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A web-based platform for the annotation and analysis of NAR-published databases

Biological databases are essential resources for life science research, but finding and selecting the most relevant and up-to-date databases can be challenging due to the large number and diversity of available databases. The Nucleic Acids Research (NAR) journal publishes annual database issues that...

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Autores principales: Friedrichs, Marcel, Königs, Cassandra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10593211/
https://www.ncbi.nlm.nih.gov/pubmed/37871106
http://dx.doi.org/10.1371/journal.pone.0293134
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author Friedrichs, Marcel
Königs, Cassandra
author_facet Friedrichs, Marcel
Königs, Cassandra
author_sort Friedrichs, Marcel
collection PubMed
description Biological databases are essential resources for life science research, but finding and selecting the most relevant and up-to-date databases can be challenging due to the large number and diversity of available databases. The Nucleic Acids Research (NAR) journal publishes annual database issues that provide a comprehensive list of databases in the molecular biology domain. However, the information provided by NAR is limited and sometimes does not reflect the current status and quality of the databases. In this article, we present a web-based platform for the annotation and analysis of NAR-published databases. The platform allows users to manually curate and enrich the NAR entries with additional information such as availability, downloadability, source code links, cross-references, and duplicates. Statistics and visualizations on various aspects of the database landscape, such as recency, status, category, and curation history are also provided. Currently, it contains a total of 2,246 database entries of which 2,025 are unique with the majority updated within the last five years. Around 75% of all databases are still available and more than half provide a download option. Cross references to Database Commons are available for 1,889 entries. The platform is freely available online at https://nardbstatus.kalis-amts.de and aims to help researchers in database selection and decision-making. It also provides insights into the current state and challenges of a subset of all databases in the life sciences.
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spelling pubmed-105932112023-10-24 A web-based platform for the annotation and analysis of NAR-published databases Friedrichs, Marcel Königs, Cassandra PLoS One Research Article Biological databases are essential resources for life science research, but finding and selecting the most relevant and up-to-date databases can be challenging due to the large number and diversity of available databases. The Nucleic Acids Research (NAR) journal publishes annual database issues that provide a comprehensive list of databases in the molecular biology domain. However, the information provided by NAR is limited and sometimes does not reflect the current status and quality of the databases. In this article, we present a web-based platform for the annotation and analysis of NAR-published databases. The platform allows users to manually curate and enrich the NAR entries with additional information such as availability, downloadability, source code links, cross-references, and duplicates. Statistics and visualizations on various aspects of the database landscape, such as recency, status, category, and curation history are also provided. Currently, it contains a total of 2,246 database entries of which 2,025 are unique with the majority updated within the last five years. Around 75% of all databases are still available and more than half provide a download option. Cross references to Database Commons are available for 1,889 entries. The platform is freely available online at https://nardbstatus.kalis-amts.de and aims to help researchers in database selection and decision-making. It also provides insights into the current state and challenges of a subset of all databases in the life sciences. Public Library of Science 2023-10-23 /pmc/articles/PMC10593211/ /pubmed/37871106 http://dx.doi.org/10.1371/journal.pone.0293134 Text en © 2023 Friedrichs, Königs https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Friedrichs, Marcel
Königs, Cassandra
A web-based platform for the annotation and analysis of NAR-published databases
title A web-based platform for the annotation and analysis of NAR-published databases
title_full A web-based platform for the annotation and analysis of NAR-published databases
title_fullStr A web-based platform for the annotation and analysis of NAR-published databases
title_full_unstemmed A web-based platform for the annotation and analysis of NAR-published databases
title_short A web-based platform for the annotation and analysis of NAR-published databases
title_sort web-based platform for the annotation and analysis of nar-published databases
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10593211/
https://www.ncbi.nlm.nih.gov/pubmed/37871106
http://dx.doi.org/10.1371/journal.pone.0293134
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