nice example of esarch

usage_rentrez.R

+library(rentrez)
+
+
+## search Rana temporaria entreies in "Nucleotide" database from NCBI
+## search returns a list of IDs
+## retmax argument is to ask more than 20 (default value) results
+query <- entrez_search(db="nucleotide", term="rana temporaria[ORGN] AND mitochondrion AND complete genome", retmax=99999)
+## see the IDs of the queries
+query$ids
+## item i can search in nucleotide database
+entrez_db_searchable('nucleotide')
+## search the gene named "mhc" and species from "actinopterygii" class organism
+query <- entrez_search(db="nucleotide",
+                       term= "(MHC[GENE] OR (major histocompatibility
+complex[MeSH])) AND actinopterygii[ORGN] AND 1992:2021[PDAT]",
+                       retmax=99999)
+
+search_year <- function(year, term){
+  query <- paste(term, " AND (", year, "[PDAT])")
+  entrez_search(db="nucleotide", term=query, retmax=0)$count
+}
+
+
+year <- 1992:2021
+publications <- sapply(year,
+                 search_year,
+                 term="(MHC[GENE] OR (major histocompatibility complex[MeSH])) AND actinopterygii[ORGN]",
+                 USE.NAMES=FALSE)
+
+plot(year, publications, type="l",  main="MHC actinopterygii")