Get GO ids from cell types

Return GO identifiers related to gene markers of specific cell types.

Usage

cell2go(celltype_qids)

Arguments

celltype_qids

A character vector of cell type Wikidata IDs

Value

A dataframe of 5 columns: The first two correspond to cell types, that is, their Wikidata Identifier and their name. The two following columns correspond to the Gene Ontology IDs given, and the last column corresponds to the cell type's marker that led to the result.

Details

This function takes in a character vector of cell type Q identifiers (QIDs), queries Wikidata (https://www.wikidata.org/) and a local RDF database to return GO IDs related to gene markers of these cell types.

See also

https://www.wikidata.org/ for information regarding Wikidata and https://panglaodb.se/index.html for the original database this information was adapted from. For an example of a cell type item in Wikidata, see https://www.wikidata.org/wiki/Q101405098

Examples

# Return GO IDs related to cell type
# 'human smooth muscle cell'
cell2go("Q101404901")
#> Rows: 2001 Columns: 5
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (5): cell_type, cell_typeLabel, go_ids, go_termLabel, geneLabel
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
if (FALSE) {
# IDs should always start with 'Q'
go2cell("101404901")
}