Database Commons: A Catalog of Worldwide Biological Databases

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.

Figure 1

The landscape of worldwide biological databases A. Top 10 countries and institutions by database count. B. Database publication trend of top 10 countries from 2001 to 2021. C. Top 10 databases, institutions, and countries by citation count. D. Top 10 databases, institutions, and countries by z-index. All statistics were obtained from Database Commons as of September 20, 2022, which is publicly available at https://ngdc.cncb.ac.cn/databasecommons/ with frequent updates by expert curation and community submission. CAS, Chinese Academy of Sciences; cBioPortal, cBio cancer genomics portal; CNCB, China National Center for Bioinformation; DAVID, Database for Annotation, Visualization and Integrated Discovery; ENCODE, Encyclopedia of DNA Elements; GEO, Gene Expression Omnibus; gnomAD, Genome Aggregation Database; IGSR, International Genome Sample Resource; KEGG, Kyoto Encyclopedia of Genes and Genomes; UCSC GB, UCSC Genome Browser; UniProt, Universal Protein Resource.