Source: https://github.com/markziemann/GeneNameErrors2020
Vew the reports: http://118.138.234.73/public/gene_name_errors/
Gene name errors result when data are imported improperly into MS Excel and other spreadsheet programs (Zeeberg et al, 2004). Certain gene names like MARCH3, SEPT2 and DEC1 are converted into date format. These errors are surprisingly common in supplementary data files in the field of genomics (Ziemann et al, 2016). This could be considered a small error because it only affects a small number of genes, however it is symptomtic of poor data processing methods. The purpose of this script is to identify gene name errors present in supplementary files of PubMed Central articles in the previous month.
library("xml2")
library("reutils")
library("readxl")
Here I will be getting PubMed Central IDs for the previous month.
Start with figuring out the date to search PubMed Central.
CURRENT_MONTH=format(Sys.time(), "%m")
CURRENT_YEAR=format(Sys.time(), "%Y")
if (CURRENT_MONTH == "01") {
PREV_YEAR=as.character(as.numeric(format(Sys.time(), "%Y"))-1)
PREV_MONTH="12"
} else {
PREV_YEAR=CURRENT_YEAR
PREV_MONTH=as.character(as.numeric(format(Sys.time(), "%m"))-1)
}
DATE=paste(PREV_YEAR,"/",PREV_MONTH,sep="")
DATE
## [1] "2020/12"
Let's see how many PMC IDs we have in the past month.
QUERY ='((genom*[Abstract]))'
ESEARCH_RES <- esearch(term=QUERY, db = "pmc", rettype = "uilist", retmode = "xml", retstart = 0,
retmax = 5000000, usehistory = TRUE, webenv = NULL, querykey = NULL, sort = NULL, field = NULL,
datetype = NULL, reldate = NULL, mindate = DATE, maxdate = DATE)
pmc <- efetch(ESEARCH_RES,retmode="text",rettype="uilist",outfile="pmcids.txt")
## Retrieving UIDs 1 to 500
## Retrieving UIDs 501 to 1000
## Retrieving UIDs 1001 to 1500
## Retrieving UIDs 1501 to 2000
## Retrieving UIDs 2001 to 2500
## Retrieving UIDs 2501 to 3000
## Retrieving UIDs 3001 to 3500
## Retrieving UIDs 3501 to 4000
## Retrieving UIDs 4001 to 4500
pmc <- read.table(pmc)
pmc <- paste("PMC",pmc$V1,sep="")
NUM_ARTICLES=length(pmc)
NUM_ARTICLES
## [1] 4472
writeLines(pmc,con="pmc.txt")
Now run the bash script. Note that false positives can occur (~1.5%) and these results have not been verified by a human.
Here are some definitions:
NUM_XLS = Number of supplementary Excel files in this set of PMC articles.
NUM_XLS_ARTICLES = Number of articles matching the PubMed Central search which have supplementary Excel files.
GENELISTS = The gene lists found in the Excel files. Each Excel file is counted once even it has multiple gene lists.
NUM_GENELISTS = The number of Excel files with gene lists.
NUM_GENELIST_ARTICLES = The number of PMC articles with supplementary Excel gene lists.
ERROR_GENELISTS = Files suspected to contain gene name errors. The dates and five-digit numbers indicate transmogrified gene names.
NUM_ERROR_GENELISTS = Number of Excel gene lists with errors.
NUM_ERROR_GENELIST_ARTICLES = Number of articles with supplementary Excel gene name errors.
ERROR_PROPORTION = This is the proportion of articles with Excel gene lists that have errors.
#system("./gene_names.sh pmc.txt")
results <- readLines("results.txt")
XLS <- results[grep("XLS",results,ignore.case=TRUE)]
NUM_XLS = length(XLS)
NUM_XLS
## [1] 1042
NUM_XLS_ARTICLES = length(unique(sapply(strsplit(XLS," "),"[[",1)))
NUM_XLS_ARTICLES
## [1] 199
GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>2]
#GENELISTS
NUM_GENELISTS <- length(unique(sapply(strsplit(GENELISTS," "),"[[",2)))
NUM_GENELISTS
## [1] 132
NUM_GENELIST_ARTICLES <- length(unique(sapply(strsplit(GENELISTS," "),"[[",1)))
NUM_GENELIST_ARTICLES
## [1] 64
ERROR_GENELISTS <- XLS[lapply(strsplit(XLS," "),length)>3]
#ERROR_GENELISTS
NUM_ERROR_GENELISTS = length(ERROR_GENELISTS)
NUM_ERROR_GENELISTS
## [1] 42
GENELIST_ERROR_ARTICLES <- unique(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
GENELIST_ERROR_ARTICLES
## [1] "PMC7758481" "PMC7746835" "PMC7744954" "PMC7732301" "PMC7732848"
## [6] "PMC7726486" "PMC7726151" "PMC7718812" "PMC7738636" "PMC7734124"
## [11] "PMC7732649" "PMC7728435" "PMC7723986" "PMC7714959" "PMC7724473"
## [16] "PMC7730811" "PMC7723042" "PMC7721725" "PMC7714695" "PMC7723770"
## [21] "PMC7717581" "PMC7710658" "PMC7711149" "PMC7707522"
NUM_ERROR_GENELIST_ARTICLES <- length(GENELIST_ERROR_ARTICLES)
NUM_ERROR_GENELIST_ARTICLES
## [1] 24
ERROR_PROPORTION = NUM_ERROR_GENELIST_ARTICLES / NUM_GENELIST_ARTICLES
ERROR_PROPORTION
## [1] 0.375
Here you can have a look at all the gene lists detected in the past month, as well as those with errors. The dates are obvious errors, these are commonly dates in September, March, December and October. The five-digit numbers represent dates as they are encoded in the Excel internal format. The five digit number is the number of days since 1900. If you were to take these numbers and put them into Excel and format the cells as dates, then these will also mostly map to dates in September, March, December and October.
