'Entrez' in R

Provides an R interface to the NCBI's 'EUtils' API, allowing users to search databases like 'GenBank' < https://www.ncbi.nlm.nih.gov/genbank/> and 'PubMed' < https://pubmed.ncbi.nlm.nih.gov/>, process the results of those searches and pull data into their R sessions.


Version 1.2.2

Maintenance release containing a number of bug fixes.

  • A fix #127 forces curl to use http/1.1, as NCBI produces errors when sing http/2 (thanks @hammer for bug report and fix)
  • fix #131 stops pubmed records with reference sections production > 1 value for the 'pmid' field. Thanks @agbarnett for the report.
  • Added clarification around the expectd input for extract_from_esummary to the docs.

Version 1.2.1

Bug fix release. Thanks @gmbecker for pointing out a problem with the way retmode was being used in entrez_fetch (PR #121).

Also updates documentation to make this clear. Removes depricated verbs from testthat code.

Version 1.2.0

rentrez updated to reflect NCBIs new API policy, allowing more requests from users with registered keys. (Issues #115 -- #117).

CITATION updated to reflect publication in The R Journal.

Minor changes

  • clarification of search syntax in docs (issue #120)
  • ORCID ids added for all authors (issue #118)

Version 1.1.0

As of this release, rentrez will use httr::POST when sending > 200 ids to the NCBI. This should make working with large ID sets easier (thanks to the NCBI for supporing the POST methods, Reed Cartwright and Chris Stubben for pushing me on issue #89).

Other minor changes: * Pass on error messages from NCBI when too many records are requested from entrez_summary (Issue #106) * Useful error message when trying to send an empty ID set to NCBI (Issue #107)

Version 1.0.4

Update to documentation and tests to accommodate versioned accessions now available from NCBI (see ?entrez_fetch and the vignette)

Version 1.0.3

Update to only use https * NCBI is goinh all https, rentrez will only use https from now on. * Added links to repo/bug reporting to DESCRIPTION * Documented changes to sequence database XML records * Allow automatic parsing of XML flavours

Version 1.0.2

Bug fix release * Tests now work with testthat 1.0.0 * All calls to ncbi specify encoding is UTF-8 (saving error messages) * HTTP Error codes associated with large requests now give the user a hint to check out the documentation for web-history features

Version 1.0.1

Bug fix release * Properly format "by_id" mode URLS (bug exposed by httr 1.0.1) * Handle case in which some IDs passed to "by_id" mode are invalide (thanks Zachary Foster for report) * Documentation updated to reflect OMIM->SNP links no longer possible * Use Rmarkdown (not knitr) as vignette builder * Return NCBI error messages are text when they exist

Version 1.0.0

* new function extract_from_esummary() for extracting like-named elements
  from a list esummary records (e.g. get all "Title" fields from a list of 
  PubMed esummaries)
* Support for `cmd` option in entrez_link (breaks backward compatibility)
    * Allows discovery of external links from and use of web_history
    * New helper function linkout_urls to get URLs form external links
* Support for 'by_id' mode for entrez_link. Pass a vector of IDs to
  entrez_link, (optionally) get a list on elink objects back (one per ID)
* New web_history object makes using NCBI Web History features easier
* All of these changes documented in new vignette
* Han Guangchun added as contributor for his pull requests 
* New tests, minor bug fixes and extended documentation

Version 0.4.1

  • Bug fix: The example for entrez_summary contained a typo which made it fail (being wrapped in dontest this hadn't previously shown up).

Version 0.4

  • entrez_summary now fetches 'version 2.0' esummary records from NCBI
    • This change may break some scripts. In particular, the names of some elements in esummary records have changed. Broken scripts shold produce a helpful error message, and using entrez_summary(..., version="1.0") should fix it. More details are given in the help to entrez_summary.
    • When version 2.0 records are requested entrez_summary fetches the json record.
  • New helper functions for einfo Eutil
    • entrez_dbs() lists avaliable databases.
    • entrez_db_summary() gets summary information about a given database.
    • entrez_db_links() lists databases against which a given db's records might be cross referenced.
    • entrez_db_searchable() lists search terms avaliable for a given database.
  • Nicer print functions for search and summary objects
  • New dependancy on jsonlite for handling json records.
  • Bunch of bugs squashed and typos cleaned up

Version 0.3.1

* Squashed a bug in the vignette which wrote to users $HOME

Version 0.3

* using httr to handle HTTP GETs and some url building
* parsing for esummary parsing for clinvar database
* Scott Chamberlain added as contributer for above
* Pubmed parser handles multi-record files
* html vignette included

Version 0.2.4

* minor release to fix bug in esummary parsing

Version 0.2.3

* Edited license/description to meet CRAN requiremens
* Added sentence to description to summarise the package

Version 0.2.2

* Parsing of esummary xmls is now much nicer. 
* S3 items to represent most results
* Tests to cover all functions

Version 0.1.1

* First release on CRAN + now part of ROpenSci
* Functions cover the whole EUtils API

Reference manual

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1.2.3 by David Winter, a year ago

https://docs.ropensci.org/rentrez/ (website) https://github.com/ropensci/rentrez/

Report a bug at https://github.com/ropensci/rentrez/issues/

Browse source code at https://github.com/cran/rentrez

Authors: David Winter [aut, cre] , Scott Chamberlain [ctb] , Han Guangchun [ctb]

Documentation:   PDF Manual  

Task views:

MIT + file LICENSE license

Imports XML, httr, jsonlite

Suggests testthat, knitr, rmarkdown

Imported by MACER, ResearchAssociate, biolink, covid19.analytics, geneHummus, pubmedR, read.gb, rotl.

Depended on by Map2NCBI.

Suggested by BoSSA, disprose, genekitr, idiogramFISH.

See at CRAN