Functional enrichment analysis allows the identification of functional or biological characteristics of genes through gene ontology terms (GO terms). However, descriptive procedures to compare GO terms between gene lists and species are limited. Here we present a descriptive computational procedure implemented in R (GOCompare) that allows comparing GO terms or categories. To test our approach, GO terms were obtained for 5,494 genes related to ten cancer traits in Homo sapiens and their orthologs in Arabidopsis thaliana. GOCompare showed some similarities for some cancer hallmarks that matched the GO terms shared between hallmarks, as there are multiple genes shared by this disease. The GO terms of central metabolism were highly weighted nodes for each species. In contrast, the combined regulation of metabolism was relevant for both species. Consequently, the R package showed good performance for use in complex data sets using only the existing relationships between GO terms in the categories.