Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
talk with NCBI entrez using R
R HTML CSS
Branch: master

README.md

Build Status Build status Coverage Status

rentrez

rentrez provides functions that work with the NCBI Eutils API to search, download data from, and otherwise interact with NCBI databases.

Install

rentrez is on CRAN, so you can get the latest stable release with install.packages("rentrez"). This repository will sometimes be a little ahead of the CRAN version, if you want the latest (and possibly greatest) version you can install the current github version using Hadley Wickham's devtools.

library(devtools)
install_github("ropensci/rentrez")

Note (April 2015): Please note that rentrez is working towards a new release, which changes some of the behaviour described below. At present, this file describes the version of rentrez available from CRAN, and not the code in this repository. As we get closer to the new release this document will be updated.

Get help

Hopefully this README, and the package's vignette and in-line documentation, , provide you with enough information to get started with rentrez. If you need more help, or if discover a bug in rentrez please let us know, either through one of the contact methods described here, or by filing an issue

The EUtils API

Each of the functions exportd by rentrez is documented, and this README and the pakage vignette provide examples of how to use the functions together as part of a workflow. The API itself is well-documented. Be sure to read the official documenation to get the most out of API. In particular, be aware of the NCBI's usage policies and try to limit very large requests to off peak (USA) times (rentrez takes care of limiting the number of requests per second, and seeting the appropriate entrez tool name in each request).

See getting information about NCBI databases

Examples

In many cases, doing something interesting with EUtils will take multiple calls. Here are a few examples of how the functions work together (check out the package vignette for others).

Getting data from that great paper you've just read

Let's say I've just read a paper on the evolution of Hox genes, Di-Poi et al. (2010), and I want to get the data required to replicate their results. First, I need the unique ID for this paper in pubmed (the PMID). Annoyingly, many journals don't give PMIDS for their papers, but we can use entrez_search to find the paper using the doi field:

library(rentrez)
hox_paper <- entrez_search(db="pubmed", term="10.1038/nature08789[doi]")
(hox_pmid <- hox_paper$ids)
#> [1] "20203609"

Now, what sorts of data are avaliable from other NCBI database for this paper?

hox_data <- entrez_link(db="all", id=hox_pmid, dbfrom="pubmed")
hox_data
#> elink result with ids from 13 databases:
#>  [1] pubmed_medgen              pubmed_mesh_major         
#>  [3] pubmed_nuccore             pubmed_nucleotide         
#>  [5] pubmed_pmc_refs            pubmed_protein            
#>  [7] pubmed_pubmed              pubmed_pubmed_citedin     
#>  [9] pubmed_pubmed_combined     pubmed_pubmed_five        
#> [11] pubmed_pubmed_reviews      pubmed_pubmed_reviews_five
#> [13] pubmed_taxonomy_entrez

Each of the character vectors in this object contain unique IDS for records in the named databases. These functions try to make the most useful bits of the returned files available to users, but they also return the original file in case you want to dive into the XML yourself.

In this case we'll get the protein sequences as genbank files, using ' entrez_fetch:

hox_proteins <- entrez_fetch(db="protein", id=hox_data$pubmed_protein, rettype="gb")

Retreiving datasets associated a particular organism.

I like spiders. So let's say I want to learn a little more about New Zealand's endemic "black widow" the katipo. Specifically, in the past the katipo has been split into two species, can we make a phylogeny to test this idea?

The first step here is to use the function entrez_search to find datasets that include katipo sequences. The popset database has sequences arising from phylogenetic or population-level studies, so let's start there.

library(rentrez)
katipo_search <- entrez_search(db="popset", term="Latrodectus katipo[Organism]")
katipo_search$count
#> [1] "6"

