By using Wikidata, go2cell links Gene Ontology terms to cell types, therefore enriching Omics results with open semantic knowledge.
You can install the latest version of go2cell from GitHub with:
install.packages("remotes")
remotes::install_github("jvfe/go2cell")Suppose we want to retrieve cell types with gene markers related to GO terms ‘muscle contraction’ and ‘glycoprotein metabolic process’:
library(go2cell)
go_ids <- c("GO:0006936", "GO:0009100")
results <- go2cell(go_ids)| cell_type | cell_typeLabel | go_ids | go_termLabel | geneLabel |
|---|---|---|---|---|
| wd:Q101404903 | human myocyte | GO:0006936 | muscle contraction | ACTN2 |
| wd:Q101405077 | human cardiomyocyte | GO:0006936 | muscle contraction | ACTN2 |
| wd:Q101404861 | human fibroblast | GO:0006936 | muscle contraction | TBX20 |
| wd:Q101405077 | human cardiomyocyte | GO:0006936 | muscle contraction | TBX20 |
| wd:Q68620817 | human hepatic stellate cell | GO:0006936 | muscle contraction | DES |
| wd:Q101404901 | human smooth muscle cell | GO:0006936 | muscle contraction | DES |