Guide to using rOpenSci packages during the US Gov’t shutdown

October 8, 2013

(This article was first published on Recology - R, and kindly contributed to R-bloggers)

Note: This is cross-posted from the rOpenSci blog, which will update with this post when our technical snafu is fixed.

With the US government shut down, many of the federal government provided data APIs are down. We write R packages to interact with many of these APIs. We have been tweeting about what APIs that are down related to R pacakges we make, but we thought we would write up a proper blog post on the issue.

NCBI services are still up! Here is the message on the NCBI page:

The information on this web site remains accessible; but, due to the lapse in government funding, the information may not be up to date, and the agency may not be able to respond to inquiries until appropriations are enacted. For updates regarding government operating status see

Most USGS services are down. Some of the message on the USGS page (both NOAA and ITIS are under USGS):

Due to the Federal government shutdown, and most associated web sites are unavailable. Only web sites necessary to protect lives and property will be maintained…

However, the USGS BISON service is still up for some reason – perhaps a different pot of money than other USGS projects?

Here’s a table of APIs we interact with, the related R package, and any notes:

API provider API still up? rOpenSci R package
USGS BISON (Biodiversity Information Serving our Nation) link Yep! rbison
NOAA Climate data link No :( rnoaa
USGS ITIS (Integrated Taxonomic Information Service) link No :( taxize
NCBI Entrez link No :( taxize,rentrez
PubMed link No :( rpubmed

For those wanting to get NOAA climate data, perhaps check out the RNCEP package.

For those using taxize, you can grab taxonomic IDs from NCBI using get_uid() rather than the ITIS version get_tsn(). With a UID from NCBI, you can do things like get a taxonomic classification using the function classification(). There are many non-government taxonomic sources in taxize, so you should be able to find what you need without ITIS. Other functions that use ITIS, and that you should avoid until the shutdown is over, are:

  • A long list carried over from the itis package that is now within taxize: getacceptednamesfromtsn(), getanymatchcount(), getcommentdetailfromtsn(), getcommonnamesfromtsn(), getcoremetadatafromtsn(), getcoveragefromtsn(), getcredibilityratingfromtsn(), getcredibilityratings(), getcurrencyfromtsn(), getdatedatafromtsn(), getdescription(), getexpertsfromtsn(), getfullhierarchyfromtsn(), getfullrecordfromlsid(), getfullrecordfromtsn(), getgeographicdivisionsfromtsn(), getgeographicvalues(), getglobalspeciescompletenessfromtsn(), gethierarchydownfromtsn(), gethierarchyupfromtsn(), getitistermsfromcommonname(), getitistermsfromscientificname(), getjurisdictionaloriginfromtsn(), getjurisdictionoriginvalues(), getjurisdictionvalues(), getkingdomnamefromtsn(), getkingdomnames(), getlastchangedate(), getlsidfromtsn(), getothersourcesfromtsn(), getparenttsnfromtsn(), getpublicationsfromtsn(), getranknames(), getrecordfromlsid(), getreviewyearfromtsn(), getscientificnamefromtsn(), getsynonymnamesfromtsn(), gettaxonauthorshipfromtsn(), gettaxonomicranknamefromtsn(), gettaxonomicusagefromtsn(), gettsnbyvernacularlanguage(), gettsnfromlsid(), getunacceptabilityreasonfromtsn(), getvernacularlanguages(), searchbycommonname(), searchbycommonnamebeginswith(), searchbycommonnameendswith(), searchbyscientificname(), searchforanymatch(), searchforanymatchpaged()
  • itis_acceptname()
  • itis_downstream()
  • itis_name()
  • itis_taxrank()
  • In tax_agg(), only use db=”ncbi”
  • In tax_name(), only use db=”ncbi”
  • In tax_rank(), only use db=”ncbi”

Let us know if you have any questions or comments.

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