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waldronlab / BugSigDB

A microbial signatures database
https://bugsigdb.org
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Some terms in body site might need review #158

Closed sdgamboa closed 1 year ago

sdgamboa commented 1 year ago

While using bugsigdbr, I noticed that most terms in 'Body site' should be in lowercase. However, some terms start in uppercase. In some cases, this leads to duplications. I don't think HIV is a body site. See the code below for details.

library(bugsigdbr)
bsdb <- importBugSigDB(cache = FALSE)
body_sites <- sort(unique(bsdb$`Body site`))
terms <- c(
    ## uppercase
    'Genitals', 'Semen', 'Vaginal fluid',

    ## repetition due to uppercase
    'posterior fornix of vagina', 
    'Posterior fornix of vagina',

    ## not a body site
    'HIV'
)
body_sites[body_sites %in% terms]
#> [1] "Genitals"                   "HIV"                       
#> [3] "posterior fornix of vagina" "Posterior fornix of vagina"
#> [5] "Semen"                      "Vaginal fluid"
df <- bsdb[bsdb$`Body site` %in% terms,]
sigs <- getSignatures(df = df)
names(sigs)
#>  [1] "bsdb:270/1/1_human-papilloma-virus-infection:HPV+_vs_HPV-_UP"                                                                                        
#>  [2] "bsdb:270/1/2_human-papilloma-virus-infection:HPV+_vs_HPV-_DOWN"                                                                                      
#>  [3] "bsdb:270/2/1_human-papilloma-virus-infection:HPV+-(persistance)_vs_HPV+-(clearance)_UP"                                                              
#>  [4] "bsdb:270/2/2_human-papilloma-virus-infection:HPV+-(persistance)_vs_HPV+-(clearance)_DOWN"                                                            
#>  [5] "bsdb:280/1/1_cervical-glandular-intraepithelial-neoplasia:high-grade-squamus-intraepithelial-lesion_vs_low-grade-squamus-intraepithelial-lesion_UP"  
#>  [6] "bsdb:280/1/2_cervical-glandular-intraepithelial-neoplasia:high-grade-squamus-intraepithelial-lesion_vs_low-grade-squamus-intraepithelial-lesion_DOWN"
#>  [7] "bsdb:297/1/1_human-papilloma-virus-infection:non-pregnant-high-risk-HPV_vs_non-pregnant-no-HPV_UP"                                                   
#>  [8] "bsdb:297/1/2_human-papilloma-virus-infection:non-pregnant-high-risk-HPV_vs_non-pregnant-no-HPV_DOWN"                                                 
#>  [9] "bsdb:297/2/1_human-papilloma-virus-infection:pregnant-high-risk-HPV_vs_pregnant-no-HPV_UP"                                                           
#> [10] "bsdb:297/2/2_human-papilloma-virus-infection:pregnant-high-risk-HPV_vs_pregnant-no-HPV_DOWN"                                                         
#> [11] "bsdb:434/1/1_human-papilloma-virus-infection:HPV-+_vs_healthy-control_UP"                                                                            
#> [12] "bsdb:434/1/2_human-papilloma-virus-infection:HPV-+_vs_healthy-control_DOWN"                                                                          
#> [13] "bsdb:434/2/1_cervical-glandular-intraepithelial-neoplasia:LSIL_vs_healthy-control_UP"                                                                
#> [14] "bsdb:434/2/2_cervical-glandular-intraepithelial-neoplasia:LSIL_vs_healthy-control_DOWN"                                                              
#> [15] "bsdb:434/3/1_cervical-glandular-intraepithelial-neoplasia:HSIL_vs_healthy-control_UP"                                                                
#> [16] "bsdb:434/3/2_cervical-glandular-intraepithelial-neoplasia:HSIL_vs_healthy-control_DOWN"                                                              
#> [17] "bsdb:434/4/1_cervical-cancer:cervical-cancer_vs_healthy-control_UP"                                                                                  
#> [18] "bsdb:434/4/2_cervical-cancer:cervical-cancer_vs_healthy-control_DOWN"                                                                                
