europepmc (version 0.3)

epmc_db: 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 https://www.ebi.ac.uk/arrayexpress/

'CHEBI'

a database and ontology of chemical entities of biological interest http://www.ebi.ac.uk/chebi/

'CHEMBL'

a database of bioactive drug-like small molecules https://www.ebi.ac.uk/chembldb/

'EMBL'

now ENA, provides a comprehensive record of the world's nucleotide sequencing information http://www.ebi.ac.uk/ena/

'INTACT'

provides a freely available, open source database system and analysis tools for molecular interaction data http://www.ebi.ac.uk/intact/

'INTERPRO'

provides functional analysis of proteins by classifying them into families and predicting domains and important sites http://www.ebi.ac.uk/interpro/

'OMIM'

a comprehensive and authoritative compendium of human genes and genetic phenotypes http://www.ncbi.nlm.nih.gov/omim

'PDB'

European resource for the collection, organisation and dissemination of data on biological macromolecular structures http://www.ebi.ac.uk/pdbe/

'UNIPROT'

comprehensive and freely accessible resource of protein sequence and functional information http://www.uniprot.org/

'PRIDE'

PRIDE Archive - proteomics data repository https://www.ebi.ac.uk/pride/archive/

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 {
  
# }
# NOT RUN {
  epmc_db("12368864", db = "uniprot", limit = 150)
  epmc_db("25249410", db = "embl")
  epmc_db("14756321", db = "uniprot")
  epmc_db("11805837", db = "pride")
  
# }