euPMC

The euPMC package formats epmc_search results from europepmc and outputs Markdown reference lists, Javascript DataTables, and publication time series. Use devtools to install the packages from GitHub.

library(devtools)
install_github("ropensci/europepmc")
install_github("cstubben/euPMC")

Try searching Europe PMC using the Shiny app to view some example tables and plots (specific terms like Yersinia pestis virulence with a few hundred matches over many years work best).

https://cstubben.shinyapps.io/euPMC/

A detailed description of search fields and example queries are available from the Europe PMC help pages. The first example searches for Yersinia pestis virulence in the title from MEDLINE sources (with pubmed IDs). The epmc_hits function returns the number of hits, which can then be used to adjust the default limit of 25 results in epmc_search.

library(europepmc)
library(euPMC)

query <- "title:(Yersinia pestis virulence) AND src:MED"
epmc_hits(query)
# [1] 148

yp <- epmc_search(query, limit=200)
# 148 records found, returning 148

dplyr::filter(yp, pmid==23357388) %>% t()
                      [,1]
id                    "23357388"
source                "MED"
pmid                  "23357388"
pmcid                 "PMC3639585"
doi                   "10.1128/IAI.01417-12"
title                 "RfaL is required for Yersinia pestis type III secretion and virulence."
authorString          "Houppert AS, Bohman L, Merritt PM, Cole CB, Caulfield AJ, Lathem WW, Marketon MM."
journalTitle          "Infect Immun"
issue                 "4"
journalVolume         "81"
pubYear               "2013"
journalIssn           "0019-9567; 1098-5522; "
pageInfo              "1186-1197"
pubType               "research support, non-u.s. gov't; research-article; journal article; research ..."
isOpenAccess          "N"
inEPMC                "Y"
inPMC                 "Y"
hasPDF                "Y"
hasBook               "N"
hasSuppl              "Y"
citedByCount          "7"
hasReferences         "Y"
hasTextMinedTerms     "Y"
hasDbCrossReferences  "N"
hasLabsLinks          "Y"
hasTMAccessionNumbers "N"
firstPublicationDate  "2013-01-28"

The next query downloads seven papers citing Houppert et al. 2013 above.

x <- epmc_search( "cites:23357388_MED")
# 7 records found, returning 7

bib_format uses helper functions authors_etal and journal_cite to format author, year, title and journal and optionally add Pubmed IDs and cited by counts into a reference list. Markdown links are added to journals, PubMed IDs and Cited By counts if displayed.

x <- arrange(x, authorString)
bib_format(x)
bib_format(x, number=TRUE, pmid=TRUE, cited =TRUE, links=TRUE)
cat(strwrap(bib_format(x, number=TRUE, links=TRUE), width=100, exdent=3), sep="\n")

1. Caulfield AJ, Walker ME, Gielda LM, Lathem WW. 2014. The Pla protease of Yersinia pestis degrades fas ligand to manipulate host cell death and inflammation. Cell Host Microbe 15(4):424-434
2. da Silva P, Manieri FZ, Herrera CM, et al. 2018. Novel Role of VisP and the Wzz System during O-Antigen Assembly in Salmonella enterica Serovar Typhimurium Pathogenesis. Infect Immun 86(8)
3. Earl SC, Rogers MT, Keen J, et al. 2015. Resistance to Innate Immunity Contributes to Colonization of the Insect Gut by Yersinia pestis. PLoS One 10(7):e0133318
4. Eddy JL, Gielda LM, Caulfield AJ, et al. 2014. Production of outer membrane vesicles by the plague pathogen Yersinia pestis. PLoS One 9(9):e107002
5. Lathem WW, Schroeder JA, Bellows LE, et al. 2014. Posttranscriptional regulation of the Yersinia pestis cyclic AMP receptor protein Crp and impact on virulence. MBio 5(1):e01038-13
6. Merritt PM, Nero T, Bohman L, et al. 2015. Yersinia pestis targets neutrophils via complement receptor 3. Cell Microbiol 17(5):666-687
7. Ritzert JT, Lathem WW. 2018. Depletion of Glucose Activates Catabolite Repression during Pneumonic Plague. J Bacteriol 200(11)

DT_format adds html links to PubMed IDs, journal and cited by counts for displaying using the DT package.

library(DT)
y<-DT_format(yp)
datatable(y, escape = c(1,5),  caption="Publications with Yersinia pestis virulence in the title")

The year_ts function creates yearly time-series objects using the publication year for plotting using the dygraphs package.

y <- year_ts(yp)
dygraph(y, xlab="Year published", ylab="Articles per year")

The final query returns publications with the species Waddlia chondrophila in the abstract.

query <- 'abstract:"Waddlia chondrophila" AND SRC:MED'
epmc_hits(query)
[1] 73

wc <- epmc_search(query, limit =100)
dplyr::count(wc, journalTitle, sort=TRUE)
# # A tibble: 43 x 2
#   journalTitle                        n
#   <chr>                           <int>
# 1 Microbes Infect                     8
# 2 PLoS One                            6
# 3 Emerg Infect Dis                    4
# 4 New Microbes New Infect             4
# 5 Clin Microbiol Infect               3
# 6 FEMS Immunol Med Microbiol          3
# 7 J Vet Diagn Invest                  3
# 8 Microbiology                        3
# 9 Vet Microbiol                       3
#10 Eur J Clin Microbiol Infect Dis     2

The package also includes a list of journals indexed in MEDLINE in the NLM catalog at NCBI. This table includes MeSH terms assigned to the journal, which can be used to summarize the publications about Waddlia chondrophila (which could be considered a new emerging zoonotic pathogen based on the journal sources).

data(nlm)
inner_join(wc, nlm, by=c(journalTitle="ta")) %>%
 tidyr::separate_rows(mesh, sep="; ") %>% dplyr::count(mesh, sort=TRUE)
# # A tibble: 57 x 2
#   mesh                              n
#   <chr>                         <int>
# 1 Microbiology*                    19
# 2 Immunity*                         9
# 3 Infection                         9
# 4 Communicable Diseases*            7
# 5 Medicine*                         7
# 6 Science                           6
# 7 Veterinary Medicine*              6
# 8 Infection*                        5
# 9 Allergy and Immunology*           4
#10 Communicable Disease Control*     4
## ... with 47 more rows