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

Description Usage Arguments Value Examples

View source: R/epmc_db.r

Description

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

Usage

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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

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  ## 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 Jan. 18, 2022, 4:47 p.m.