Table 1. Frequency of relations in the gene ontology and suggested semantic correspondence classes to reduce ambiguity†.
| Relationship | Frequency in GO (CC+BP+MF) |
Frequency in GO CC | Frequency in GO BP | Frequency in GO MF | Correspondence Class | Correspondence Members |
|---|---|---|---|---|---|---|
| is_a | 72455 | 5591 | 54689 | 12175 | Scoping (hyponymy) | hyponym "is_a" hypernym |
| part_of | 8613 | 1702 | 5751 | 1160 | Scaling (meronymy) | meronym "part_of" holonym |
| has_part | 736 | 156 | 339 | 241 | Scaling (meronymy) | holonym "has_part" meronym |
| happens_during | 24 | 0 | 24 | 0 | Spatiotemporal (process-process) |
process "happens_during" process |
| ends_during | 1 | 0 | 1 | 0 | Spatiotemporal (process-process) |
process "ends_during" process |
| occurs_in | 181 | 0 | 180 | 1 | Spatiotemporal (process-entity or process-process) | process "occurs_in" entity OR process "occurs_in" process |
| regulates | 3368 | 0 | 3322 | 46 | Active (actor-subject) | actor "regulates" subject |
| positively_regulates | 2916 | 0 | 2880 | 36 | Active (actor-subject) | actor "positively_regulates" subject |
| negatively_regulates | 2937 | 0 | 2285 | 52 | Active (actor-subject) | actor "negatively_regulates" subject |
| regulated_by‡ | 0 | 0 | 0 | 0 | Active (actor-subject) | subject "regulated_by" actor |
| before‡ | 0 | 0 | 0 | 0 | Spatiotemporal (prior-latter) |
prior "before" latter |
† GO-core data-version: releases/2016-01-12 (available in Scripts Directory)
‡ These relationships are not found in GO but are part of the Relations Ontology