GENELISTS
## [1] "PMC7771963 /pmc/articles/PMC7771963/bin/elife-55793-supp1.xlsx Dmelanogaster"
## [2] "PMC7771963 /pmc/articles/PMC7771963/bin/elife-55793-supp1.xlsx Hsapiens"
## [3] "PMC7771206 /pmc/articles/PMC7771206/bin/12920_2020_828_MOESM2_ESM.xlsx Hsapiens"
## [4] "PMC7771076 /pmc/articles/PMC7771076/bin/12920_2020_836_MOESM4_ESM.xlsx Hsapiens"
## [5] "PMC7771076 /pmc/articles/PMC7771076/bin/12920_2020_836_MOESM5_ESM.xlsx Hsapiens"
## [6] "PMC7771076 /pmc/articles/PMC7771076/bin/12920_2020_836_MOESM6_ESM.xlsx Hsapiens"
## [7] "PMC7769233 /pmc/articles/PMC7769233/bin/PBI-19-109-s001.xls Athaliana"
## [8] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_2.XLSX Mmusculus"
## [9] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_2.XLSX Hsapiens"
## [10] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_3.XLSX Mmusculus"
## [11] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_3.XLSX Mmusculus"
## [12] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_3.XLSX Hsapiens"
## [13] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_3.XLSX Hsapiens"
## [14] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_4.XLSX Hsapiens"
## [15] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_4.XLSX Hsapiens"
## [16] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_4.XLSX Hsapiens"
## [17] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_5.XLSX Hsapiens"
## [18] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_6.XLSX Hsapiens"
## [19] "PMC7769845 /pmc/articles/PMC7769845/bin/Table_6.XLSX Hsapiens"
## [20] "PMC7768046 /pmc/articles/PMC7768046/bin/Table_1.xlsx Hsapiens"
## [21] "PMC7768046 /pmc/articles/PMC7768046/bin/Table_1.xlsx Hsapiens"
## [22] "PMC7767998 /pmc/articles/PMC7767998/bin/Table_10.XLSX Hsapiens"
## [23] "PMC7767998 /pmc/articles/PMC7767998/bin/Table_11.XLSX Hsapiens"
## [24] "PMC7767998 /pmc/articles/PMC7767998/bin/Table_12.XLSX Hsapiens"
## [25] "PMC7767998 /pmc/articles/PMC7767998/bin/Table_12.XLSX Hsapiens"
## [26] "PMC7767998 /pmc/articles/PMC7767998/bin/Table_12.XLSX Hsapiens"
## [27] "PMC7767998 /pmc/articles/PMC7767998/bin/Table_1.XLSX Hsapiens"
## [28] "PMC7767998 /pmc/articles/PMC7767998/bin/Table_3.XLSX Hsapiens"
## [29] "PMC7767998 /pmc/articles/PMC7767998/bin/Table_6.XLSX Hsapiens"
## [30] "PMC7767998 /pmc/articles/PMC7767998/bin/Table_7.XLSX Hsapiens"
## [31] "PMC7762822 /pmc/articles/PMC7762822/bin/mmc2.xlsx Hsapiens"
## [32] "PMC7758710 /pmc/articles/PMC7758710/bin/mmc1.xlsx Hsapiens"
## [33] "PMC7758710 /pmc/articles/PMC7758710/bin/mmc1.xlsx Hsapiens"
## [34] "PMC7758710 /pmc/articles/PMC7758710/bin/mmc1.xlsx Hsapiens"
## [35] "PMC7758710 /pmc/articles/PMC7758710/bin/mmc1.xlsx Hsapiens"
## [36] "PMC7758710 /pmc/articles/PMC7758710/bin/mmc1.xlsx Hsapiens"
## [37] "PMC7751343 /pmc/articles/PMC7751343/bin/Supplementary_Data2.xlsx Hsapiens"
## [38] "PMC7749177 /pmc/articles/PMC7749177/bin/41467_2020_20086_MOESM4_ESM.xlsx Hsapiens"
## [39] "PMC7749177 /pmc/articles/PMC7749177/bin/41467_2020_20086_MOESM4_ESM.xlsx Hsapiens"
## [40] "PMC7749177 /pmc/articles/PMC7749177/bin/41467_2020_20086_MOESM4_ESM.xlsx Hsapiens"
## [41] "PMC7749177 /pmc/articles/PMC7749177/bin/41467_2020_20086_MOESM4_ESM.xlsx Hsapiens"
## [42] "PMC7749177 /pmc/articles/PMC7749177/bin/41467_2020_20086_MOESM4_ESM.xlsx Hsapiens"
## [43] "PMC7749177 /pmc/articles/PMC7749177/bin/41467_2020_20086_MOESM4_ESM.xlsx Hsapiens"
## [44] "PMC7749177 /pmc/articles/PMC7749177/bin/41467_2020_20086_MOESM4_ESM.xlsx Hsapiens"
## [45] "PMC7749177 /pmc/articles/PMC7749177/bin/41467_2020_20086_MOESM4_ESM.xlsx Hsapiens"
## [46] "PMC7738172 /pmc/articles/PMC7738172/bin/ppat.1009113.s002.xlsx Celegans"
## [47] "PMC7738172 /pmc/articles/PMC7738172/bin/ppat.1009113.s002.xlsx Celegans"
## [48] "PMC7767460 /pmc/articles/PMC7767460/bin/cancers-12-03867-s001.xlsx Hsapiens"
## [49] "PMC7767460 /pmc/articles/PMC7767460/bin/cancers-12-03867-s001.xlsx Hsapiens"
## [50] "PMC7767460 /pmc/articles/PMC7767460/bin/cancers-12-03867-s001.xlsx Hsapiens"
## [51] "PMC7767460 /pmc/articles/PMC7767460/bin/cancers-12-03867-s001.xlsx Hsapiens"
## [52] "PMC7765024 /pmc/articles/PMC7765024/bin/ijms-21-09500-s001.xlsx Hsapiens"
## [53] "PMC7765024 /pmc/articles/PMC7765024/bin/ijms-21-09500-s001.xlsx Hsapiens"
## [54] "PMC7765024 /pmc/articles/PMC7765024/bin/ijms-21-09500-s001.xlsx Hsapiens"
## [55] "PMC7758481 /pmc/articles/PMC7758481/bin/DataSheet_1.xlsx Hsapiens 1 43532"
## [56] "PMC7758481 /pmc/articles/PMC7758481/bin/DataSheet_3.xlsx Hsapiens 3 43713 43714 43717"
## [57] "PMC7758481 /pmc/articles/PMC7758481/bin/DataSheet_6.xlsx Hsapiens"
## [58] "PMC7758481 /pmc/articles/PMC7758481/bin/DataSheet_6.xlsx Hsapiens"
## [59] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [60] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [61] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [62] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [63] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [64] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [65] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [66] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [67] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [68] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [69] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [70] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [71] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [72] "PMC7758323 /pmc/articles/PMC7758323/bin/Data_Sheet_1.xlsx Hsapiens"
## [73] "PMC7753206 /pmc/articles/PMC7753206/bin/Table_3.XLSX Hsapiens"
## [74] "PMC7753206 /pmc/articles/PMC7753206/bin/Table_4.XLSX Hsapiens"
## [75] "PMC7747725 /pmc/articles/PMC7747725/bin/41598_2020_79037_MOESM4_ESM.xlsx Hsapiens"
## [76] "PMC7736716 /pmc/articles/PMC7736716/bin/mmc2.xls Ggallus"
## [77] "PMC7736716 /pmc/articles/PMC7736716/bin/mmc3.xlsx Hsapiens"
## [78] "PMC7749173 /pmc/articles/PMC7749173/bin/42003_2020_1527_MOESM3_ESM.xlsx Hsapiens"
## [79] "PMC7749173 /pmc/articles/PMC7749173/bin/42003_2020_1527_MOESM3_ESM.xlsx Hsapiens"
## [80] "PMC7739048 /pmc/articles/PMC7739048/bin/vdaa142_suppl_supplementary_tables.xlsx Hsapiens"
