uniprot: the universal protein knowledgebase in 2021

How often is UniProt released?

every 8 weeksUniProt releases are published every 8 weeks (4 weeks until the last 2019 release, 2019_11), with possible exceptions in January and summer due to reduced staff during holidays.26-Jan-2021

How many protein sequences are in UniProt?

UniProtKB entries are available in three file formats - Flat Text, XML and RDF/XML. UniProtKB entries in these formats each contain only one protein sequence, the so-called 'canonical' sequence.23-Nov-2021

How reliable is UniProt?

UniProtKB encompasses several individual protein sequence resources that are depicted on this page. If you are talking about a sequence that is from SwissProt (manually reviewed/curated sequences) or UniRef100 clusters then that sequence is likely perfectly accurate.26-Oct-2018

Is UniProt a protein database?

The UniProt Knowledgebase (UniProtKB) is an expertly curated database, a central access point for integrated protein information with cross-references to multiple sources.

What is UniProt Knowledgebase?

The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.22-Nov-2021

What is UniProt code?

UniProtKB/TrEMBL entry names The UniProtKB/TrEMBL entry name consists of up to 16 uppercase alphanumeric characters with a naming convention similar to that of UniProtKB/Swiss-Prot, where: ... Y is a mnemonic species identification code of at most 5 alphanumeric characters.10-Apr-2018

Is UniProt and Swiss-Prot same?

UniProtKB/TrEMBL is a computer-annotated (unreviewed) supplement to Swiss-Prot, which strives to gather all protein sequences that are not yet represented in Swiss-Prot.

How large is UniProt?

The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of which over half a million sequences have been curated by experts who critically review experimental and predicted data for each protein.28-Nov-2016

Is UniProt a primary database?

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects....UniProt.ContentPrimary citationUniProt ConsortiumAccessData formatCustom flat file, FASTA, GFF, RDF, XML.Websitewww.uniprot.org www.uniprot.org/news/16 more rows

Why is UniProt used?

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. EMBL-EBI and SIB together used to produce Swiss-Prot and TrEMBL, while PIR produced the Protein Sequence Database (PIR-PSD). ...02-Feb-2021

Is UniProt curated?

Accurate and comprehensive representation of biological knowledge, as well as easy access to this data for working scientists and a basis for computational analysis, are primary goals of biocuration. In order to respond to the flood of sequencing data, UniProt provides both manual curation and automatic annotation.14-May-2021

Why do we use UniProt?

UniProt helps with this in the following ways: It provides an up-to-date, comprehensive body of protein information at a single site. It aids scientific discovery by collecting, interpreting and organising this information so that it is easy to access and use. ... It provides tools to help with protein sequence analysis.

How often is UniProt released?

Due to the ever-increasing number of sequence records UniProt is processing with every release cycle, as of release 2020_01 (26 February 2020), UniProt releases are now published every eight weeks. This gives our production team the time required to complete data import, proteome redundancy removal, data checking, integration of external data and automatic annotation of unreviewed records prior to starting the release process.

What is the purpose of UniProt Knowledgebase?

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 article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

How many proteomes are there in UniProt?

UniProt release 2020_04 contains over 189 million sequence records (Figure 1 ), with >292 000 proteomes, the complete set of proteins believed to be expressed by an organism, originating from completely sequenced viral, bacterial, archaeal and eukaryotic genomes available through the UniProtKB Proteomes portal ( https://www.uniprot.org/proteomes/ ). The majority of these proteomes continue to be based on the translation of genome sequence submissions to the INSDC source databases—ENA, GenBank and the DDBJ ( 4 )—supplemented by genomes sequenced and/or annotated by groups such as Ensembl ( 5 ), NCBI RefSeq ( 6 ), Vectorbase ( 7) and WormBase ParaSite ( 8 ). Viral proteomes are manually checked and verified and periodically added to the database.

What is UniProt working on?

UniProt is continually evolving to meet new challenges while still working to capture all available protein sequence data and to curate the ever-increasing amount of functional data described in the scientific literature.

What is UniProt database?

The UniProt databases exist to support biological and biomedical research by providing a complete compendium of all known protein sequence data linked to a summary of the experimentally verified, or computationally predicted, functional information about that protein.

What is the role of Uniprot?

UniProt continues to play its pivotal role in the fields of biology and biomedicine, collecting, standardizing and organizing knowledge of proteins and their functions to create a reference framework for multiscale biomedical data integration and analysis. Organisms are being routinely sequenced at the whole genome level, and eukaryotic, prokaryotic, and metagenomic sequencing projects are all contributing to the increased diversity of sequence data in the UniProt databases. It is of increasing importance that our automatic annotation pipelines continue to develop in parallel to ensure that these unreviewed genomes, the vast majority of which are not being experimentally studied at the protein level, are richly and comprehensively annotated with functional information. Expert curation of those proteins biochemically characterized remains a key focus of our activities, to both inform on these well-studied entities and also to act as template entries for information transfer to proteins in related species. As the complexity and depth of our value-added data increases, we are exploring new ways to present the data to users and will continue to serve the community with new and improved website access designed to improve and enhance the user experience and upgraded programmatic access, with ease of use always a priority.

What is the purpose of a single protein sequence?

This allows users to get a gene-centric subset of representative proteins for a given genome, as opposed to the full proteome which includes all proteins (e.g. including isoforms) that map to the genome. Figure 2.

What is the purpose of UniProt Knowledgebase?

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 article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

How does NLP help in biological sequence analysis?

Remarkable advances in high-throughput sequencing have resulted in rapid data accumulation, and analyzing biological (DNA/RNA/protein) sequences to discover new insights in biology has become more critical and challenging. To tackle this issue, the application of natural language processing (NLP) to biological sequence analysis has received increased attention, because biological sequences are regarded as sentences and k-mers in these sequences as words. Embedding is an essential step in NLP, which converts words into vectors. This transformation is called representation learning and can be applied to biological sequences. Vectorized biological sequences can be used for function and structure estimation, or as inputs for other probabilistic models. Given the importance and growing trend in the application of representation learning in biology, here, we review the existing knowledge in representation learning for biological sequence analysis.

Introduction

• The UniProt databases exist to support biological and biomedical research by providing a complete compendium of all known protein sequence data linked to a summary of the experimentally verified, or computationally predicted, functional information about that protein. The UniProt Knowledgebase (UniProtKB) combines reviewed UniProtKB/Swiss-Prot entr...

See more on academic.oup.com

Progress and New Developments

Data Availability

Conclusions

Acknowledgements

Funding