Bioinformatic databases survey

<h1>Bioinformatic databases survey</h1> <p>The dataset surveys bioinformatic databases published in the <a href="https://academic.oup.com/nar">NAR database issue</a> from 1995 to 2022. It evaluates the current number of citations and availability of each ressources.</p> <h2>Data content</h2> <p>The dataset is composed of two tables :</p> <p><strong>A. Databases table :</strong> Contains the information of each database published in the NAR database issue.</p> <ul> <li>db_id : Database ID in the dataset</li> <li>resource_name : Name(s) of the database</li> <li>current_access : Latest known web address of the database</li> <li>is_a_pun : The database name is a play on word</li> <li>available_2022 : The database was accessible online during the 2022 survey</li> <li>last_accessible_year : If not accessible, latest point in time where the database was found online (using the Internet web archive snapshots)</li> <li>unavailable_message : If not accessible, the message/error when trying to access the ressource</li> <li>year_first_publication : Year of first publication of the database</li> <li>year_last_publication : Year of latest publication of the database (including database update publications)</li> <li>total_citations_2022 : Cumulative number of citation for all articles of the database</li> <li>nb_authors_max : Maximum number of authors associated to any articles published for that database</li> <li>nb_articles_2022 : Number of articles published for that database in 2022</li> </ul> <p><strong>B. Articles table :</strong> Contains the information collected for the NAR articles</p> <ul> <li>collector : Person who contributed to add this database in the dataset</li> <li>article_global_id : DOI of the article surveyed</li> <li>db_id : Database ID of the ressource described in the article</li> <li>article_id : Article unique ID</li> <li>article_year : Article publication year</li> <li>Authors : list of authors of the article. Separated by ";"</li> <li>Author.ID : list of ORCID of the authors of the article. Separated by ";"</li> <li>Title : Title of the atricle</li> <li>Source.title : Journal name</li> <li>Volume : Volume number</li> <li>Issue : Issue number</li> <li>Funding.Details : Funding information of the article</li> <li>Funding.Text : Funding text provided by the authors</li> <li>PubMed.ID : Pubmed ID of the article</li> <li>citations_2016 : Number of citations of the article in 2016 (if published)</li> <li>citations_2022 : Number of citations of the article in 2022</li> <li>nb_authors : Number of authors in the article</li> <li>Index.Keywords : Keywords associated to the publication</li> </ul> <h2>Data sources</h2> <p>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 : <a href="https://doi.org/10.13012/B2IDB-4311325_V1">https://doi.org/10.13012/B2IDB-4311325_V1</a>&nbsp;</p> <p>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 <a href="https://hurwitzlab.shinyapps.io/DS_Heroes/">https://hurwitzlab.shinyapps.io/DS_Heroes/</a>. Students could elect to be added or not as author to this Zenodo repository.</p> <p>The <a href="https://ur.arizona.edu/content/course-based-research-undergraduate-experiences-cures">CURE class BAT102</a> "<strong>Data Science Heroes: An undergraduate research experience in Open Data Science Practices"</strong> 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.</p>