Slimming or not slimming with Gene Ontology: which tool should be used?

Question

[tlorin]

Many people use Gene Ontology analyses to look for enrichment of specific terms, and some of them further include GO Slim results to get "higher rank" terms.

Many tools exist for both, and here is a related post and a related paper emphasizing the major role of database update.

For GO Slim, things are less clear to me. I know of PANTHER, GO Slimmer, GO Term Mapper, WebGestalt (and even a command-line one, map2slim). Would you have any advice on

1. whether the GO Slim approach is meaningful, given that we can provide the specific terms that we want to slim for
2. how can we choose these specific terms ("transcription factor", etc.) before even doing the analysis
3. which program (web or not) to use

I know this is kind of a broad question but I haven't seen any recent post related to GO Slim (this one is quite old) on Biostars and thought this could be useful not only to me but to others. Many thanks!

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