In this search count is the total number of hits returned for the search term. We can use entrez_summary to learn a little about these datasets. rentrez will parse this xml into a list of esummary records, with each list entry corresponding to one of the IDs it is passed. In this case we get six records, and we see what each one contains like so:

summaries <- entrez_summary(db="popset", id=katipo_search$ids)
summaries[[1]]
#> esummary result with 16 items:
#>  [1] uid        caption    title      extra      gi         settype   
#>  [7] createdate updatedate flags      taxid      authors    article   
#> [13] journal    statistics properties oslt
sapply(summaries, "[[", "title")
#>                                                                                                                                                                                                                  167843272 
#> "Latrodectus katipo 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence." 
#>                                                                                                                                                                                                                  167843256 
#>                                                                                                                                  "Latrodectus katipo cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial." 
#>                                                                                                                                                                                                                  145206810 
#>        "Latrodectus 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence." 
#>                                                                                                                                                                                                                  145206746 
#>                                                                                                                                         "Latrodectus cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial." 
#>                                                                                                                                                                                                                   41350664 
#>                                                                                             "Latrodectus tRNA-Leu (trnL) gene, partial sequence; and NADH dehydrogenase subunit 1 (ND1) gene, partial cds; mitochondrial." 
#>                                                                                                                                                                                                                   39980346 
#>                                                                                                                                         "Theridiidae cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial."

Let's just get the two mitochondrial loci (COI and trnL), using entrez_fetch:

COI_ids <- katipo_search$ids[c(2,6)]
trnL_ids <- katipo_search$ids[5]
COI <- entrez_fetch(db="popset", id=COI_ids, rettype="fasta")
trnL <- entrez_fetch(db="popset", id=trnL_ids, rettype="fasta")

The "fetched" results are fasta formatted characters, which can be written to disk easily:

write(COI, "Test/COI.fasta")
write(trnL, "Test/trnL.fasta")

Once you've got the sequences you can do what you want with them, but I wanted a phylogeny so let's do that with ape:

library(ape)
coi <- read.dna("Test/COI.fasta", "fasta")
coi_aligned <- clustal(coi)
tree <- nj(dist.dna(coi_aligned))

Making use of httr configuration options

As of version 0.3, rentrez uses httr to manage calls to the Eutils API. This allows users to take advantage of some of httr's configuration options.

Any rentrez function that interacts with the Eutils api will pass the value of the argument config along to httr's GET function. For instance, if you acess the internet through a proxy you use the httr function use_proxy() to provide connection details to an entrez call:

entrez_search(db="pubmed",
              term="10.1038/nature08789[doi]",
              config=use_proxy("0.0.0.0", port=80,username="user", password="****")

Other options include verbose() which prints a detailed account of what's going on during a request, timeout() which sets the number of seconds to wait for a response before giving up, and, in the development version of httr, progress() which prints a progress bar to screen.

rentrez functions will also be effected by the global httr configuration set by httr::set_config(). For example, it's possible to have all calls to Eutils pass through a proxy and produce verbose output

httr::set_config(use_proxy("0.0.0.0", port=80,username="user", password="****"),
                 verbose() )
entrez_search(db="pubmed",  term="10.1038/nature08789[doi]")

WebEnv and big queries

The NCBI provides search history features, which can be useful for dealing with large lists of IDs (which will not fit in a single URL) or repeated searches. As an example, we will go searching for COI sequences from all the snail (Gastropod) species we can find in the nucleotide database:

snail_search <- entrez_search(db="nuccore", "Gastropoda[Organism] AND COI[Gene]", retmax=200, usehistory="y")

Because we set usehistory to "y" the snail_search object contains a unique ID for the search (WebEnv) and the particular query in that search history (QueryKey). Instead of using the 200 ids we turned up to make a new URL and fetch the sequences we can use the webhistory features.

cookie <- snail_search$WebEnv
qk <- snail_search$QueryKey
snail_coi <- entrez_fetch(db="nuccore", WebEnv=cookie, query_key=qk, rettype="fasta", retmax=10)

Getting information about NCBI databases

Most of the exmples above required some background information about what databases NCBI has to offer, and how they can be searched. rentrez provides a set of functions with names starting entrez_db that help you to discover this information in an interactive session.

