How to cite us If you find UniProt useful, please consider citing our latest publication: The UniProt Consortium UniProt: the universal protein knowledgebase in 2021 Nucleic Acids Res. 49:D1 (2021)...or choose the publication that best covers the UniProt aspects or components you used in your work:
Full Answer
What is the aim of UniProt KnowledgeBase?
1 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. 2 ACKNOWLEDGEMENTS. ... 3 REFERENCES. ...
What are the UniProt reference clusters?
The UniProt Reference Clusters (UniRef) consist of three databases of clustered sets of protein sequences from UniProtKB and selected UniParc records.
How can I download data from UniProt?
In addition to providing customizable views and downloads in a range of formats via the website, and file sets at the FTP site ( www.uniprot.org/downloads ), UniProt supplies users with a number of different options for computational access to the data ( www.uniprot.org/help/programmatic_access ).
How many sequences are there in UniProt?
This portion of UniProt currently contains around 80 million sequences and is growing exponentially. Although entries in UniProtKB/TrEMBL are not manually curated they are supplemented by automatically generated annotation.
Can I cite UniProt?
https://www.uniprot.org/uniparc/UPI00000002E4. Remarks: A UniProtKB accession number (AC) is a stable identifier and therefore allows unambiguous citation of a UniProtKB entry. This is not the case for the 'Entry name'.10-Apr-2018
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 Swiss-Prot and UniProt 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.
What is the UniProt database?
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).02-Feb-2021
How do I find my UniProt ID?
Select the Retrieve/ID mapping tab of the toolbar and enter or upload a list of identifiers (or gene names) to do one of the following: Retrieve the corresponding UniProt entries to download them or work with them on this website.26-Jan-2021
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
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
How do you cite Pdbsum?
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank....PDBsum.ContentAuthorsRoman Laskowski & al. (1997)Primary citationPMID 9433130AccessWebsitewww.ebi.ac.uk/pdbsum/8 more rows
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
What is the function of UniProt?
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
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.
What data and tools does UniProt provide?
To build upon this protein data and to aid analysis, UniProt provides three main tools; 'BLAST' (Basic Local Alignment Search Tool), 'Align' multiple sequence alignment tool and 'Retrieve/ID Mapping' for batch retrievals of UniProt entries and ID mapping between UniProt and external databases.24-Mar-2016
What is a UniProt reference cluster?
The UniProt Reference Clusters (UniRef) consist of three databases of clustered sets of protein sequences from UniProtKB and selected UniParc records. The UniRef100 database combines identical sequences and sequence fragments (from any organism) into a single UniRef entry. The sequence of a representative protein, the accession numbers of all the merged entries and links to the corresponding UniProtKB and UniParc records are displayed. UniRef100 sequences are clustered using the CD-HIT algorithm to build UniRef90 and UniRef50. Each cluster is composed of sequences that have at least 90% or 50% sequence identity, respectively, to the longest sequence. Clustering sequences significantly reduces database size, enabling faster sequence searches.
What is UniProt database?
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.
What is UniProt consortium?
The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services.
Why does Uniparc only store one sequence?
In order to avoid redundancy, UniParc stores each unique sequence only once. Identical sequences are merged, regardless of whether they are from the same or different species. Each sequence is given a stable and unique identifier (UPI), making it possible to identify the same protein from different source databases.
When was Swiss Prot created?
Swiss-Prot was created in 1986 by Amos Bairoch during his PhD and developed by the Swiss Institute of Bioinformatics and subsequently developed by Rolf Apweiler at the European Bioinformatics Institute.
What is Swiss Prot?
UniProtKB/Swiss-Prot is a manually annotated, non-redundant protein sequence database. It combines information extracted from scientific literature and biocurator -evaluated computational analysis. The aim of UniProtKB/Swiss-Prot is to provide all known relevant information about a particular protein. Annotation is regularly reviewed to keep up with current scientific findings. The manual annotation of an entry involves detailed analysis of the protein sequence and of the scientific literature.
Who is Uniprot funded by?
