I could have, for example, genetics data which point to involvement of gene X, and gene X functions in lipid droplet formation, and by extension is relevant to dyslipidemia, obesity, cardiovascular disease and type 2 diabetes. A logical next step might be to collect all entities - gene, protein, metabolite, lipids/fatty acids, etc - found in the lipid droplet, or in the adipocyte, in order to learn how gene X fits into the larger lipid droplet picture.

To accomplish this, it would be easier to query a database built around cell or tissue attributes, as opposed to gene/protein/metabolite or disease databases, which are more often encountered. Do any such databases exist? For human?

I know of a couple for non-human species. One is the cell lineage maps of Caenorhabditis elegans. Another is early embryogenesis of a number of disparate organisms. Cell did publish a SnapShot of the lipid droplet - in graphical form - but if I put that info into a database, I would want to borrow from an established schema.

One incarnation of this could be something like state₁ --> state₂ --> state₃, where the transition from one state to the next requires {list of entities}. OK, this is differentiation based and that is fine. Another, simpler example would be a catalog of entities identified in an organelle, cell or tissue.

Any ideas along these lines for looking at a pathway or process from the perspective of the cell/tissue as opposed to the genes/proteins/metabolites?