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UniProtKB Swiss-Prot

Source: vignettes/articles/swiss_prot_ids.Rmd
swiss_prot_ids.Rmd

The MGI report MRK_SwissProt.rpt provides associations between MGI genetic markers and UniProtKB/Swiss-Prot identifiers.

To read this report using the key "swiss_prot_ids", use the following code:

# To read all records (~ 17,000), use `read_report("swiss_prot_ids")`.
(assoc_to_swiss_ids <- read_report(report_key = "swiss_prot_ids", n_max = 150L))
## # A tibble: 150 × 7
##    marker_status marker_id  marker_symbol marker_name chromosome genetic_map_pos
##    <fct>         <chr>      <chr>         <chr>       <fct>                <dbl>
##  1 O             MGI:19156… 0610030E20Rik RIKEN cDNA… 6                     32.3
##  2 O             MGI:19235… 0610040J01Rik RIKEN cDNA… 5                     32.8
##  3 O             MGI:19150… 1110002E22Rik RIKEN cDNA… 3                     64.0
##  4 O             MGI:19292… 1110004F10Rik RIKEN cDNA… 7                     61.4
##  5 O             MGI:19159… 1110032F04Rik RIKEN cDNA… 3                     32.1
##  6 O             MGI:21523… 1110038F14Rik RIKEN cDNA… 15                    36.3
##  7 O             MGI:19134… 1110059E24Rik RIKEN cDNA… 19                    15.5
##  8 O             MGI:19134… 1110059G10Rik RIKEN cDNA… 9                     73.3
##  9 O             MGI:19161… 1110065P20Rik RIKEN cDNA… 4                     57.9
## 10 O             MGI:19161… 1190005I06Rik RIKEN cDNA… 8                     69.9
## # ℹ 140 more rows
## # ℹ 1 more variable: swiss_prt_id <list>

UniProtKB/Swiss-Prot identifiers

The list-column swiss_prt_id provides associated ProtKB/Swiss-Prot identifiers. To unnest swiss_prt_id use:

assoc_to_swiss_ids |>
  dplyr::select("marker_id", "marker_symbol","swiss_prt_id") |>
  dplyr::filter(marker_id == "MGI:1098687") |>
  tidyr::unnest("swiss_prt_id")
## # A tibble: 2 × 3
##   marker_id   marker_symbol swiss_prt_id
##   <chr>       <chr>         <chr>       
## 1 MGI:1098687 Aak1          Q3UHJ0      
## 2 MGI:1098687 Aak1          Q6PIU9

Variables

marker_status

marker_status: genetic marker status is a factor of two levels: 'O' for official, and 'W' for withdrawn. Official indicates a currently in-use genetic marker, whereas withdrawn means that the symbol or name was once approved but has since been replaced.

marker_id

marker_id: MGI accession identifier. A unique alphanumeric character string that is used to unambiguously identify a particular record in the Mouse Genome Informatics database. The format is MGI:nnnnnn, where n is a digit.

marker_symbol

marker_symbol: marker symbol is a unique abbreviation of the marker name.

marker_name

marker_name: marker name is a word or phrase that uniquely identifies the genetic marker, e.g. a gene or allele name.

chromosome

chromosome: mouse chromosome name. Possible values are names for the autosomal, sexual or mitochondrial chromosomes.

genetic_map_pos

genetic_map_pos: genetic map position in centiMorgan (cM): a unit of length in a genetic map. Two loci are 1 cM apart if recombination is detected between them in 1% of meioses.

swiss_prt_id

swiss_prt_id: UniProtKB/Swiss-Prot identifier(s), a list-column.