rplos tutorial


for v0.5.6


The rplos package interacts with the API services of PLoS (Public Library of Science) Journals. You used to need an API key to work with this package - that is no longer needed!

This tutorial will go through three use cases to demonstrate the kinds of things possible in rplos.

  • Search across PLoS papers in various sections of papers
  • Search for terms and visualize results as a histogram OR as a plot through time
  • Text mining of scientific literature

Installation

install.packages("rplos")

Or development version

if (!require("devtools")) install.packages("devtools")
devtools::install_github("ropensci/rplos")

library("rplos")

Usage

Search across PLoS papers in various sections of papers

searchplos is a general search, and in this case searches for the term Helianthus and returns the DOI’s of matching papers

searchplos(q= "Helianthus", fl= "id", limit = 5)

#> $meta
#>   numFound start maxScore
#> 1      422     0       NA
#>
#> $data
#>                             id
#> 1 10.1371/journal.pone.0148280
#> 2 10.1371/journal.pone.0111982
#> 3 10.1371/journal.pone.0057533
#> 4 10.1371/journal.pone.0139188
#> 5 10.1371/journal.pone.0045899

Get only full article DOIs

searchplos(q="*:*", fl='id', fq='doc_type:full', start=0, limit=5)

#> $meta
#>   numFound start maxScore
#> 1   184983     0       NA
#>
#> $data
#>                                                        id
#> 1                            10.1371/journal.pone.0107420
#> 2 10.1371/annotation/492fdf80-c999-4947-b569-96af8cb4e9d9
#> 3 10.1371/annotation/7a3d2279-0f96-433c-bb3f-d7fda1759633
#> 4 10.1371/annotation/78d328b9-2c8c-4978-84b1-7e6a0b12ada1
#> 5 10.1371/annotation/7983e1b9-09e4-4123-b1d5-aaaa0121e76a

Get DOIs for only PLoS One articles

searchplos(q="*:*", fl='id', fq='cross_published_journal_key:PLoSONE', start=0, limit=5)

#> $meta
#>   numFound start maxScore
#> 1  1344674     0       NA
#>
#> $data
#>                                        id
#> 1            10.1371/journal.pone.0107420
#> 2      10.1371/journal.pone.0107420/title
#> 3   10.1371/journal.pone.0107420/abstract
#> 4 10.1371/journal.pone.0107420/references
#> 5       10.1371/journal.pone.0107420/body

Get DOIs for full article in PLoS One

searchplos(q="*:*", fl='id',
   fq=list('cross_published_journal_key:PLoSONE', 'doc_type:full'),
   start=0, limit=5)

#> $meta
#>   numFound start maxScore
#> 1   157139     0       NA
#>
#> $data
#>                                                        id
#> 1                            10.1371/journal.pone.0107420
#> 2 10.1371/annotation/492fdf80-c999-4947-b569-96af8cb4e9d9
#> 3 10.1371/annotation/7a3d2279-0f96-433c-bb3f-d7fda1759633
#> 4 10.1371/annotation/78d328b9-2c8c-4978-84b1-7e6a0b12ada1
#> 5 10.1371/annotation/7983e1b9-09e4-4123-b1d5-aaaa0121e76a

Search for many terms

q <- c('ecology','evolution','science')
lapply(q, function(x) searchplos(x, limit=2))

#> [[1]]
#> [[1]]$meta
#>   numFound start maxScore
#> 1    32852     0       NA
#>
#> [[1]]$data
#>                             id
#> 1 10.1371/journal.pone.0059813
#> 2 10.1371/journal.pone.0001248
#>
#>
#> [[2]]
#> [[2]]$meta
#>   numFound start maxScore
#> 1    53560     0       NA
#>
#> [[2]]$data
#>                                                        id
#> 1 10.1371/annotation/9773af53-a076-4946-a3f1-83914226c10d
#> 2 10.1371/annotation/c55d5089-ba2f-449d-8696-2bc8395978db
#>
#>
#> [[3]]
#> [[3]]$meta
#>   numFound start maxScore
#> 1   157210     0       NA
#>
#> [[3]]$data
#>                             id
#> 1 10.1371/journal.pbio.0020122
#> 2 10.1371/journal.pbio.1001166

Search on specific sections

A suite of functions were created as light wrappers around searchplos as a shorthand to search specific sections of a paper.

