DOI: 10.5281/zenodo.12790447
title: Bioinformatic databases survey

description: Bioinformatic databases survey

The dataset surveys bioinformatic databases published in the NAR database issue from 1995 to 2022. It evaluates the current number of citations and availability of each ressources.

Data content

The dataset is composed of two tables :

A. Databases table : Contains the information of each database published in the NAR database issue.



db_id : Database ID in the dataset

resource_name : Name(s) of the database

current_access : Latest known web address of the database

is_a_pun : The database name is a play on word

available_2022 : The database was accessible online during the 2022 survey

last_accessible_year : If not accessible, latest point in time where the database was found online (using the Internet web archive snapshots)

unavailable_message : If not accessible, the message/error when trying to access the ressource

year_first_publication : Year of first publication of the database

year_last_publication : Year of latest publication of the database (including database update publications)

total_citations_2022 : Cumulative number of citation for all articles of the database

nb_authors_max : Maximum number of authors associated to any articles published for that database

nb_articles_2022 : Number of articles published for that database in 2022


B. Articles table : Contains the information collected for the NAR articles



collector : Person who contributed to add this database in the dataset

article_global_id : DOI of the article surveyed

db_id : Database ID of the ressource described in the article

article_id : Article unique ID

article_year : Article publication year

Authors : list of authors of the article. Separated by ";"

Author.ID : list of ORCID of the authors of the article. Separated by ";"

Title : Title of the atricle

Source.title : Journal name

Volume : Volume number

Issue : Issue number

Funding.Details : Funding information of the article

Funding.Text : Funding text provided by the authors

PubMed.ID : Pubmed ID of the article

citations_2016 : Number of citations of the article in 2016 (if published)

citations_2022 : Number of citations of the article in 2022

nb_authors : Number of authors in the article

Index.Keywords : Keywords associated to the publication


Data sources

Note that the presented dataset leverage and expand on the dataset gathered and published in Imker, H.J., 2020. Who Bears the Burden of Long-Lived Molecular Biology Databases?. Data Science Journal, 19(1), p.8. The original dataset collected by Dr. Imker is available at : https://doi.org/10.13012/B2IDB-4311325_V1 

The dataset was collected and is maintained by undergraduate students of a CURE class (Course-based Undergraduate Research Experience) held at the University of Arizona. All students of the class have participated to the collection, update and curation the dataset that is available as a database and a web-portal at https://hurwitzlab.shinyapps.io/DS_Heroes/. Students could elect to be added or not as author to this Zenodo repository.

The CURE class BAT102 "Data Science Heroes: An undergraduate research experience in Open Data Science Practices" gives the students an opportunity to learn about open science and investigate open data practices in bioinformatics through a survey of the databases published in the NAR database issue.