given a data.frame with uri and tm produced by edamize (or mkdf), check against the frozen EDAM term tables in biocEDAM, filtering records to those whose uri matches a known id.

given a data.frame with uri and tm produced by edamize (or mkdf), check against the frozen EDAM term tables in biocEDAM, filtering records to those whose uri matches a known id.

Usage

verify(datf)

Arguments

datf

data.frame with at least a uri column containing EDAM URIs (e.g. "http://edamontology.org/topic_3308")

Value

a data.frame with the same structure as datf, restricted to rows whose uri matches a term in the bundled EDAM vocabulary tables

Examples

df <- data.frame(
    uri = c("http://edamontology.org/topic_3308",
            "http://edamontology.org/topic_9999"),   # 9999 is not a real term
    tm  = c("Transcriptomics", "Made-up term"),
    stringsAsFactors = FALSE)
verify(df)  # returns only the row whose uri is in the known vocabulary
#>                                  uri              tm
#> 1 http://edamontology.org/topic_3308 Transcriptomics