#> [19] "bsdb:436/1/1_cervical-glandular-intraepithelial-neoplasia:CIN2+/cervical-cancer_vs_healthy-control_UP"                                               
#> [20] "bsdb:522/2/1_endometriosis:Endometriosis-patients_vs_Controls-undergoing-laparoscopic-surgery-for-benign-tumors_DOWN"                                
#> [21] "bsdb:522/2/2_endometriosis:Endometriosis-patients_vs_Controls-undergoing-laparoscopic-surgery-for-benign-tumors_UP"                                  
#> [22] "bsdb:525/1/1_endometriosis:Women-with-EM-associated-CPPS_vs_Women-without-CPPS-presenting-for-routine-examinations_DOWN"                             
#> [23] "bsdb:525/1/2_endometriosis:Women-with-EM-associated-CPPS_vs_Women-without-CPPS-presenting-for-routine-examinations_UP"                               
#> [24] "bsdb:525/2/1_endometriosis:Women-with-EM-associated-CPPS_vs_Women-without-CPPS-presenting-for-routine-examinations_UP"                               
#> [25] "bsdb:525/2/2_endometriosis:Women-with-EM-associated-CPPS_vs_Women-without-CPPS-presenting-for-routine-examinations_DOWN"                             
#> [26] "bsdb:553/1/1_spontaneous-abortion:First-or-second-trimester-miscarriage_vs_Viable-control-pregnancy_DOWN"                                            
#> [27] "bsdb:553/2/1_spontaneous-abortion:First-trimester-miscarriage_vs_Viable-control-pregnancy_DOWN"                                                      
#> [28] "bsdb:553/2/2_spontaneous-abortion:First-trimester-miscarriage_vs_Viable-control-pregnancy_UP"                                                        
#> [29] "bsdb:553/3/1_spontaneous-abortion:complete/incomplete-miscarriage_vs_missed-miscarriage_DOWN"                                                        
#> [30] "bsdb:590/1/1_infection:HIV-1-infection_vs_HIV-1-negative_DOWN"                                                                                       
#> [31] "bsdb:590/1/2_infection:HIV-1-infection_vs_HIV-1-negative_UP"                                                                                         
#> [32] "bsdb:590/1/3_infection:HIV-1-infection_vs_HIV-1-negative_UP"                                                                                         
#> [33] "bsdb:594/1/1_periodontitis:HIV+_vs_HIV–_UP"                                                                                                          
#> [34] "bsdb:594/1/2_periodontitis:HIV+_vs_HIV–_DOWN"                                                                                                        
#> [35] "bsdb:596/1/1_HIV-infection:HIV-infected-men_vs_HIV-uninfected-men_DOWN"                                                                              
#> [36] "bsdb:596/1/2_HIV-infection:HIV-infected-men_vs_HIV-uninfected-men_UP"                                                                                
#> [37] "bsdb:598/1/1_HIV-infection:HIV-seroconverted_vs_HIV-seronegative_UP"                                                                                 
#> [38] "bsdb:598/1/2_HIV-infection:HIV-seroconverted_vs_HIV-seronegative_UP"                                                                                 
#> [39] "bsdb:598/2/1_HIV-infection:HIV-seroconverted_vs_HIV-seronegative_UP"
sessioninfo::session_info()
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#> ──────────────────────────────────────────────────────────────────────────────

Created on 2023-02-01 with reprex v2.0.2

lgeistlinger commented 1 year ago

Thanks @sdgamboa.

This will be fixed in the next release of BugSigDB and is already fixed in the devel version of BugSigDB. Note that all body site terms are exported in capitalized form according to #111.

dat <- bugsigdbr::importBugSigDB(version = "devel", cache = FALSE)
terms <- c("HIV", "posterior fornix of vagina")
> terms %in% dat$Condition
[1] FALSE FALSE