wiki:PrePostComposeGO

Guidelines for pre-composed vs. post-composed GO terms

Case: Process affecting specific gene product

These will always be post-composed. GO term requests should not be made when the curator would like to describe activities or locations that are not evidently mechanistically or compositionally distinct from an existing GO term.

Case: component X during phase Y

These will always be post-composed.

Case: localization of X

  • pre-compose if X is a protein complex
  • post-compose if X is a gene product

Case: process X during Y extension vs. pre-composed process

GO now tries to avoid using "during" in term names*; they use "X involved in Y" or "A by B" wordings.

So if we have enough data to define and use a "process X involved in process Y" term, request the pre-composed term. Otherwise (if we only know that X happens at the same time as Y), annotate to the process X term with an annotation extension using "during" (i.e. happens_during or exists_during)

*reason: "during" only says that things happen at the same time, not whether one is part of the other, so it's not very informative. Happening at the same time could be a coincidence.

Case: process X involved in process Y

Usually we would precompose these. An exception to this rule is when a signalling pathway is activated by a number of different stresses. In this case the stress will be added as a "during..." extension. The rationale for this exception is that the specific annotations do not offer any obvious benefits to users (for enrichments etc). This would change if 2 distinct pathways were observed with distinct gene products annotated for each pathway (this test can be used to make decisions about further proposed exceptions). Note that you should continue to make a concurrent "response to x stress" for these gene products.

Last modified 6 years ago Last modified on Feb 25, 2015, 4:27:28 PM