## [81] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [82] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [83] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [84] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [85] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [86] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [87] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [88] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [89] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [90] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [91] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [92] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [93] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [94] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [95] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [96] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [97] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [98] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [99] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [100] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [101] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [102] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [103] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [104] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [105] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [106] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [107] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [108] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [109] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [110] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [111] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [112] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [113] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [114] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [115] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [116] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [117] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [118] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [119] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [120] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [121] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens 1 43896"
## [122] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [123] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [124] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [125] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [126] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [127] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [128] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [129] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [130] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [131] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [132] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [133] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [134] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [135] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [136] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [137] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [138] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [139] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [140] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [141] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [142] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [143] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [144] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [145] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [146] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [147] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [148] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens"
## [149] "PMC7744954 /pmc/articles/PMC7744954/bin/ACEL-19-e13278-s002.xlsx Mmusculus 26 42248 39326 41883 40238 38777 40787 40238 37681 37135 41153 40603 39692 40422 40238 38961 39508 40238 38047 38231 40238 39873 40057 40422 40238 37865 37681"
## [150] "PMC7744954 /pmc/articles/PMC7744954/bin/ACEL-19-e13278-s002.xlsx Mmusculus"
## [151] "PMC7734003 /pmc/articles/PMC7734003/bin/CAS-111-4594-s002.xls Hsapiens"
## [152] "PMC7734003 /pmc/articles/PMC7734003/bin/CAS-111-4594-s002.xls Hsapiens"
## [153] "PMC7732301 /pmc/articles/PMC7732301/bin/aging-12-103859-s001..xlsx Hsapiens 1 43893"
## [154] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens"
## [155] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens"
## [156] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens"
## [157] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens 3 37165 37530 37865"
## [158] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens"
## [159] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens"
## [160] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens 3 42248 39692 40057"
## [161] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens 2 39692 40057"
## [162] "PMC7732068 /pmc/articles/PMC7732068/bin/pone.0232101.s008.xlsx Dmelanogaster"
## [163] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM10_ESM.xlsx Hsapiens"
## [164] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM10_ESM.xlsx Hsapiens"
## [165] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM10_ESM.xlsx Hsapiens"
## [166] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM12_ESM.xlsx Hsapiens"
## [167] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM20_ESM.xlsx Hsapiens"
## [168] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM21_ESM.xlsx Hsapiens"
## [169] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM21_ESM.xlsx Mmusculus"
## [170] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM4_ESM.xlsx Hsapiens"
## [171] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM4_ESM.xlsx Hsapiens"
## [172] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM4_ESM.xlsx Hsapiens"
## [173] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM4_ESM.xlsx Hsapiens"
## [174] "PMC7729872 /pmc/articles/PMC7729872/bin/41467_2020_20079_MOESM4_ESM.xlsx Hsapiens"
## [175] "PMC7728285 /pmc/articles/PMC7728285/bin/ppat.1009028.s005.xlsx Hsapiens"
## [176] "PMC7728285 /pmc/articles/PMC7728285/bin/ppat.1009028.s005.xlsx Hsapiens"
## [177] "PMC7728285 /pmc/articles/PMC7728285/bin/ppat.1009028.s007.xlsx Hsapiens"
## [178] "PMC7726486 /pmc/articles/PMC7726486/bin/mmc2.xlsx Hsapiens 1 43712"
## [179] "PMC7726486 /pmc/articles/PMC7726486/bin/mmc3.xlsx Hsapiens 1 43712"
## [180] "PMC7726486 /pmc/articles/PMC7726486/bin/mmc4.xlsx Hsapiens"
## [181] "PMC7726486 /pmc/articles/PMC7726486/bin/mmc5.xlsx Hsapiens"
## [182] "PMC7726151 /pmc/articles/PMC7726151/bin/41467_2020_20136_MOESM3_ESM.xlsx Hsapiens"
## [183] "PMC7726151 /pmc/articles/PMC7726151/bin/41467_2020_20136_MOESM3_ESM.xlsx Hsapiens"
## [184] "PMC7726151 /pmc/articles/PMC7726151/bin/41467_2020_20136_MOESM3_ESM.xlsx Hsapiens"
## [185] "PMC7726151 /pmc/articles/PMC7726151/bin/41467_2020_20136_MOESM3_ESM.xlsx Hsapiens"
## [186] "PMC7726151 /pmc/articles/PMC7726151/bin/41467_2020_20136_MOESM6_ESM.xlsx Hsapiens 21 44078 44081 43896 44085 44085 44085 44085 44085 43897 44080 44080 43893 44084 44082 43896 44089 44080 