I found this paper "https://www.nature.com/articles/s41556-018-0220-2" very useful for my research. I read their paper and supplementary materials. However, in their protein-protein interaction network of Figure 5 , I could not understand how they inferred that a protein in their network to be labelled as "Direct binding of PtdIns(4,5)P2 " (green nodes) or to be labelled as "Indirect PtdIns(4,5)P2 association" (yellow nodes).
I would highly appreciate if you can let me have your useful ideas and clarification for my better understanding about this . Also, did they infer this direct and indirect labelling information (green and yellow node colloring) from only literature review and published papers, or from some software analyses or specific databases?
Also, how they did this color labelling using String database?