mapped to the gene sets annotated to each KE.	File provided as a tab-separated text file. File contains two columns, one for the KEs and one for the genes. Genes expressed as Ensembl identifiers.	Genes_to_KEs.txt
Gene set identifier to name mapping	Mapping between gene set identifiers and the names used for matching KE descriptions to gene sets. File may be needed if genes are obtained from external sources.	File provided as a tab-separated text file. File contains two columns: term_name and exact_source.	Name_to_ID_mapping.txt
KE to biological system annotation	Annotation of KEs to relevant biological systems at the level of the system, organ/tissue, cell, and cell component.	A spreadsheet with a column for KE name, id, and level, as well as distinct column for each annotation by level, including the secondary annotations, and indication of duplication. Equal annotations are separated by “/”.	Biological_system_annotations.xlsx
Dictionary	A complete listing of all the systems, tissues/organs, cell types, and cell components used in the biological context annotations.	A spreadsheet with five sheets. Complete dictionary covers all combinations of system, organ/tissue, and cell type annotations. Individual dictionaries provide a complete list of systems, organs/tissues, cell types, and cell components.	Dictionary.xlsx