43892 44076 43896 44083"
## [187] "PMC7726151 /pmc/articles/PMC7726151/bin/41467_2020_20136_MOESM6_ESM.xlsx Hsapiens"
## [188] "PMC7726151 /pmc/articles/PMC7726151/bin/41467_2020_20136_MOESM6_ESM.xlsx Hsapiens"
## [189] "PMC7718812 /pmc/articles/PMC7718812/bin/tvst-9-13-8_s004.xlsx Hsapiens 3 42980 42987 42985"
## [190] "PMC7718812 /pmc/articles/PMC7718812/bin/tvst-9-13-8_s005.xlsx Hsapiens"
## [191] "PMC7718792 /pmc/articles/PMC7718792/bin/peerj-08-10457-s002.xls Athaliana"
## [192] "PMC7718792 /pmc/articles/PMC7718792/bin/peerj-08-10457-s003.xls Athaliana"
## [193] "PMC7718792 /pmc/articles/PMC7718792/bin/peerj-08-10457-s004.xlsx Athaliana"
## [194] "PMC7718792 /pmc/articles/PMC7718792/bin/peerj-08-10457-s005.xlsx Athaliana"
## [195] "PMC7738636 /pmc/articles/PMC7738636/bin/Table_1.xls Ggallus"
## [196] "PMC7738636 /pmc/articles/PMC7738636/bin/Table_3.xls Hsapiens"
## [197] "PMC7738636 /pmc/articles/PMC7738636/bin/Table_4.xlsx Ggallus 2 43891 44085"
## [198] "PMC7738636 /pmc/articles/PMC7738636/bin/Table_4.xlsx Hsapiens 1 44082"
## [199] "PMC7738636 /pmc/articles/PMC7738636/bin/Table_6.xlsx Hsapiens"
## [200] "PMC7738636 /pmc/articles/PMC7738636/bin/Table_6.xlsx Hsapiens"
## [201] "PMC7738478 /pmc/articles/PMC7738478/bin/Table_3.xlsx Hsapiens"
## [202] "PMC7731467 /pmc/articles/PMC7731467/bin/12876_2020_1560_MOESM4_ESM.xlsx Hsapiens"
## [203] "PMC7731467 /pmc/articles/PMC7731467/bin/12876_2020_1560_MOESM6_ESM.xlsx Hsapiens"
## [204] "PMC7731467 /pmc/articles/PMC7731467/bin/12876_2020_1560_MOESM9_ESM.xlsx Hsapiens"
## [205] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s003.xlsx Hsapiens"
## [206] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s003.xlsx Hsapiens"
## [207] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s005.xlsx Hsapiens"
## [208] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s005.xlsx Hsapiens"
## [209] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s006.xlsx Hsapiens"
## [210] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s006.xlsx Hsapiens"
## [211] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s007.xlsx Hsapiens"
## [212] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s007.xlsx Hsapiens"
## [213] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s008.xlsx Hsapiens"
## [214] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s008.xlsx Hsapiens"
## [215] "PMC7721185 /pmc/articles/PMC7721185/bin/pgen.1009163.s009.xlsx Hsapiens"
## [216] "PMC7734124 /pmc/articles/PMC7734124/bin/Table_2.XLSX Mmusculus 23 44075 44081 44082 44084 44078 43901 44077 43895 43898 44076 43891 43897 43893 43891 43896 43899 44080 44085 44083 44079 43892 43900 43892"
## [217] "PMC7734124 /pmc/articles/PMC7734124/bin/Table_8.XLSX Mmusculus"
## [218] "PMC7734124 /pmc/articles/PMC7734124/bin/Table_8.XLSX Mmusculus"
## [219] "PMC7734124 /pmc/articles/PMC7734124/bin/Table_8.XLSX Mmusculus"
## [220] "PMC7734124 /pmc/articles/PMC7734124/bin/Table_8.XLSX Mmusculus"
## [221] "PMC7732649 /pmc/articles/PMC7732649/bin/Table_2.xls Hsapiens"
## [222] "PMC7732649 /pmc/articles/PMC7732649/bin/Table_2.xls Hsapiens"
## [223] "PMC7732649 /pmc/articles/PMC7732649/bin/Table_3.xls Hsapiens"
## [224] "PMC7732649 /pmc/articles/PMC7732649/bin/Table_4.xls Hsapiens 1 44075"
## [225] "PMC7732649 /pmc/articles/PMC7732649/bin/Table_5.xls Hsapiens"
## [226] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [227] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [228] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [229] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [230] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [231] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [232] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [233] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [234] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [235] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [236] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [237] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_3.XLSX Hsapiens"
## [238] "PMC7729193 /pmc/articles/PMC7729193/bin/Table_5.XLSX Hsapiens"
## [239] "PMC7728698 /pmc/articles/PMC7728698/bin/Table_1.XLSX Athaliana"
## [240] "PMC7728698 /pmc/articles/PMC7728698/bin/Table_1.XLSX Hsapiens"
## [241] "PMC7728435 /pmc/articles/PMC7728435/bin/elife-59980-fig1-data8.xlsx Hsapiens 30 2020/09/11 2020/09/09 2020/09/03 2020/03/03 2020/03/01 2020/09/03 2020/09/06 2020/09/06 2020/03/05 2020/09/02 2020/03/08 2020/03/02 2020/09/10 2020/03/02 2020/03/07 2020/03/06 2020/09/02 2020/03/06 2020/09/07 2020/03/02 2020/03/05 2020/09/08 2020/03/09 2020/03/02 2020/09/06 2020/09/02 2020/09/05 2020/09/15 2020/03/08 2020/09/01"
## [242] "PMC7728435 /pmc/articles/PMC7728435/bin/elife-59980-fig2-data2.xlsx Hsapiens"
## [243] "PMC7728435 /pmc/articles/PMC7728435/bin/elife-59980-fig2-data3.xlsx Hsapiens 13 2020/03/06 2020/03/02 2020/03/02 2020/03/01 2020/03/03 2020/03/06 2020/03/07 2020/03/02 2020/03/05 2020/03/08 2020/03/09 2020/03/05 2020/03/08"
## [244] "PMC7725876 /pmc/articles/PMC7725876/bin/Table_2.xls Hsapiens"
## [245] "PMC7723986 /pmc/articles/PMC7723986/bin/Table_3.XLSX Hsapiens"
## [246] "PMC7723986 /pmc/articles/PMC7723986/bin/Table_4.xlsx Hsapiens"
## [247] "PMC7723986 /pmc/articles/PMC7723986/bin/Table_6.XLSX Hsapiens 5 2020/03/02 2020/03/02 2020/03/02 2020/03/02 2020/03/02"
## [248] "PMC7723986 /pmc/articles/PMC7723986/bin/Table_6.XLSX Hsapiens 5 2020/03/02 2020/03/02 2020/03/02 2020/03/02 2020/03/02"
## [249] "PMC7723986 /pmc/articles/PMC7723986/bin/Table_9.XLSX Ggallus"
## [250] "PMC7723986 /pmc/articles/PMC7723986/bin/Table_9.XLSX Hsapiens"
## [251] "PMC7718028 /pmc/articles/PMC7718028/bin/Table_4.xlsx Hsapiens"
## [252] "PMC7718028 /pmc/articles/PMC7718028/bin/Table_4.xlsx Hsapiens"
## [253] "PMC7718028 /pmc/articles/PMC7718028/bin/Table_4.xlsx Hsapiens"
## [254] "PMC7718028 /pmc/articles/PMC7718028/bin/Table_4.xlsx Hsapiens"
## [255] "PMC7718028 /pmc/articles/PMC7718028/bin/Table_4.xlsx Hsapiens"
## [256] "PMC7718028 /pmc/articles/PMC7718028/bin/Table_4.xlsx Hsapiens"
## [257] "PMC7718028 /pmc/articles/PMC7718028/bin/Table_4.xlsx Hsapiens"
## [258] "PMC7714959 /pmc/articles/PMC7714959/bin/Table_1.xlsx Hsapiens"
## [259] "PMC7714959 /pmc/articles/PMC7714959/bin/Table_1.xlsx Hsapiens 2 43894 44085"
## [260] "PMC7714959 /pmc/articles/PMC7714959/bin/Table_2.xlsx Hsapiens 5 44078 44080 44166 43900 44079"
## [261] "PMC7714959 /pmc/articles/PMC7714959/bin/Table_2.xlsx Hsapiens 3 43891 43891 43899"
## [262] "PMC7714959 /pmc/articles/PMC7714959/bin/Table_3.xlsx Hsapiens"
## [263] "PMC7724473 /pmc/articles/PMC7724473/bin/mmc2.xlsx Mmusculus 12 40057 38412 39692 39326 41883 40422 37500 37135 40787 37316 42248 38961"
## [264] "PMC7724473 /pmc/articles/PMC7724473/bin/mmc3.xlsx Mmusculus 9 39142 39692 39326 40422 37500 37135 40057 40787 38961"
## [265] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [266] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [267] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens 40 43525 43529 43532 43532 43533 43534 43534 43717 43717 43717 43717 43528 43528 43528 43528 43531 43710 43525 43525 43525 43525 43525 43527 43527 43716 43716 43715 43800 43800 43800 43800 43800 43800 43800 43800 43800 43800 43800 43800 43800"
## [268] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens 6 43892 43891 43898 44082 43896 44081"
## [269] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens 1 43892"
## [270] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [271] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [272] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [273] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [274] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [275] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [276] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [277] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [278] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [279] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [280] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [281] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [282] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [283] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [284] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [285] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [286] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens 3 43716 43532 43709"
## [287] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [288] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [289] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [290] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [291] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [292] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [293] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [294] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [295] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [296] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [297] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [298] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [299] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [300] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens"
## [301] "PMC7726308 /pmc/articles/PMC7726308/bin/Supplementary_Data1.xlsx Hsapiens"
## [302] "PMC7723042 /pmc/articles/PMC7723042/bin/41467_2020_19813_MOESM15_ESM.xlsx Hsapiens 22 43349 43348 43353 43161 43345 43167 43344 43168 43160 43161 43351 43162 43165 43170 43352 43169 43347 43166 43160 43164 43346 43350"
## [303] "PMC7721725 /pmc/articles/PMC7721725/bin/42003_2020_1479_MOESM10_ESM.xlsx Hsapiens 9 40057 40057 40057 39508 40057 40787 40057 40057 40057"
## [304] "PMC7721725 /pmc/articles/PMC7721725/bin/42003_2020_1479_MOESM4_ESM.xlsx Hsapiens"
## [305] "PMC7721725 /pmc/articles/PMC7721725/bin/42003_2020_1479_MOESM5_ESM.xlsx Hsapiens"
## [306] "PMC7721725 /pmc/articles/PMC7721725/bin/42003_2020_1479_MOESM6_ESM.xlsx Hsapiens"
## [307] "PMC7721725 /pmc/articles/PMC7721725/bin/42003_2020_1479_MOESM8_ESM.xlsx Hsapiens 5 39508 40057 40057 39692 40057"
## [308] "PMC7721725 /pmc/articles/PMC7721725/bin/42003_2020_1479_MOESM9_ESM.xlsx Ggallus 8 40057 40057 40057 37226 36951 36951 40057 40057"
## [309] "PMC7721644 /pmc/articles/PMC7721644/bin/mmc2.xlsx Hsapiens"
## [310] "PMC7714695 /pmc/articles/PMC7714695/bin/41594_2020_466_MOESM3_ESM.xlsx Hsapiens"
## [311] "PMC7714695 /pmc/articles/PMC7714695/bin/41594_2020_466_MOESM3_ESM.xlsx Hsapiens"
## [312] "PMC7714695 /pmc/articles/PMC7714695/bin/41594_2020_466_MOESM3_ESM.xlsx Hsapiens"
## [313] "PMC7714695 /pmc/articles/PMC7714695/bin/41594_2020_466_MOESM3_ESM.xlsx Hsapiens"
## [314] "PMC7714695 /pmc/articles/PMC7714695/bin/41594_2020_466_MOESM5_ESM.xlsx Hsapiens"
## [315] "PMC7714695 /pmc/articles/PMC7714695/bin/41594_2020_466_MOESM5_ESM.xlsx Hsapiens 1 42256"
## [316] "PMC7714695 /pmc/articles/PMC7714695/bin/41594_2020_466_MOESM5_ESM.xlsx Hsapiens"
## [317] "PMC7708349 /pmc/articles/PMC7708349/bin/Table_1.xlsx Dmelanogaster"
## [318] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-003.xlsx Hsapiens"
## [319] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-003.xlsx Ggallus"
## [320] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-003.xlsx Hsapiens"
## [321] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-003.xlsx Hsapiens"
## [322] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-003.xlsx Hsapiens"
## [323] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-003.xlsx Hsapiens"
## [324] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-003.xlsx Hsapiens"
## [325] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-003.xlsx Hsapiens"
## [326] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-004.xlsx Hsapiens"
## [327] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-004.xlsx Hsapiens"
## [328] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-004.xlsx Hsapiens"
## [329] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-004.xlsx Hsapiens"
## [330] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-004.xlsx Hsapiens"
## [331] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-004.xlsx Hsapiens"
## [332] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-004.xlsx Hsapiens"
## [333] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-004.xlsx Hsapiens"
## [334] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-005.xlsx Hsapiens"
## [335] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-005.xlsx Hsapiens"
## [336] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-005.xlsx Hsapiens"
## [337] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-005.xlsx Hsapiens"
## [338] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-005.xlsx Hsapiens"
## [339] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-005.xlsx Hsapiens"
## [340] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-005.xlsx Hsapiens"
## [341] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-005.xlsx Hsapiens"
## [342] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-006.xlsx Hsapiens"
## [343] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-006.xlsx Hsapiens"
## [344] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-006.xlsx Hsapiens"
## [345] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-006.xlsx Hsapiens"
## [346] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-006.xlsx Hsapiens"
## [347] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-006.xlsx