Mining PLoS
Carlos Rodriguez Contreras
October 2, 2016
Intro
This document reports the results of some basic searchs to PLoS - Public Library of Science using the rplos package, which is part of the R Open Science echo system 
The rplos package interacts with the API services of PLoS Journals. It was used to need an API key to work with this package, fortunately such API key is no longer needed.
rplos package allows to:
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
Once the package is installed (through CRAN or GitHub) it can be loaded with the require command.
A simple search for all fields available for doing searches is done with the plosfields command which produces next output:
## field description
## 10 abstract Abstract section
## 49 abstract_ngram <NA>
## 11 abstract_primary_display Abstract section
## 21 accepted_date Accepted Date
## 38 affiliate Affiliate
## 50 affiliate_facet <NA>
## 5 alternate_title Alternative Title
## 25 article_type Article Type
## 51 article_type_facet <NA>
## 6 author Author
## 52 author_affiliate <NA>
## 9 author_collab_only_display Author
## 7 author_display Author
## 53 author_facet <NA>
## 39 author_notes Author Notes
## 8 author_without_collab_display Author
## 18 body Most sections of the article
## 54 body_ngram <NA>
## 55 body_rev <NA>
## 40 competing_interest Competing Interest Statement
## 15 conclusions Conclusions section
## 45 copyright copyright-statement
## 42 counter_total_all Total views, all time
## 43 counter_total_month Total views, last 30 days
## 48 cross_published_journal_eissn no description
## 47 cross_published_journal_key Cross Published Journal Key
## 46 cross_published_journal_name Cross Published Journal Name
## 56 doc_partial_body <NA>
## 57 doc_partial_parent_id <NA>
## 58 doc_partial_type <NA>
## 59 doc_type <NA>
## 36 editor Editor
## 60 editor_affiliate <NA>
## 37 editor_display Editor
## 61 editor_facet <NA>
## 28 eissn electronic ISSN
## 30 elocation_id Electronic Location
## 2 everything All text in the article
## 62 everything_ngram <NA>
## 63 everything_noprocess <NA>
## 64 everything_rev <NA>
## 65 figure_table_caption <NA>
## 41 financial_disclosure Financial Disclosure Statement
## 1 id DOI (Digital Object Identifier)
## 12 introduction Introduction section
## 24 issue Issue
## 22 journal Full Journal Name
## 32 journal_id_nlm_ta Journal ID at NLM
## 31 journal_id_pmc Journal ID at PMC
## 33 journal_id_publisher Publisher of this Journal
## 13 materials_and_methods Materials and Methods section
## 35 pagecount Total number of pages
## 29 pissn print ISSN
## 19 publication_date Publication Date
## 34 publisher Publisher of this Article
## 20 received_date Received Date
## 17 reference Reference section
## 14 results_and_discussion Results and discussion section
## 26 subject Subject Category
## 66 subject_facet <NA>
## 67 subject_hierarchy <NA>
## 27 subject_level_1 Subject Category
## 68 subject2 <NA>
## 69 subject2_facet <NA>
## 70 subject2_hierarchy <NA>
## 71 subject2_level_1 <NA>
## 16 supporting_information Supporting Information section
## 44 timestamp Time of last index
## 3 title Article Title
## 4 title_display Article Title
## 72 title_ngram <NA>
## 23 volume VolumeThe searchplos command
One of the most powerful rplos commands is searchplos which penetrates PLoS by using the API. This command automaticaly looks for ‘subject’ in all publications of PLoS. It is possible to retrieve all 72 fields listed above.
A basic search by subject ‘zika’ is shown next. The search looks for following fields: ‘id’, ‘journal’, ‘publication date’, ‘authors’ and ‘title’. The first three columns, which contain irrelevant data, were deleted, and the remaining columns’ names were edited. The first two publications of the results, are shown below.
## Currently, there are 263 papers containing the term zika as subject.## DOI Journal
## 1 10.1371/journal.pntd.0004984 PLOS Neglected Tropical Diseases
## 2 10.1371/journal.pmed.1002157 PLOS Medicine
## Publication Date
## 1 2016-11-10T00:00:00Z
## 2 2016-10-25T00:00:00Z
## Author
## 1 Pengcheng Zhou; Juan Wang; Yixiang Zheng; Rongrong Zhou; Xue-Gong Fan
## 2 Christian L Althaus; Nicola Low
## Title
## 1 Zika Virus May Affect the Universal Two-Child Policy: A New Challenge for China
## 2 How Relevant Is Sexual Transmission of Zika Virus?The output was edited and formated as a standardized dataset.
This dataset is reachable in the author’s figshare repository 
The plosword command
It is possible to search various subjects at the same time in all PLoS publications by using the plosword command. Next, a search for subjects ‘zika’, ‘dengue’ and ‘chikungunya’ is executed. The command generates a table with the results, and it also generates a graphic vis a vis with these related deseases.
## No_Articles Term
## 1 263 zika
## 2 3626 dengue
## 3 1013 chikungunya
The plot_throughtime command
It is also possible to generate a time series graphic in rplos by using the plot_throughtime command. The next three graphics show the publications generation through the time for the three related deseases: Zika, Dengue and Chikungunya.
LAST MINUTE UPGRADE
The searchplos command extracts the searched term in all fields availale in PLoS journals. This includes a lot of Editorials, which are not articles reporting researches results. There is also the risk of over-considerate a reserach submission which, under the same title and authors, contains some support material like datasets, scripts, procedures and separated graphics.
A better search can be executed using one of the wrappers for searchplos, for a more specific search the wrapper plostitle is used, this looks for the term ‘zika’ only in the title of articles in all journals of PLoS. The two first articles of this new search are shown below.
## Currently, there are 72 research articles containing the term zika in the title.## DOI Journal
## 1 10.1371/journal.pntd.0005132 PLOS Neglected Tropical Diseases
## 2 10.1371/journal.pntd.0004589 PLOS Neglected Tropical Diseases
## Publication Date
## 1 2017-01-19T00:00:00Z
## 2 2016-03-18T00:00:00Z
## Author
## 1 Priscila C Albuquerque; Mauro Jorge C Castro; Juliana Santos-Gandelman; Ana Claudia Oliveira; José M Peralta; Marcio L Rodrigues
## 2 Philip K Russell
## Title
## 1 Bibliometric Indicators of the Zika Outbreak
## 2 The Zika Pandemic - A Perfect Storm?This new dataset is also reachable in the author’s figshare repository
This work is licenced under a Creative Commons Attribution-NoDerivatives 4.0 International Licence 