First up, entrez_dbs() gives you a list of database names

entrez_dbs()
#>  [1] "pubmed"          "protein"         "nuccore"        
#>  [4] "nucleotide"      "nucgss"          "nucest"         
#>  [7] "structure"       "genome"          "assembly"       
#> [10] "genomeprj"       "bioproject"      "biosample"      
#> [13] "blastdbinfo"     "books"           "cdd"            
#> [16] "clinvar"         "clone"           "gap"            
#> [19] "gapplus"         "grasp"           "dbvar"          
#> [22] "epigenomics"     "gene"            "gds"            
#> [25] "geoprofiles"     "homologene"      "medgen"         
#> [28] "journals"        "mesh"            "ncbisearch"     
#> [31] "nlmcatalog"      "omim"            "orgtrack"       
#> [34] "pmc"             "popset"          "probe"          
#> [37] "proteinclusters" "pcassay"         "biosystems"     
#> [40] "pccompound"      "pcsubstance"     "pubmedhealth"   
#> [43] "seqannot"        "snp"             "sra"            
#> [46] "taxonomy"        "toolkit"         "toolkitall"     
#> [49] "toolkitbook"     "unigene"         "gencoll"        
#> [52] "gtr"

Some of the names are a little opaque, so you can get some more descriptve information about each with entrez_db_summary()

entrez_db_summary("cdd")
#>  DbName: cdd
#>  MenuName: Conserved Domains
#>  Description: Conserved Domain Database
#>  DbBuild: Build150108-1904.1
#>  Count: 50415
#>  LastUpdate: 2015/01/09 00:21

entrez_db_searchable() lets you discover the fields avalible for search terms for a given database. You get back a named-list, with names are fields. Each element has additional information about each named search field (you can also use as.data.frame to create a dataframe, with one search-field per row):

search_fields <- entrez_db_searchable("pmc")
search_fields$GRNT
#>  Name: GRNT
#>  FullName: Grant Number
#>  Description: NIH Grant Numbers
#>  TermCount: 2135694
#>  IsDate: N
#>  IsNumerical: N
#>  SingleToken: Y
#>  Hierarchy: N
#>  IsHidden: N

Finally, entrez_db_links takes a database name, and returns a list of other NCBI databases which might contain linked-records.

entrez_db_links("omim")
#> Databases with linked records for database 'omim'
#>  [1] biosample   biosystems  books       clinvar     dbvar      
#>  [6] gene        genetests   geoprofiles gtr         homologene 
#> [11] mapview     medgen      medgen      nuccore     nucest     
#> [16] nucgss      omim        pcassay     pccompound  pcsubstance
#> [21] pmc         protein     pubmed      pubmed      snp        
#> [26] snp         snp         sra         structure   unigene

Trendy topics in genetics

This is one is a little more trivial, but you can also use entrez to search pubmed and the EUtils API allows you to limit searches by the year in which the paper was published. That gives is a chance to find the trendiest -omics going around (this has quite a lot of repeated searching, so it you want to run your own version be sure to do it in off peak times).

Let's start by making a function that finds the number of records matching a given search term for each of several years (using the mindate and maxdate terms from the Eutils API):

library(rentrez)
papers_by_year <- function(years, search_term){
            return(sapply(years, function(y) entrez_search(db="pubmed",term=search_term, mindate=y, maxdate=y, retmax=0)$count))
        }

With that we can fetch the data for earch term and, by searching with no term, find the total number of papers published in each year:

years <- 1990:2014
total_papers <- as.numeric(papers_by_year(years, ""))
omics <- c("genomic", "epigenomic", "metagenomic", "proteomic", "transcriptomic", "pharmacogenomic", "connectomic" )
trend_data <- sapply(omics, function(t) papers_by_year(years, t))
trend_props <- as.numeric(trend_data)/total_papers

That's the data, let's plot it:

library(reshape)
library(ggplot2)
trend_df <- melt(data.frame(years, trend_props), id.vars="years")
p <- ggplot(trend_df, aes(years, value, colour=variable))
p + geom_line(size=1) + scale_y_log10("number of papers")

Giving us... well this:


This package is part of a richer suite called fulltext, along with several other packages, that provides the ability to search for and retrieve full text of open access scholarly articles.


Something went wrong with that request. Please try again.