starplast.metabolites

The metabolite table: rows are compounds, not genes.

Three slots on the metabolism axis ask about metabolites -- their steady-state levels, the flux through them, the composition of membrane lipids -- and none of them can be answered by a table whose rows are genes. A metabolite is not a gene, and the mapping between them is a metabolic model rather than a measurement. Those slots carry unit="metabolite" for that reason, and this is the table they resolve against.

It is the same shape as the host tables instruction 39 describes: a second table, keyed by its own identifier, reached through slots that declare their unit rather than through rows bolted onto the parasite table.

What identifies a row

The compound name as the study reported it, normalised for case and punctuation only. There is no Toxoplasma-wide metabolite identifier the way there is for genes -- studies report names, sometimes HMDB or KEGG accessions, often neither -- so joining two studies means matching names, and matching names is lossy. With one study in the table that cost is not yet paid; the moment a second arrives it is the first problem to solve, and it should be solved with an identifier and not with fuzzy matching.