API: EpiBibR

Access bibliographic data on Covid-19 and other medical references through the EpiBibR API.

Table of Contents


By using SKEMA Quantum Studio framework (Warin 2019), this course will teach you how to use the EpiBibR package created by our team!

Database description

EpiBibR is a R wrapper to easily access bibliographic data on Covid-19 and other medical references. In this global crisis, knowledge and open data can have an impact. In this regard, our team thought it could be significant to make available more than 20 000 references (journal articles,letter,news) through R.

The references were collected via PubMed, a free resource that is developed and maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM), located at the National Institutes of Health (NIH). PubMed includes over 30 million citations from biomedical literature.

More specifically, to retrieve our references, we adopted the procedure used by the Allen Institute for AI for their CORD-19 project. We apply the same query on PubMed (“COVID-19” OR Coronavirus OR “Corona virus” OR “2019-nCoV” OR “SARS-CoV” OR “MERS-CoV” OR “Severe Acute Respiratory Syndrome” OR “Middle East Respiratory Syndrome” ) to build our own bibliographic data.

To navigate through our bibliographic data, EpiBibR has numerous search arguments: author, author’s country of origin, keyword in the title, keyword in the abstract, year and the name of the journal. Each of them can truly help scientists and R users to filter references and find the relevant articles.

In an effort to rally our package with the open source community, the format of our dataframe has been designed to facilitate the use of the R package Bibliometrix on our data.

Functions

EpiBibR allows you to search bibligraphic references using several arguments : Author, author’s country of origin, author + year, keywords in the title, keywords in the abstract, year and source name. The functions listed below allow you to retrieve these informations and each of them are detailed below and some examples are provided.

EpiBib_references()

To get the entire bibliographic dataframe contaning more than 25 000 references.


EpiBib_data <- EpiBib_references()

EpiBib_author()

It can be truly helpful to search references by the name of the author. For example, we will search all the articles writtin by Philippe Colson.


colson_articles <- EpiBib_author("Colson")

EpiBib_country()

Search by author’s country of origin.


canada_articles <- EpiBib_country("canada")

EpiBib_AU_YE

Search by author and year


yang2019 <- EpiBib_AU_YE(author = "yang", year = 2019)

EpiBib_title()

Search by keywords in title


covid_articles <- EpiBib_title("covid")

EpiBib_abstract()

Search by keywords in the abstract


coronavirus_articles <- EpiBib_abstract("coronavirus")

EpiBib_year()

Search by year


A2020_articles <- EpiBib_year(2020)

EpiBib_source()

Search by source


bio_articles <- EpiBib_source("bio")

Data Summary

Field Tag Description
AU Authors
TI Document Title
AB Abstract
PY Year
DT Document Type
MESH Medical Subject Headings Vocabulary
TC Times Cited
SO Publication Name (or Source)
J9 Source Abbreviation
JI ISO Source Abbreviation
DI Digital Object Identifier (DOI)
ISSN Source Code
VOL Volume
ISSUE Issue Number
LT Language
C1 Author Address
RP Reprint Address
ID PubMed ID
DE Authors’ Keywords
UT Unique Article Identifier
AU_CO Author’s Country of Origin
DB Bibliographic Database

Note: Once you’ve retrieved all the wanted data, you can check here how to use it with the R package Bibliometrix.

tl;dr


# Load EpiBibR package 
library(EpiBibR)

# Retrieve bibliographic data
EpiBib_data <- EpiBib_references()

# Retrieve by author
colson_articles <- EpiBib_author("Colson")

# Retrieve by author's country of origin
canada_articles <- EpiBib_country("canada")

# Retrieve by author and year
yang2019 <- EpiBib_AU_YE(author = "yang", year = 2019)

# Retrieve by keywords in title
covid_articles <- EpiBib_title("covid")

# Retrieve by keywords in the abstract
coronavirus_articles <- EpiBib_abstract("coronavirus")

# Retrieve by year
A2020_articles <- EpiBib_year(2020)

# Retrieve by source
bio_articles <- EpiBib_source("bio")

Code learned this week

Command Detail
EpiBib_references() Retrieve bibliographic data
EpiBib_author() Retrieve data by author
EpiBib_country() Retrieve data by country
EpiBib_AU_YE() Retrieve data by author and year
EpiBib_title() Retrieve data by keywords in title
EpiBib_abstract() Retrieve data by keywords in the abstract
EpiBib_year() Retrieve data by year
EpiBib_source() Retrieve data by year

References

This course uses the EpiBibR package documentation


Warin, Thierry. 2019. “SKEMA Quantum Studio: A Technological Framework for Data Science in Higher Education.” https://doi.org/10.6084/m9.figshare.8204195.v2.

Citation

For attribution, please cite this work as

Warin (2020, April 7). Virtual Campus: API: EpiBibR. Retrieved from https://virtualcampus.skemagloballab.io/posts/api-epibibr/

BibTeX citation

@misc{warin2020api:,
  author = {Warin, Thierry},
  title = {Virtual Campus: API: EpiBibR},
  url = {https://virtualcampus.skemagloballab.io/posts/api-epibibr/},
  year = {2020}
}