1, Note that annotating to a term implies annotation to all parents via any path. Usually, an annotation should be the most detailed level in the ontology that describes the biology. However, sometimes, one cannot be certain about the level, then annotating with a pair of parent-offspring GO terms is recommended. Go even permits you annotate a gene product with conflicting terms if the biology is in controversial.
[ref] http://www.geneontology.org/GO.annotation.conventions.shtml
2, GoSlim is the cut down version of GO. Some detailed information is neglect in order to just give a broad overview. GoSlim could be curated by different users to meet their own needs. A perl script map2slim.pl was developed to help map Go annotation to the nearest parent GoSlim node.
[ref] http://www.geneontology.org/GO.slims.shtml
3, Pay attention to the regulate relationship.
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