Automated PubMed literature search

literature_search() searches for articles for protein-disease pairs in PubMed. A list of proteins and diseases is provided as input. The function retrieves the articles for each protein-disease pair. The input should be in the correct format, a list with diseases as names and protein vectors associated with each disease as elements (see examples).

Usage

literature_search(prot_dis_list, max_articles = 10)

Arguments

prot_dis_list

A list of proteins and diseases. The names of the list are the diseases and the elements are vectors of proteins.

max_articles

The maximum number of articles to retrieve for each protein-disease pair. Default is 10.

Value

A list of tibbles. Each tibble contains the articles found for a protein-disease pair.

Details

The disease and gene names should be correct in order for the query to be successful. For example AML should be written as "acute myeloid leukemia".

Examples

# Prepare the list of protein-disease pairs
prot_dis_list <- list("acute myeloid leukemia" = c("FLT3", "EPO"),
                      "chronic lymphocytic leukemia" = c("PARP1", "FCER2"))

# Run the literature search
lit_search_results <- literature_search(prot_dis_list, max_articles = 1)
#> Searching for articles on FLT3 and acute myeloid leukemia
#> Searching for articles on EPO and acute myeloid leukemia
#> Searching for articles on PARP1 and chronic lymphocytic leukemia
#> Searching for articles on FCER2 and chronic lymphocytic leukemia

# Results for FLT3 in acute myeloid leukemia
lit_search_results[["acute myeloid leukemia"]][["FLT3"]]
#>       pmid  First_author year              journal
#> 1 39287653 Duan, Wenbing 2024 Annals of hematology
#>                                                                                                                                                                                                                                title
#> 1 Only FLT3-ITD co-mutation did not have a deleterious effect on acute myeloid leukemia patients with NPM1 mutation, but concomitant with DNMT3A co-mutation or a&#x2009;&lt;&#x2009;3log reduction of MRD2 predicted poor survival.