UniProt: the Universal Protein Knowledgebase in 2023

Abstract

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data processing pipeline and to our website to adapt to an ever-increasing information content. The number of sequences in UniProtKB has risen to over 227 million and we are working towards including a reference proteome for each taxonomic group. We continue to extract detailed annotations from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations provided by automated systems using a variety of machine-learning techniques. In addition, the scientific community continues their contributions of publications and annotations to UniProt entries of their interest. Finally, we describe our new website (https://www.uniprot.org/), designed to enhance our users' experience and make our data easily accessible to the research community. This interface includes access to AlphaFold structures for more than 85% of all entries as well as improved visualisations for subcellular localisation of proteins.

Figure 1

(A) Growth of UniProt databases over the last 10 years and (B) Growth of Reference Proteomes and taxonomic breakdown.

Figure 2.

Statistics of UniProt crowdsourcing activity. (A) Cumulative number of submissions, unique publications and proteins covered, and number of contributors for selected releases. Release 2019_08 was the first release where community submissions appeared, and 2022_03 is the latest release at the time of this manuscript preparation. (B) Taxonomic distribution of unique protein entries that have at least one publication submitted by the community. (C) Block chart showing the relative distribution of annotations by categories.

Figure 3

(A) Card view of results following a search of the UniProt website and (B). Table view of results following the same search.

Figure 4.

UniProtKB entry CL18A_HUMAN (UniProtKB: A5D8T8) shows an embedded SwissBioPics image: the generic animal cell (Eumetazoa) is selected based on organism taxonomy. It contains 71 interactive locations, of which the endoplasmic reticulum, Golgi apparatus, endosome and secretory space are highlighted using annotations from the UniProt entry.