Turn an IMPC phenotype response into a table — impc_parse

Pure.

Usage

impc_parse_phenotypes(body, mgi = NA_character_)

Arguments

body: A parsed IMPC genotype-phenotype/select response.
mgi: The MGI marker accession that was queried.

Value

A tibble of mp_id, mp_name, allele, allele_symbol, zygosity, and source_url, one row per distinct phenotype term. NULL when there are none.

One row per term, not per observation

IMPC reports a document per phenotype, sex, zygosity, and parameter combination, so the same term recurs many times over. Rows are collapsed to distinct mp_id, keeping the first occurrence. Counting the raw documents would report a gene's phenotype breadth several times over.

mp_id is an MP term for most phenotypes and an MPATH term for pathology findings. Both appear in the same field.

References

Groza et al. (2023). The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease. Nucleic Acids Research 51(D1), D1038-D1045. doi:10.1093/nar/gkac972

Service documentation: https://www.mousephenotype.org/

Examples

body <- list(response = list(docs = list(
  list(
    mp_term_id = "MP:0011100",
    mp_term_name = "preweaning lethality, complete penetrance",
    allele_accession_id = "MGI:4364806",
    zygosity = "homozygote"
  )
)))
impc_parse_phenotypes(body, "MGI:97306")
#> # A tibble: 1 × 6
#>   mp_id      mp_name                    allele allele_symbol zygosity source_url
#>   <chr>      <chr>                      <chr>  <chr>         <chr>    <chr>     
#> 1 MP:0011100 preweaning lethality, com… MGI:4… NA            homozyg… https://w…