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()
- EpiBib_author()
- EpiBib_country()
- EpiBib_AU_YE()
- EpiBib_title()
- EpiBib_abstract()
- EpiBib_year()
- EpiBib_source()
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