GO Trimming algorithm flowchart. A) Phase 1 of GO Trimming: identification of parent-child relationships in GO hierarchy. B) Phase 2 of GO Trimming: strict and soft trimming using 0% and 40% uniqueness thresholds. Green boxes represent start and endpoints for the algorithm. Blue parallelograms represent input and output steps. Red rectangles represent an action required by the user and yellow diamonds represent questions that determine the flow of the algorithm. Input for the algorithm is the query list (list of enriched GO terms) and the GO tree (hierarchy of all GO terms). Output is a list of GO terms with soft and strict trimmed terms removed.