epmc_db: Retrieve external database entities referenced in a given...

In ropensci/europepmc: R Interface to the Europe PubMed Central RESTful Web Service

Retrieve external database entities referenced in a given publication

Description

This function returns EBI database entities referenced in a publication from Europe PMC RESTful Web Service.

Usage

epmc_db(
  ext_id = NULL,
  data_src = "med",
  db = NULL,
  limit = 100,
  verbose = TRUE
)

Arguments

ext_id	character, publication identifier
data_src	character, data source, by default Pubmed/MedLine index will be searched. The following three letter codes represent the sources Europe PubMed Central supports: agr Agricola is a bibliographic database of citations to the agricultural literature created by the US National Agricultural Library and its co-operators. cba Chinese Biological Abstracts ctx CiteXplore eth EthOs Theses, i.e. PhD theses (British Library) hir NHS Evidence med PubMed/Medline NLM nbk Europe PMC Book metadata pat Biological Patents pmc PubMed Central
db	character, specify database: 'ARXPR' Array Express, a database of functional genomics experiments 'CHEBI' a database and ontology of chemical entities of biological interest 'CHEMBL' a database of bioactive drug-like small molecules 'EMBL' now ENA, provides a comprehensive record of the world's nucleotide sequencing information 'INTACT' provides a freely available, open source database system and analysis tools for molecular interaction data 'INTERPRO' provides functional analysis of proteins by classifying them into families and predicting domains and important sites 'OMIM' a comprehensive and authoritative compendium of human genes and genetic phenotypes 'PDB' European resource for the collection, organisation and dissemination of data on biological macromolecular structures 'UNIPROT' comprehensive and freely accessible resource of protein sequence and functional information 'PRIDE' PRIDE Archive - proteomics data repository
limit	integer, number of results. By default, this function returns 100 records.
verbose	logical, print some information on what is going on.

Value

Cross-references as data.frame

Examples

  ## Not run: 
  epmc_db("12368864", db = "uniprot", limit = 150)
  epmc_db("25249410", db = "embl")
  epmc_db("14756321", db = "uniprot")
  epmc_db("11805837", db = "pride")
  
## End(Not run)

ropensci/europepmc documentation built on Nov. 30, 2023, 12:43 a.m.