  • plosauthor searchers in authors
  • plosabstract searches in abstracts
  • plostitle searches in titles
  • plosfigtabcaps searches in figure and table captions
  • plossubject searches in subject areas

plosauthor searches across authors, and in this case returns the authors of the matching papers. the fl parameter determines what is returned

plosauthor(q = "Eisen", fl = "author", limit = 5)

#> $meta
#>   numFound start maxScore
#> 1      833     0       NA
#>
#> $data
#>             author
#> 1 Jonathan A Eisen
#> 2 Jonathan A Eisen
#> 3 Jonathan A Eisen
#> 4 Jonathan A Eisen
#> 5 Jonathan A Eisen

plosabstract searches across abstracts, and in this case returns the id and title of the matching papers

plosabstract(q = 'drosophila', fl='id,title', limit = 5)

#> $meta
#>   numFound start maxScore
#> 1     2925     0       NA
#>
#> $data
#>                             id
#> 1 10.1371/journal.pbio.0040198
#> 2 10.1371/journal.pbio.0030246
#> 3 10.1371/journal.pone.0012421
#> 4 10.1371/journal.pbio.0030389
#> 5 10.1371/journal.pone.0002817
#>                                                                             title
#> 1                                                                     All for All
#> 2                                     School Students as Drosophila Experimenters
#> 3                            Host Range and Specificity of the Drosophila C Virus
#> 4                     New Environments Set the Stage for Changing Tastes in Mates
#> 5 High-Resolution, In Vivo Magnetic Resonance Imaging of Drosophila at 18.8 Tesla

plostitle searches across titles, and in this case returns the title and journal of the matching papers

plostitle(q='drosophila', fl='title,journal', limit=5)

#> $meta
#>   numFound start maxScore
#> 1     1892     0       NA
#>
#> $data
#>                      journal
#> 1               PLoS Biology
#> 2               PLoS Biology
#> 3              PLoS Genetics
#> 4 PLoS Computational Biology
#> 5                   PLoS ONE
#>                                                   title
#> 1      Reinforcement of Gametic Isolation in Drosophila
#> 2         Identification of Drosophila MicroRNA Targets
#> 3 Phenotypic Plasticity of the Drosophila Transcriptome
#> 4            Parametric Alignment of Drosophila Genomes
#> 5              A Tripartite Synapse Model in Drosophila

Search for terms and visualize results as a histogram OR as a plot through time

plosword allows you to search for 1 to K words and visualize the results as a histogram, comparing number of matching papers for each word

out <- plosword(list("monkey", "Helianthus", "sunflower", "protein", "whale"),
    vis = "TRUE")
out$table

#>   No_Articles       Term
#> 1       10289     monkey
#> 2         422 Helianthus
#> 3        1144  sunflower
#> 4      114997    protein
#> 5        1331      whale

out$plot

plot of chunk plosword1plot

You can also pass in curl options, in this case get verbose information on the curl call.

plosword('Helianthus', callopts=list(verbose=TRUE))

#> Number of articles with search term
#>                                 422

Visualize terms

plot_throughtime allows you to search for up to 2 words and visualize the results as a line plot through time, comparing number of articles matching through time. Visualize with the ggplot2 package, only up to two terms for now.

library("ggplot2")
plot_throughtime(terms = "phylogeny", limit = 200) + geom_line(size=2, color='black')

plot of chunk throughtime1

In addition to searchplos() and related searching functions, there are a few slightly different ways to search: faceting and highlighted searches. Faceting allows you to ask, e.g., how many articles are published in each of the PLOS journals. Highlighting allows you to ask, e.g., highlight terms that I search for in the text results given back, which can make downstream processing easier, and help visualize search results (see highbrow() below).

