TABLE 3.

Comparison of the top-level view vs. Activity Flow vs Process Description layers in a hierarchically-organised map. Resources: KEGG: Kyoto Encyclopaedia of Genes and Genomes (KEGG) (Kanehisa and Goto, 2000), OmniPath (Türei et al., 2016), SIGnaling Network Open Resource (SIGNOR) (Licata et al., 2020), Reactome (Gillespie et al., 2022), Recon and ReconMap (Thiele et al., 2013; Noronha et al., 2017), PANTHER (Mi et al., 2019).

Features	Top layer: top-level view	Intermediate layer: AF	Detailed layer: PD
SBGN language	Activity Flow or free format b	Activity Flow	Process Description
Connectivity	Interactions	Interactions	Processes
Granularity	Least detailed: focus on key molecules and cell types	Intermediate level of details	Most detailed, the level of processes
Compatible databases	Not available a	KEGG signalling pathways, BioCarta, OmniPath, SIGNOR	Reactome, PANTHER, Recon X, KEGG metabolic pathways
Application/Use	Communication with domain experts for defining disease hallmarks	omics visualisation, network analysis, Boolean modelling, integration with machine learning inferred networks	omics visualisation, network analysis, ODE modelling, Boolean modelling (via CaSQ)

^a The closest similar visualisations are figures with an overview of disease mechanisms in review papers, representations with cell types, tissues and organs shown.

^b By free-format here we mean flexible representation with one necessary function: all lower-layer sub-pathways in a hierarchically-organised structure are represented by an element on the top-level view and this way integrate them into a single virtual map.