UniProt is funded by grants from the National Human Genome Research Institute, the National Institutes of Health (NIH), the European Commission, the Swiss Federal Government through the Federal Office of Education and Science, NCI-caBIG, and the US Department of Defense.
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.
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 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/.
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 are the UniProt rules?
These are UniRule, in which rules are created as part of the process of expert curation of UniProtKB/Swiss-Prot, and SAAS, in which rules are derived automatically from UniProtKB/Swiss-Prot entries sharing common annotations and characteristics. Both UniRules and SAAS use the hierarchical InterPro classification of protein family and domain signatures ( 15) as a basis for protein classification and functional annotation. These rules share a common syntax that specifies annotations—including protein nomenclature, function and important residues—and necessary conditions, such as the requirement for conserved functional residues and motifs. InterPro integrates signatures from the HAMAP ( 16) and PIRSF ( 17) projects within the UniProt consortium. The creation of family signatures in HAMAP and PIRSF is tightly linked to the expert curation of literature characterized template entries in UniProtKB/Swiss-Prot, which allows highly specific functional annotation even within large and functionally diverse superfamilies. As an example the HAMAP signature MF_01864 see Figure 4, which encapsulates the information from only seven peer-reviewed publications covering four experimentally characterized proteins that serve as templates to annotate the function of the bacterial tRNA-2-methylthio-N (6)-dimethylallyladenosine synthase family to over 11 000 UniProtKB/TrEMBL records. The UniRule pipeline also leverages the manual curation of UniProtKB/Swiss-Prot for the continuous validation of rules: annotations are refreshed at each release of UniProtKB/TrEMBL, and the consistency of each rule evaluated by comparing the predicted annotations with those of the current version of UniProtKB/Swiss-Prot. Only those rules whose predictions perfectly match UniProtKB/Swiss-Prot are retained for the current production cycle.
What is expert curation?
Literature-based expert curation is a core UniProt activity. It provides high-quality annotation for experimentally characterized proteins across diverse protein families and taxonomic groups in the UniProtKB/Swiss-Prot section of UniProt. Although labour-intensive, the benefits of creating such a rich annotated data set are manifold, both for wet-lab researchers by providing an up-to-date knowledgebase containing experimental information, and computer scientists by providing high-quality training sets for development and enhancement of bioinformatics algorithms. Last but not least, it also serves as an essential source for the generation of automatic annotation for uncharacterized proteins, a key challenge in the era of next generation sequencing. The wealth of curation experience accumulated over the years within the consortium has created an expert team in this field. During 2013 we curated over 8400 papers and created over 3300 new UniProtKB/Swiss-Prot entries.
What is a UniProt?
UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This growth in sequences has prompted an extension of UniProt accession number space from 6 to 10 characters. An increasing fraction of new sequences are identical to a sequence that already exists in the database with the majority of sequences coming from genome sequencing projects. We have created a new proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies to help users track the provenance of sequences. We present a new website that has been designed using a user-experience design process. We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein. These scores will be helpful in identifying which proteins are the best characterized and most informative for comparative analysis. All UniProt data is provided freely and is available on the web at http://www.uniprot.org/.
How does next generation sequencing help in the development of protein sequence databases?
In addition, there are new data types being introduced by developing high-throughput technologies in proteomics and genomics. The combination of both provides new opportunities for the life sciences and the biomedical domain. Therefore, it is crucial to identify experimental characterizations of proteins in the literature and to capture and integrate this knowledge into a framework in combination with high-throughput data and automatic annotation approaches to allow it to be fully exploited. UniProt facilitates scientific discovery by organizing biological knowledge and enabling researchers to rapidly comprehend complex areas of biology.
What are the changes in Uniprot?
