#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")
##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:
hox_paper <- entrez_search(db="pubmed", term="10.1038/nature08789[doi]")
(hox_pmid <- hox_paper$ids)## [1] "20203609"
Now, what sorts of data are avaliable from other NCBI database for this paper?
hox_data <- entrez_link(db="all", id=hox_pmid, dbfrom="pubmed")
hox_data## elink result with ids from 13 databases:
## [1] pubmed_medgen pubmed_mesh_major
## [3] pubmed_nuccore pubmed_nucleotide
## [5] pubmed_pmc_refs pubmed_protein
## [7] pubmed_pubmed pubmed_pubmed_citedin
## [9] pubmed_pubmed_combined pubmed_pubmed_five
## [11] pubmed_pubmed_reviews pubmed_pubmed_reviews_five
## [13] pubmed_taxonomy_entrez
Each of the character vectors in this object contain unique IDS for records in the named databases. These functions try to make the most useful bits of the returned files available to users, but they also return the original file in case you want to dive into the XML yourself.
In this case we'll get the protein sequences as genbank files, using '
entrez_fetch:
hox_proteins <- entrez_fetch(db="protein", ids=hox_data$pubmed_protein, rettype="gb")## Error: Function requires either id or WebEnv to be set as arguments
###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]")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 MenuName
## "cdd" "Conserved Domains"
## Description DbBuild
## "Conserved Domain Database" "Build141002-1144.3"
## Count LastUpdate
## "49955" "2014/10/06 18:00"
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
## [1] "GRNT"
##
## $FullName
## [1] "Grant Number"
##
## $Description
## [1] "NIH Grant Numbers"
##
## $TermCount
## [1] "2094173"
##
## $IsDate
## [1] "N"
##
## $IsNumerical
## [1] "N"
##
## $SingleToken
## [1] "Y"
##
## $Hierarchy
## [1] "N"
##
## $IsHidden
## [1] "N"
Finally, entrez_db_links takes a database name, and returns a list of other
NCBI databases which might contain linked-records.
entrez_db_links("omim")## Databases with linked records for database 'omim'
## [1] biosample biosystems books clinvar dbvar
## [6] gene genetests geoprofiles gtr homologene
## [11] mapview medgen medgen nuccore nucest
## [16] nucgss omim pcassay pccompound pcsubstance
## [21] pmc protein pubmed pubmed snp
## [26] snp snp sra structure unigene
###Trendy topics in genetics
This is one is a little more trivial, but you can also use entrez to search pubmed and the EUtils API allows you to limit searches by the year in which the paper was published. That gives is a chance to find the trendiest -omics going around (this has quite a lot of repeated searching, so it you want to run your own version be sure to do it in off peak times).
Let's start by making a function that finds the number of records matching a given
search term for each of several years (using the mindate and maxdate terms from
the Eutils API):
library(rentrez)
papers_by_year <- function(years, search_term){
return(sapply(years, function(y) entrez_search(db="pubmed",term=search_term, mindate=y, maxdate=y, retmax=0)$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 <- 1990:2013
total_papers <- 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 <- trend_data/total_papersThat'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.