Hsapiens"
## [348] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-006.xlsx Hsapiens"
## [349] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-006.xlsx Hsapiens"
## [350] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-007.xlsx Ggallus"
## [351] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-007.xlsx Hsapiens"
## [352] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-009.xlsx Hsapiens"
## [353] "PMC7726493 /pmc/articles/PMC7726493/bin/EXCLI-19-1459-s-009.xlsx Hsapiens"
## [354] "PMC7723770 /pmc/articles/PMC7723770/bin/mmc1.xlsx Hsapiens"
## [355] "PMC7723770 /pmc/articles/PMC7723770/bin/mmc1.xlsx Hsapiens"
## [356] "PMC7723770 /pmc/articles/PMC7723770/bin/mmc1.xlsx Hsapiens"
## [357] "PMC7723770 /pmc/articles/PMC7723770/bin/mmc3.xlsx Hsapiens 23 44086 44078 44085 44079 43896 44081 43900 44084 43894 44088 43895 44166 43897 44077 43899 44083 43898 43892 43893 43891 43892 43891 44075"
## [358] "PMC7723770 /pmc/articles/PMC7723770/bin/mmc3.xlsx Hsapiens"
## [359] "PMC7723770 /pmc/articles/PMC7723770/bin/mmc4.xlsx Hsapiens"
## [360] "PMC7723770 /pmc/articles/PMC7723770/bin/mmc5.xlsx Hsapiens"
## [361] "PMC7723770 /pmc/articles/PMC7723770/bin/mmc5.xlsx Hsapiens"
## [362] "PMC7717581 /pmc/articles/PMC7717581/bin/pgen.1009110.s029.xlsx Dmelanogaster 5 44078 44078 44078 44078 44078"
## [363] "PMC7717581 /pmc/articles/PMC7717581/bin/pgen.1009110.s029.xlsx Dmelanogaster 1 44078"
## [364] "PMC7717581 /pmc/articles/PMC7717581/bin/pgen.1009110.s029.xlsx Dmelanogaster 2 44078 44078"
## [365] "PMC7714144 /pmc/articles/PMC7714144/bin/ppat.1009055.s007.xlsx Hsapiens"
## [366] "PMC7714144 /pmc/articles/PMC7714144/bin/ppat.1009055.s008.xlsx Hsapiens"
## [367] "PMC7710658 /pmc/articles/PMC7710658/bin/mmc2.xlsx Mmusculus"
## [368] "PMC7710658 /pmc/articles/PMC7710658/bin/mmc2.xlsx Mmusculus 1 43898"
## [369] "PMC7710658 /pmc/articles/PMC7710658/bin/mmc2.xlsx Mmusculus"
## [370] "PMC7710658 /pmc/articles/PMC7710658/bin/mmc2.xlsx Mmusculus"
## [371] "PMC7710658 /pmc/articles/PMC7710658/bin/mmc2.xlsx Mmusculus"
## [372] "PMC7710658 /pmc/articles/PMC7710658/bin/mmc2.xlsx Mmusculus"
## [373] "PMC7710658 /pmc/articles/PMC7710658/bin/mmc2.xlsx Mmusculus"
## [374] "PMC7693437 /pmc/articles/PMC7693437/bin/Table_1.XLSX Mmusculus"
## [375] "PMC7693437 /pmc/articles/PMC7693437/bin/Table_1.XLSX Mmusculus"
## [376] "PMC7689744 /pmc/articles/PMC7689744/bin/CPT-108-1067-s012.xlsx Hsapiens"
## [377] "PMC7689744 /pmc/articles/PMC7689744/bin/CPT-108-1067-s012.xlsx Hsapiens"
## [378] "PMC7689744 /pmc/articles/PMC7689744/bin/CPT-108-1067-s012.xlsx Hsapiens"
## [379] "PMC7711149 /pmc/articles/PMC7711149/bin/sj-xls-2-mpx-10.1177_1744806920966902.xls Hsapiens 47 2020/03/06 2020/12/01 2020/03/04 2020/03/01 2020/03/01 2020/03/01 2020/09/09 2020/03/03 2020/03/11 2020/09/11 2020/03/01 2020/03/08 2020/09/08 2020/09/02 2020/09/03 2020/03/01 2020/03/01 2020/03/01 2020/09/07 2020/12/01 2020/03/06 2020/09/09 2020/09/11 2020/09/02 2020/03/11 2020/03/11 2020/03/10 2020/03/01 2020/03/01 2020/03/11 2020/09/09 2020/03/11 2020/12/01 2020/03/02 2020/03/03 2020/09/09 2020/09/09 2020/09/07 2020/03/03 2020/03/01 2020/03/04 2020/03/03 2020/03/04 2020/03/08 2020/09/09 2020/03/08 2020/03/02"
## [380] "PMC7711149 /pmc/articles/PMC7711149/bin/sj-xls-3-mpx-10.1177_1744806920966902.xls Hsapiens 2 2020/03/01 2020/03/01"
## [381] "PMC7707522 /pmc/articles/PMC7707522/bin/ppat.1008593.s011.xlsx Hsapiens 2 40787 37500"
## [382] "PMC7292296 /pmc/articles/PMC7292296/bin/NPR2-39-301-s002.xlsx Hsapiens"
## [383] "PMC7292296 /pmc/articles/PMC7292296/bin/NPR2-39-301-s002.xlsx Hsapiens"
ERROR_GENELISTS
## [1] "PMC7758481 /pmc/articles/PMC7758481/bin/DataSheet_1.xlsx Hsapiens 1 43532"
## [2] "PMC7758481 /pmc/articles/PMC7758481/bin/DataSheet_3.xlsx Hsapiens 3 43713 43714 43717"
## [3] "PMC7746835 /pmc/articles/PMC7746835/bin/DataSheet_3.xlsx Hsapiens 1 43896"
## [4] "PMC7744954 /pmc/articles/PMC7744954/bin/ACEL-19-e13278-s002.xlsx Mmusculus 26 42248 39326 41883 40238 38777 40787 40238 37681 37135 41153 40603 39692 40422 40238 38961 39508 40238 38047 38231 40238 39873 40057 40422 40238 37865 37681"
## [5] "PMC7732301 /pmc/articles/PMC7732301/bin/aging-12-103859-s001..xlsx Hsapiens 1 43893"
## [6] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens 3 37165 37530 37865"
## [7] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens 3 42248 39692 40057"
## [8] "PMC7732848 /pmc/articles/PMC7732848/bin/42003_2020_1497_MOESM3_ESM.xlsx Hsapiens 2 39692 40057"
## [9] "PMC7726486 /pmc/articles/PMC7726486/bin/mmc2.xlsx Hsapiens 1 43712"
## [10] "PMC7726486 /pmc/articles/PMC7726486/bin/mmc3.xlsx Hsapiens 1 43712"
## [11] "PMC7726151 /pmc/articles/PMC7726151/bin/41467_2020_20136_MOESM6_ESM.xlsx Hsapiens 21 44078 44081 43896 44085 44085 44085 44085 44085 43897 44080 44080 43893 44084 44082 43896 44089 44080 43892 44076 43896 44083"
## [12] "PMC7718812 /pmc/articles/PMC7718812/bin/tvst-9-13-8_s004.xlsx Hsapiens 3 42980 42987 42985"
## [13] "PMC7738636 /pmc/articles/PMC7738636/bin/Table_4.xlsx Ggallus 2 43891 44085"
## [14] "PMC7738636 /pmc/articles/PMC7738636/bin/Table_4.xlsx Hsapiens 1 44082"
## [15] "PMC7734124 /pmc/articles/PMC7734124/bin/Table_2.XLSX Mmusculus 23 44075 44081 44082 44084 44078 43901 44077 43895 43898 44076 43891 43897 43893 43891 43896 43899 44080 44085 44083 44079 43892 43900 43892"
## [16] "PMC7732649 /pmc/articles/PMC7732649/bin/Table_4.xls Hsapiens 1 44075"
## [17] "PMC7728435 /pmc/articles/PMC7728435/bin/elife-59980-fig1-data8.xlsx Hsapiens 30 2020/09/11 2020/09/09 2020/09/03 2020/03/03 2020/03/01 2020/09/03 2020/09/06 2020/09/06 2020/03/05 2020/09/02 2020/03/08 2020/03/02 2020/09/10 2020/03/02 2020/03/07 2020/03/06 2020/09/02 2020/03/06 2020/09/07 2020/03/02 2020/03/05 2020/09/08 2020/03/09 2020/03/02 2020/09/06 2020/09/02 2020/09/05 2020/09/15 2020/03/08 2020/09/01"
## [18] "PMC7728435 /pmc/articles/PMC7728435/bin/elife-59980-fig2-data3.xlsx Hsapiens 13 2020/03/06 2020/03/02 2020/03/02 2020/03/01 2020/03/03 2020/03/06 2020/03/07 2020/03/02 2020/03/05 2020/03/08 2020/03/09 2020/03/05 2020/03/08"
## [19] "PMC7723986 /pmc/articles/PMC7723986/bin/Table_6.XLSX Hsapiens 5 2020/03/02 2020/03/02 2020/03/02 2020/03/02 2020/03/02"
## [20] "PMC7723986 /pmc/articles/PMC7723986/bin/Table_6.XLSX Hsapiens 5 2020/03/02 2020/03/02 2020/03/02 2020/03/02 2020/03/02"
## [21] "PMC7714959 /pmc/articles/PMC7714959/bin/Table_1.xlsx Hsapiens 2 43894 44085"
## [22] "PMC7714959 /pmc/articles/PMC7714959/bin/Table_2.xlsx Hsapiens 5 44078 44080 44166 43900 44079"
## [23] "PMC7714959 /pmc/articles/PMC7714959/bin/Table_2.xlsx Hsapiens 3 43891 43891 43899"
## [24] "PMC7724473 /pmc/articles/PMC7724473/bin/mmc2.xlsx Mmusculus 12 40057 38412 39692 39326 41883 40422 37500 37135 