Database Commons: A Catalog of Worldwide Biological Databases

Lina Ma; Dong Zou; Lin Liu; Huma Shireen; Amir A Abbasi; Alex Bateman; Jingfa Xiao; Wenming Zhao; Yiming Bao; Zhang Zhang

doi:10.1016/j.gpb.2022.12.004

Database Commons: A Catalog of Worldwide Biological Databases

Genomics Proteomics Bioinformatics. 2023 Oct;21(5):1054-1058. doi: 10.1016/j.gpb.2022.12.004. Epub 2022 Dec 23.

Authors

Lina Ma¹, Dong Zou², Lin Liu², Huma Shireen³, Amir A Abbasi³, Alex Bateman⁴, Jingfa Xiao⁵, Wenming Zhao⁵, Yiming Bao⁵, Zhang Zhang⁶

Affiliations

¹ National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: malina@big.ac.cn.
² National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
³ National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.
⁴ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge CB10 1SD, United Kingdom.
⁵ National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
⁶ National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: zhangzhang@big.ac.cn.

Abstract

Biological databases serve as a global fundamental infrastructure for the worldwide scientific community, which dramatically aid the transformation of big data into knowledge discovery and drive significant innovations in a wide range of research fields. Given the rapid data production, biological databases continue to increase in size and importance. To build a catalog of worldwide biological databases, we curate a total of 5825 biological databases from 8931 publications, which are geographically distributed in 72 countries/regions and developed by 1975 institutions (as of September 20, 2022). We further devise a z-index, a novel index to characterize the scientific impact of a database, and rank all these biological databases as well as their hosting institutions and countries in terms of citation and z-index. Consequently, we present a series of statistics and trends of worldwide biological databases, yielding a global perspective to better understand their status and impact for life and health sciences. An up-to-date catalog of worldwide biological databases, as well as their curated meta-information and derived statistics, is publicly available at Database Commons (https://ngdc.cncb.ac.cn/databasecommons/).

Keywords: Biological database; Catalog; Citation; Database Commons; z-index.

MeSH terms

Big Data*
Databases, Factual