# Human and Mouse Homology with phenotype annotations from MGI
# http://www.informatics.jax.org/mgihome/projects/overview.shtml
## last database update
05/28/2024
MGI 6.23
# 12/27/2022 MGI 6.22 108
# 06/23/2022 MGI 6.20 106
# 06/08/2021 MGI 6.17 ??? Empty table!
# 12/08/2020 MGI 6.16
# 5/05/2020 MGI 6.15
# 09/25/2019 MGI 6.14
# 04/16/2019 MGI 6.13
# 10/09/2018 MGI 6.12
url <- "http://www.informatics.jax.org/downloads/reports/HMD_HumanPhenotype.rpt"
# add empty column 8 to avoid parsing failures
message("Downloading ", url)
x <- read_tsv(url, col_names=c("human", "entrez_gene", "homologene", "x1", "mouse", "id", "phenotype_id", "x2"))
# > ensembl 108
x <- read_tsv(url, col_names=c("human", "entrez_gene", "mouse", "id", "mp", "x1"))
## duplicated mouse genes
table(duplicated(x$mouse))
FALSE TRUE
20121 9479
# Group by gene names
mgi <- group_by(x, id, mouse) %>% summarize(n=n(), human = paste(human, collapse=",")) %>%
ungroup() %>% filter(n !=41) %>% arrange( grepl("Rik$", mouse), mouse)
## 1798 in mgi 6.23
z <- filter(mgi, n>1)
filter(z, str_detect(human, fixed(mouse, ignore_case=TRUE)) )
filter(z, str_detect(human, fixed(mouse, ignore_case=TRUE)) )
# A tibble: 632 × 4
id mouse n human
<chr> <chr> <int> <chr>
1 MGI:1916934 Aarsd1 2 AARSD1,PTGES3L-AARSD1
2 MGI:1351657 Abcf2 2 ABCF2,ABCF2-H2BK1
3 MGI:1349396 Acot1 2 ACOT1,ACOT2
4 MGI:2159605 Acot2 2 ACOT1,ACOT2
5 MGI:2385289 Acsm2 2 ACSM2A,ACSM2B
6 MGI:1347095 Adgre5 2 ADGRE2,ADGRE5
7 MGI:87921 Adh1 3 ADH1A,ADH1B,ADH1C
filter(mgi, n>1)
attr(mgi, "downloaded") <- Sys.Date()
setwd("~/Documents/R/packages/hciRdata/data")
save(mgi, file="mgi.rda")
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