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waldronlab / BugSigDB

A microbial signatures database
https://bugsigdb.org
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Change value of EFO in colorectal adenoma #159

Closed seandavi closed 1 year ago

seandavi commented 1 year ago

Current: EFO:0000232 Suggested: EFO:0005406

lgeistlinger commented 1 year ago

Thanks @seandavi. Which version of BugSigDB are you using?

Currently:

"Colorectal adenoma" points to EFO:0005406 on BugSigDB's condition page and also when linked on individual studies as eg on Experiment 1 of Study 631.

On the other hand, it is exported as EFO:0005406 in the latest snapshot:

> dat <- bugsigdbr::importBugSigDB(version = "devel", cache = FALSE)
  |======================================================================| 100%

> spl <- split(dat[["EFO ID"]], dat[["Condition"]])
> spl[["colorectal adenoma"]]
 [1] "EFO:0005406" "EFO:0005406" "EFO:0005406" "EFO:0005406" "EFO:0005406"
 [6] "EFO:0005406" "EFO:0005406" "EFO:0005406" "EFO:0005406" "EFO:0005406"
[11] "EFO:0005406" "EFO:0005406" "EFO:0005406" "EFO:0005406" "EFO:0005406"
[16] "EFO:0005406" "EFO:0005406" "EFO:0005406" "EFO:0005406" "EFO:0005406"
[21] "EFO:0005406" "EFO:0005406" "EFO:0005406" "EFO:0005406"
seandavi commented 1 year ago

Sorry, @lgeistlinger. I meant the other way around. There is a curation value in Study 1 that has the name "adenoma" which actually refers to "colorectal adenoma." The literal meaning of EFO:0000232 is correct, but the paper is referring to EFO:0005406.

lgeistlinger commented 1 year ago

Got you. That's been updated on bugsigdb.org and should propagate into the export on Sunday. Thanks!