Facet by journal

facetplos(q='*:*', facet.field='journal')

#> $facet_queries
#> NULL
#>
#> $facet_fields
#> $facet_fields$journal
#>                                 X1      X2
#> 1                         plos one 1285831
#> 2                    plos genetics   50706
#> 3                   plos pathogens   44134
#> 4       plos computational biology   37646
#> 5 plos neglected tropical diseases   35979
#> 6                     plos biology   29392
#> 7                    plos medicine   20335
#> 8             plos clinical trials     521
#> 9                     plos medicin       9
#>
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> NULL

Using facet.query to get counts

facetplos(q='*:*', facet.field='journal', facet.query='cell,bird')

#> $facet_queries
#>        term value
#> 1 cell,bird    24
#>
#> $facet_fields
#> $facet_fields$journal
#>                                 X1      X2
#> 1                         plos one 1285831
#> 2                    plos genetics   50706
#> 3                   plos pathogens   44134
#> 4       plos computational biology   37646
#> 5 plos neglected tropical diseases   35979
#> 6                     plos biology   29392
#> 7                    plos medicine   20335
#> 8             plos clinical trials     521
#> 9                     plos medicin       9
#>
#>
#> $facet_dates
#> NULL
#>
#> $facet_ranges
#> NULL

Date faceting

facetplos(q='*:*', url=url, facet.date='publication_date',
  facet.date.start='NOW/DAY-5DAYS', facet.date.end='NOW', facet.date.gap='+1DAY')

#> $facet_queries
#> NULL
#>
#> $facet_fields
#> NULL
#>
#> $facet_dates
#> $facet_dates$publication_date
#>                   date value
#> 1 2016-04-27T00:00:00Z  2247
#> 2 2016-04-28T00:00:00Z  2187
#> 3 2016-04-29T00:00:00Z   848
#> 4 2016-04-30T00:00:00Z     0
#> 5 2016-05-01T00:00:00Z     0
#> 6 2016-05-02T00:00:00Z     0
#>
#>
#> $facet_ranges
#> NULL

Search for the term alcohol in the abstracts of articles, return only 10 results

highplos(q='alcohol', hl.fl = 'abstract', rows=2)

#> $`10.1371/journal.pmed.0040151`
#> $`10.1371/journal.pmed.0040151`$abstract
#> [1] "Background: <em>Alcohol</em> consumption causes an estimated 4% of the global disease burden, prompting"
#>
#>
#> $`10.1371/journal.pone.0027752`
#> $`10.1371/journal.pone.0027752`$abstract
#> [1] "Background: The negative influences of <em>alcohol</em> on TB management with regard to delays in seeking"

Search for the term alcohol in the abstracts of articles, and return fragment size of 20 characters, return only 5 results

highplos(q='alcohol', hl.fl='abstract', hl.fragsize=20, rows=2)

#> $`10.1371/journal.pmed.0040151`
#> $`10.1371/journal.pmed.0040151`$abstract
#> [1] "Background: <em>Alcohol</em>"
#>
#>
#> $`10.1371/journal.pone.0027752`
#> $`10.1371/journal.pone.0027752`$abstract
#> [1] " of <em>alcohol</em> on TB management"

Search for the term experiment across all sections of an article, return id (DOI) and title fl only, search in full articles only (via fq='doc_type:full'), and return only 10 results

highplos(q='everything:"experiment"', fl='id,title', fq='doc_type:full',
   rows=2)

#> $`10.1371/journal.pone.0154334`
#> $`10.1371/journal.pone.0154334`$everything
#> [1] " and designed the <em>experiments</em>: RJ CM AOC. Performed the <em>experiments</em>: RJ AOC. Analyzed the data: RJ. Contributed"
#>
#>
#> $`10.1371/journal.pone.0039681`
#> $`10.1371/journal.pone.0039681`$everything
#> [1] " Selection of Transcriptomics <em>Experiments</em> Improves Guilt-by-Association Analyses Transcriptomics <em>Experiment</em>"

Visualize highligted searches

Browse highlighted fragments in your default browser

This first examle, we only looko at 10 results

out <- highplos(q='alcohol', hl.fl = 'abstract', rows=10)
highbrow(out)

highbrow1

But it works quickly with lots of results too

out <- highplos(q='alcohol', hl.fl = 'abstract', rows=1200)
highbrow(out)

highbrow2

Citing

To cite rplos in publications use:


Scott Chamberlain, Carl Boettiger and Karthik Ram (2016). rplos: Interface to PLOS Journals search API. R package version 0.5.6 https://github.com/ropensci/rplos

License and bugs

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