epmc_db function

Retrieve external database entities referenced in a given publication

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

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.

Returns

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)