40787 37316 42248 38961"
## [25] "PMC7724473 /pmc/articles/PMC7724473/bin/mmc3.xlsx Mmusculus 9 39142 39692 39326 40422 37500 37135 40057 40787 38961"
## [26] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens 40 43525 43529 43532 43532 43533 43534 43534 43717 43717 43717 43717 43528 43528 43528 43528 43531 43710 43525 43525 43525 43525 43525 43527 43527 43716 43716 43715 43800 43800 43800 43800 43800 43800 43800 43800 43800 43800 43800 43800 43800"
## [27] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens 6 43892 43891 43898 44082 43896 44081"
## [28] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens 1 43892"
## [29] "PMC7730811 /pmc/articles/PMC7730811/bin/13148_2020_983_MOESM1_ESM.xlsx Hsapiens 3 43716 43532 43709"
## [30] "PMC7723042 /pmc/articles/PMC7723042/bin/41467_2020_19813_MOESM15_ESM.xlsx Hsapiens 22 43349 43348 43353 43161 43345 43167 43344 43168 43160 43161 43351 43162 43165 43170 43352 43169 43347 43166 43160 43164 43346 43350"
## [31] "PMC7721725 /pmc/articles/PMC7721725/bin/42003_2020_1479_MOESM10_ESM.xlsx Hsapiens 9 40057 40057 40057 39508 40057 40787 40057 40057 40057"
## [32] "PMC7721725 /pmc/articles/PMC7721725/bin/42003_2020_1479_MOESM8_ESM.xlsx Hsapiens 5 39508 40057 40057 39692 40057"
## [33] "PMC7721725 /pmc/articles/PMC7721725/bin/42003_2020_1479_MOESM9_ESM.xlsx Ggallus 8 40057 40057 40057 37226 36951 36951 40057 40057"
## [34] "PMC7714695 /pmc/articles/PMC7714695/bin/41594_2020_466_MOESM5_ESM.xlsx Hsapiens 1 42256"
## [35] "PMC7723770 /pmc/articles/PMC7723770/bin/mmc3.xlsx Hsapiens 23 44086 44078 44085 44079 43896 44081 43900 44084 43894 44088 43895 44166 43897 44077 43899 44083 43898 43892 43893 43891 43892 43891 44075"
## [36] "PMC7717581 /pmc/articles/PMC7717581/bin/pgen.1009110.s029.xlsx Dmelanogaster 5 44078 44078 44078 44078 44078"
## [37] "PMC7717581 /pmc/articles/PMC7717581/bin/pgen.1009110.s029.xlsx Dmelanogaster 1 44078"
## [38] "PMC7717581 /pmc/articles/PMC7717581/bin/pgen.1009110.s029.xlsx Dmelanogaster 2 44078 44078"
## [39] "PMC7710658 /pmc/articles/PMC7710658/bin/mmc2.xlsx Mmusculus 1 43898"
## [40] "PMC7711149 /pmc/articles/PMC7711149/bin/sj-xls-2-mpx-10.1177_1744806920966902.xls Hsapiens 47 2020/03/06 2020/12/01 2020/03/04 2020/03/01 2020/03/01 2020/03/01 2020/09/09 2020/03/03 2020/03/11 2020/09/11 2020/03/01 2020/03/08 2020/09/08 2020/09/02 2020/09/03 2020/03/01 2020/03/01 2020/03/01 2020/09/07 2020/12/01 2020/03/06 2020/09/09 2020/09/11 2020/09/02 2020/03/11 2020/03/11 2020/03/10 2020/03/01 2020/03/01 2020/03/11 2020/09/09 2020/03/11 2020/12/01 2020/03/02 2020/03/03 2020/09/09 2020/09/09 2020/09/07 2020/03/03 2020/03/01 2020/03/04 2020/03/03 2020/03/04 2020/03/08 2020/09/09 2020/03/08 2020/03/02"
## [41] "PMC7711149 /pmc/articles/PMC7711149/bin/sj-xls-3-mpx-10.1177_1744806920966902.xls Hsapiens 2 2020/03/01 2020/03/01"
## [42] "PMC7707522 /pmc/articles/PMC7707522/bin/ppat.1008593.s011.xlsx Hsapiens 2 40787 37500"
Let's investigate the errors in more detail.
# By species
SPECIES <- sapply(strsplit(ERROR_GENELISTS," "),"[[",3)
table(SPECIES)
## SPECIES
## Dmelanogaster Ggallus Hsapiens Mmusculus
## 3 2 32 5
barplot(table(SPECIES))
# Number of affected Excel files per paper
DIST <- table(sapply(strsplit(ERROR_GENELISTS," "),"[[",1))
DIST
##
## PMC7707522 PMC7710658 PMC7711149 PMC7714695 PMC7714959 PMC7717581 PMC7718812
## 1 1 2 1 3 3 1
## PMC7721725 PMC7723042 PMC7723770 PMC7723986 PMC7724473 PMC7726151 PMC7726486
## 3 1 1 2 2 1 2
## PMC7728435 PMC7730811 PMC7732301 PMC7732649 PMC7732848 PMC7734124 PMC7738636
## 2 4 1 1 3 1 2
## PMC7744954 PMC7746835 PMC7758481
## 1 1 2
summary(as.numeric(DIST))
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.00 1.00 1.50 1.75 2.00 4.00
hist(DIST,main="Number of affected Excel files per paper")
# PMC Articles with the most errors
DIST_DF <- as.data.frame(DIST)
DIST_DF <- DIST_DF[order(-DIST_DF$Freq),,drop=FALSE]
DIST_DF
## Var1 Freq
## 16 PMC7730811 4
## 5 PMC7714959 3
## 6 PMC7717581 3
## 8 PMC7721725 3
## 19 PMC7732848 3
## 3 PMC7711149 2
## 11 PMC7723986 2
## 12 PMC7724473 2
## 14 PMC7726486 2
## 15 PMC7728435 2
## 21 PMC7738636 2
## 24 PMC7758481 2
## 1 PMC7707522 1
## 2 PMC7710658 1
## 4 PMC7714695 1
## 7 PMC7718812 1
## 9 PMC7723042 1
## 10 PMC7723770 1
## 13 PMC7726151 1
## 17 PMC7732301 1
## 18 PMC7732649 1
## 20 PMC7734124 1
## 22 PMC7744954 1
## 23 PMC7746835 1
MOST_ERR_FILES = as.character(DIST_DF[1,1])
MOST_ERR_FILES
## [1] "PMC7730811"
# Number of errors per paper
NERR <- as.numeric(sapply(strsplit(ERROR_GENELISTS," "),"[[",4))
names(NERR) <- sapply(strsplit(ERROR_GENELISTS," "),"[[",1)
NERR <-tapply(NERR, names(NERR), sum)
NERR
## PMC7707522 PMC7710658 PMC7711149 PMC7714695 PMC7714959 PMC7717581 PMC7718812
## 2 1 49 1 10 8 3
## PMC7721725 PMC7723042 PMC7723770 PMC7723986 PMC7724473 PMC7726151 PMC7726486
## 22 22 23 10 21 21 2
## PMC7728435 PMC7730811 PMC7732301 PMC7732649 PMC7732848 PMC7734124 PMC7738636
## 43 50 1 1 8 23 3
## PMC7744954 PMC7746835 PMC7758481
## 26 1 4
hist(NERR,main="number of errors per PMC article")
NERR_DF <- as.data.frame(NERR)
NERR_DF <- NERR_DF[order(-NERR_DF$NERR),,drop=FALSE]
NERR_DF
## NERR
## PMC7730811 50
## PMC7711149 49
## PMC7728435 43
## PMC7744954 26
## PMC7723770 23
## PMC7734124 23
## PMC7721725 22
## PMC7723042 22
## PMC7724473 21
## PMC7726151 21
## PMC7714959 10
## PMC7723986 10
## PMC7717581 8
## PMC7732848 8
## PMC7758481 4
## PMC7718812 3
## PMC7738636 3
## PMC7707522 2
## PMC7726486 2
## PMC7710658 1
## PMC7714695 1
## PMC7732301 1
## PMC7732649 1
## PMC7746835 1
MOST_ERR = rownames(NERR_DF)[1]
MOST_ERR
## [1] "PMC7730811"
GENELIST_ERROR_ARTICLES <- gsub("PMC","",GENELIST_ERROR_ARTICLES)
ARTICLES <- esummary(GENELIST_ERROR_ARTICLES ,db = "pmc")
JOURNALS <- as.data.frame(table(ARTICLES$xmlValue("//FullJournalName")))
JOURNALS <- JOURNALS[order(-JOURNALS$Freq),]
JOURNAL_WINNER = as.character(JOURNALS[1,1])
JOURNALS
## Var1 Freq
## 10 Frontiers in Oncology 5
## 5 Communications Biology 2
## 13 Nature Communications 2
## 1 Aging (Albany NY) 1
## 2 Aging Cell 1
## 3 Cell 1
## 4 Clinical Epigenetics 1
## 6 Computational and Structural Biotechnology Journal 1
## 7 eLife 1
## 8 Frontiers in Cardiovascular Medicine 1
## 9 Frontiers in Cell and Developmental Biology 1
## 11 Molecular Pain 1
## 12 Molecular Therapy. Methods & Clinical Development 1
## 14 Nature Structural & Molecular Biology 1
## 15 PLoS Genetics 1
## 16 PLoS Pathogens 1
## 17 Stem Cell Reports 1
## 18 Translational Vision Science & Technology 1
JOURNALS <- JOURNALS[order(JOURNALS$Freq),]
par(mar=c(5,25,4,2))
barplot(JOURNALS$Freq,names.arg = JOURNALS$Var1,horiz=TRUE,las=1,
xlab="Papers with gene name errors in supp files",
main="Top journals this month")
Congrats to our Journal of the Month winner!
