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searchPubMed.R
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sink(file = "./logofsearchPubMed.txt")
# Daily PBPath Journal Watch ----
print(paste0("Daily PBPath Journal Watch from PubMed Started at: ", Sys.time()))
# load library ----
print(paste0("Load Library Started at: ", Sys.time()))
source("R/loadLibrary.R")
print(paste0("Load Library Ended at: ", Sys.time()))
# Get PMID list from PubMed ----
## search topic ----
print(paste0("define topics Started at: ", Sys.time()))
source("R/topic.R")
print(paste0("define topics Ended at: ", Sys.time()))
## journal list ----
print(paste0("Read Journal List Started at: ", Sys.time()))
source("R/journals.R")
print(paste0("Read Journal List Ended at: ", Sys.time()))
## searchQuery ----
print(paste0("Read searchQuery Started at: ", Sys.time()))
source("R/searchQuery.R")
print(paste0("Read searchQuery Ended at: ", Sys.time()))
## date range ----
source("R/dateRange.R")
## generate search formula ----
print(paste0("Read searchFormula Started at: ", Sys.time()))
source("R/searchFormula.R")
print(paste0("Read searchFormula Ended at: ", Sys.time()))
# Search ----
print(paste0("Search Started at: ", Sys.time()))
source("R/search.R")
print(paste0("Search Ended at: ", Sys.time()))
# Fetch ----
print(paste0("Fetch Started at: ", Sys.time()))
source("R/fetch.R")
print(paste0("Fetch Ended at: ", Sys.time()))
# Get PMIDs ----
print(paste0("Get PMIDs Started at: ", Sys.time()))
source("R/getPMID.R")
print(paste0("Get PMIDs Ended at: ", Sys.time()))
# Save PMIDs ----
print(paste0("Save PMIDs Started at: ", Sys.time()))
source("R/savePMID.R")
print(paste0("Save PMIDs Ended at: ", Sys.time()))
# Save dataframes ----
print(paste0("Save DFs Started at: ", Sys.time()))
source("R/saveDF.R")
print(paste0("Save DFs Ended at: ", Sys.time()))
sink()
# Search: (pancreas) AND (American Journal of Surgical Pathology[Jour] OR Human Pathology[Jour] OR American journal of clinical pathology[Jour] OR Journal of Pathology[Jour] OR International Journal of Surgical Pathology[Jour] OR Histopathology[Jour] OR Archives of Pathology[Jour] OR Modern Pathology[Jour])
#
#
# Pancrea* AND tumor* OR cancer* OR adenocarcinoma* OR carcinoma*
# Gallbladder AND tumor* OR polyp* OR cancer* OR adenocarcinoma* OR carcinoma*
# Ampulla* AND tumor* OR polyp* OR cancer* OR adenocarcinoma* OR carcinoma*
# Biliary* tumor* OR OR cancer* OR adenocarcinoma* OR carcinoma* OR polyp*
# Bile duct* AND tumor* OR polyp* OR cancer* OR adenocarcinoma* OR carcinoma*
# Neuroendocrine AND pancrea*
# Acinar cell carcinoma
# Pancreatoblastoma*
# Cholangiocarcinoma*
# Solid pseudopapillary neoplasm*
# Intraductal papillary mucinous neoplasm*
# Mucinous cystic neoplasm*
# Intraductal papillary neoplasm* of bile duct
#
# List of journals to be reviewed:
# 1. AJSP
# 2. Pancreatology
# 3. Gastroenterology
# 4. Hepatology
# 5. Modern Path
# 6. Histopathology
# 7. Journal of molecular diagnostics
# 8. Virchows Archives
# 9. Human Pathology
# 10. Am J Gastroenterol
# 11. Pancreas
# 12. Clin Gastroenterol and Hepatol
# 13. Gut
# 14. American J Clin Pathol
# 15. Archives of Pathol and Lab Med
# 16. Seminars in Diagnostic Patthology
# 17. Cancer Cytopathology
# 18. Journal of American Society of Cytopathology
# 19. Diagnostic Cytopathology
# 20. Annals of Surgical Oncology
# 21. Annals of Surgery
# 22. Endocrine Pathology
# 23. Cancer
# 24. International Journal of Surgical Pathology