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PubMed literature search

Source: R/lit_search.R
hd_literature_search.Rd

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

Usage

hd_literature_search(
  feature_class_list,
  max_articles = 10,
  keywords = NULL,
  fields = "All Fields",
  api_key = NULL,
  verbose = TRUE
)

Arguments

feature_class_list

A list of features (gene names) and classes (diseases). The names of the list are the classes and the elements are vectors of features. See examples.

max_articles

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

keywords

Additional keywords to include in the search. They are added to the query as "AND keywords". Default is NULL.

fields

The fields to search for the keywords. Default is "All Fields". Other options are "Title", "Abstract", "Author", "Journal", "Affiliation", "MeSH Terms", "Other Terms".

api_key

user-specific API key to increase the limit of queries per second. You can obtain your key from NCBI but not required. Default is NULL.

verbose

Whether to print progress messages. Default is TRUE.

Value

A list of tibbles. Each tibble contains the articles found for a gene-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". The query is constructed as "gene[field] AND disease[field] AND keywords". For more details check the easyPubMed package documentation. For more complicated queries, you can use the easyPubMed package directly or use the PubMed website directly.

Examples

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

# Run the literature search
lit_search_results <- hd_literature_search(feature_class_list, max_articles = 1)
#> Searching for articles onFLT3andacute myeloid leukemia
#> Warning: The get_pubmed_ids() function has become obsolete. You should use the EPM_query() function instead. Please, have a look at the manual or the vignette. The get_pubmed_ids() function will be retired in the second half of 2024.
#> This warning is displayed once per session.
#> Invalid response from PubMed API
#> Searching for articles onEPOandacute myeloid leukemia
#> Invalid response from PubMed API
#> Searching for articles onPARP1andchronic lymphocytic leukemia
#> Invalid response from PubMed API

# Results for FLT3 in acute myeloid leukemia
lit_search_results$`acute myeloid leukemia`$FLT3
#> NULL