JOURNAL_WINNER
## [1] "Frontiers in Oncology"
There are two categories:
Paper with the most suplementary files affected by gene name errors (MOST_ERR_FILES)
Paper with the most gene names converted to dates (MOST_ERR)
Sometimes, one paper can win both categories. Congrats to our winners.
MOST_ERR_FILES <- gsub("PMC","",MOST_ERR_FILES)
article <- esummary(MOST_ERR_FILES,db = "pmc")
article
## Object of class 'esummary'
## <?xml version="1.0" encoding="UTF-8"?>
## <!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary pmc 20160609//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20160609/esummary_pmc.dtd">
## <eSummaryResult>
## <DocumentSummarySet status="OK">
## <DbBuild>Build210111-0115m.1</DbBuild>
## <DocumentSummary uid="7730811">
## <PubDate>2020 Dec 11</PubDate>
## <EPubDate>2020 Dec 11</EPubDate>
## <PrintPubDate/>
## <Source>Clin Epigenetics</Source>
## <Authors>
## <Author>
## <Name>Good M</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Chu T</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Shaw P</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>McClain L</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Chamberlain A</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Castro C</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Rimer JM</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Mihi B</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Gong Q</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Nolan LS</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Cooksey K</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Linneman L</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Agrawal P</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Finegold DN</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Peters D</Name>
## <AuthType>Author</AuthType>
## </Author>
## </Authors>
## <Title>Global hypermethylation of intestinal epithelial cells is a hallmark feature of neonatal surgical necrotizing enterocolitis</Title>
## <Volume>12</Volume>
## <Issue/>
## <Pages>190</Pages>
## <ArticleIds>
## <ArticleId>
## <IdType>pmid</IdType>
## <Value>33308304</Value>
## </ArticleId>
## <ArticleId>
## <IdType>doi</IdType>
## <Value>10.1186/s13148-020-00983-6</Value>
## </ArticleId>
## <ArticleId>
## <IdType>pmcid</IdType>
## <Value>PMC7730811</Value>
## </ArticleId>
## </ArticleIds>
## <FullJournalName>Clinical Epigenetics</FullJournalName>
## <SortDate>2020/12/11 00:00</SortDate>
## <PmcLiveDate>2020/12/11</PmcLiveDate>
## </DocumentSummary>
## </DocumentSummarySet>
## </eSummaryResult>
##
## ESummary query using the database 'pmc'.
#journal <- article$xmlValue("//FullJournalName")
MOST_ERR <- gsub("PMC","",MOST_ERR)
article <- esummary(MOST_ERR,db = "pmc")
article
## Object of class 'esummary'
## <?xml version="1.0" encoding="UTF-8"?>
## <!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary pmc 20160609//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20160609/esummary_pmc.dtd">
## <eSummaryResult>
## <DocumentSummarySet status="OK">
## <DbBuild>Build210111-0115m.1</DbBuild>
## <DocumentSummary uid="7730811">
## <PubDate>2020 Dec 11</PubDate>
## <EPubDate>2020 Dec 11</EPubDate>
## <PrintPubDate/>
## <Source>Clin Epigenetics</Source>
## <Authors>
## <Author>
## <Name>Good M</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Chu T</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Shaw P</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>McClain L</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Chamberlain A</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Castro C</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Rimer JM</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Mihi B</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Gong Q</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Nolan LS</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Cooksey K</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Linneman L</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Agrawal P</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Finegold DN</Name>
## <AuthType>Author</AuthType>
## </Author>
## <Author>
## <Name>Peters D</Name>
## <AuthType>Author</AuthType>
## </Author>
## </Authors>
## <Title>Global hypermethylation of intestinal epithelial cells is a hallmark feature of neonatal surgical necrotizing enterocolitis</Title>
## <Volume>12</Volume>
## <Issue/>
## <Pages>190</Pages>
## <ArticleIds>
## <ArticleId>
## <IdType>pmid</IdType>
## <Value>33308304</Value>
## </ArticleId>
## <ArticleId>
## <IdType>doi</IdType>
## <Value>10.1186/s13148-020-00983-6</Value>
## </ArticleId>
## <ArticleId>
## <IdType>pmcid</IdType>
## <Value>PMC7730811</Value>
## </ArticleId>
## </ArticleIds>
## <FullJournalName>Clinical Epigenetics</FullJournalName>
## <SortDate>2020/12/11 00:00</SortDate>
## <PmcLiveDate>2020/12/11</PmcLiveDate>
## </DocumentSummary>
## </DocumentSummarySet>
## </eSummaryResult>
##
## ESummary query using the database 'pmc'.
TODO: To plot the trend over the past 6 months.
Zeeberg, B.R., Riss, J., Kane, D.W. et al. Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics. BMC Bioinformatics 5, 80 (2004). https://doi.org/10.1186/1471-2105-5-80
Ziemann, M., Eren, Y. & El-Osta, A. Gene name errors are widespread in the scientific literature. Genome Biol 17, 177 (2016). https://doi.org/10.1186/s13059-016-1044-7
sessionInfo()
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] readxl_1.3.1 reutils_0.2.3 xml2_1.3.2
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.5 XML_3.99-0.3 assertthat_0.2.1 digest_0.6.25
## [5] bitops_1.0-6 cellranger_1.1.0 magrittr_1.5 evaluate_0.14
## [9] rlang_0.4.7 stringi_1.5.3 rmarkdown_2.3 tools_3.6.3
## [13] stringr_1.4.0 RCurl_1.98-1.2 xfun_0.16 yaml_2.2.1
## [17] compiler_3.6.3 htmltools_0.5.0 knitr_1.29