Usage of terms describing protein or chemical production

Production terms were created to handle annotation of experimental data involving the measurement of a cytokine/protein/non-protein mediator in intracellular or extracellular media where the exact process leading to the appearance of the substance is not necessarily clear. Typically the appearance of a protein or other biochemical in the extracellular media following a stimulation could be the result of de novo synthesis and secretion, as is common for many proteins, or secretion or release from preexisting cellular stores of the protein/biochemical, such as for interferon-1 alpha and beta, histamine, etc. Because the time course of many stimulation assays is several hours and the assays themselves often ELISAs, it cannot always be determined if de novo protein synthesis is involved, or if simply the liberation of the protein from a preexisting source is occurring, as appears to be the case here.

The GO "production" terms allow for annotation of this type of data without the necessary resolution of the mechanism involved in the appearance of the measured substance. In cases where the experimental data definitely shows that a stimulation leads to, for instance, biosynthesis, an appropriate "positive regulation of biosynthesis" term may be used for annotation instead.

Example

Annotation of: 'GO:0002532 production of molecular mediator involved in inflammatory response' for mouse ADAM17 from PMID:20610799

ADAM17 is somehow involved in the appearance of sLRP because treatment of cells with siRNA to ADAM17 interfere with the appearance of sLRP. Presumably, this is due to the direct metalloprotease activity of ADAM17 on LRP, but the paper does not show this directly. Thus, the production term works well in this instance to capture the experimental result. One could argue for a "positive regulation of production" term, but given that ADAM17 is probably directly involved in the release of sLRP from the cell, curator judgment allows one to select the "production" term directly.

The genesis of these production terms is found in this SF entry of 2003: https://sourceforge.net/tracker/?func=detail&aid=863084&group_id=36855&atid=440764

Guidance contributed by Alex Diehl, 23-12-2011: GO Discuss mailing list