The past year has seen numerous important changes for UniProt. In particular many changes, such as the expansion of accession numbers, have been necessary to cope with the increase in sequences. However, we have several strategies to help our users deal with the deluge of protein data, such as the inclusion of proteome identifiers and the addition of further reference proteomes, to better navigate the deluge of new sequencing data. The provision of annotation scores will help users identify the proteins with the highest level of functional characterization, which should greatly aid comparative protein sequence analysis. We are particularly pleased to have released a completely redeveloped website that has been designed with the primary goal of enhancing the user's experience as they navigate our data. As well as these new developments we continue to focus upon our core mission to extract and organize experimental information on proteins from the literature and thus help scientists around the world to make further important discoveries. We encourage all our users to give us feedback on our data and website and to contact us via the e-mail [email protected], through the web at http://www.uniprot.org/contact or through our social media channels.
How many sequences are in UniProt?
The section of UniProt that contains manually curated and reviewed entries is known as UniProtKB/Swiss-Prot and currently contains about half a million sequences. This section grows as new proteins are experimentally characterized ( 1 ).
How to Cite Us
- If you find UniProt useful, please consider citing our latest publication: The UniProt Consortium UniProt: the universal protein knowledgebase in 2021 Nucleic Acids Res. 49:D1 (2021) ...or choose the publication that best covers the UniProt aspects or components you used in your work:
2019
- The UniProt Consortium UniProt: a worldwide hub of protein knowledge Nucleic Acids Res. 47:D506-515 (2019) Morgat A, Lombardot T, Coudert E, Axelsen K, Neto TB, Gehant S, Bansal P, Bolleman J, Gasteiger E, de Castro E, Baratin D, Pozzato M, Xenarios I, Poux S, Redaschi N, Bridge A, UniProt Consortium. Enzyme annotation in UniProtKB using Rhea Bioinformatics 36(6):1896-1901 (2019)
2018
- The UniProt Consortium UniProt: the universal protein knowledgebase Nucleic Acids Res. 46:2699 (2018) Pichler K, Warner K, Magrane M, UniProt Consortium SPIN: Submitting Sequences Determined at Protein Level to UniProt Curr. Protoc. Bioinformatics 62(1):e52 (2018)
2017
- The UniProt Consortium UniProt: the universal protein knowledgebase Nucleic Acids Res. 45:D158-D169 (2017) Chen C, Huang H, Wu CH. Protein Bioinformatics Databases and Resources Methods Mol. Biol. 1558:3-39 (2017) Ding R, Boutet E, Lieberherr D, Schneider M, Tognolli M, Wu CH, Vijay-Shanker K, Arighi CN. eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality D…
2016
- Boutet E, Lieberherr D, Tognolli M, Schneider M, Bansal P, Bridge AJ, Poux S, Bougueleret L, Xenarios I. UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View Methods Mol. Biol. 1374:23-54 (2016) Breuza L, Poux S, Estreicher A, Famiglietti ML, Magrane M, Tognolli M, Bridge A, Baratin D, Redaschi N, UniProt Consortium The UniProtKB guide to the human proteome Database (Oxf…
2015
- Alpi E, Griss J, da Silva AW, Bely B, Antunes R, Zellner H, Rios D, O'Donovan C, Vizcaino JA, Martin MJ. Analysis of the tryptic search space in UniProt databases Proteomics 15:48-57 (2015) Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations Database (…
2014
- Famiglietti ML, Estreicher A, Gos A, Bolleman J, Gehant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I. Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation. Hum. Mutat. 35:927-935 (2014) Huntley RP, Sawford T, Martin MJ, O'Donovan C. Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt Gigascience 3:4 (2014) Masson P, Hulo C, de C…
2013
- Chen C, Li Z, Huang H, Suzek BE, Wu CH; UniProt Consortium A fast Peptide Match service for UniProt Knowledgebase Bioinformatics 29:2808-2809 (2013) Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Martin MJ, O'Donovan C, Apweiler R. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans Database (Oxford) bas062 (2013) Pedruzzi I, Rivoire C, Auchincloss AH, Coude…
2012
- Burge S, Attwood TK, Bateman A, Berardini TZ, Cherry M, O'Donovan C, Xenarios I, Gaudet P. Biocurators and Biocuration: surveying the 21st century challenges Database (Oxford) (2012) Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quin…
2011
- Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. The impact of focused Gene Ontology curation of specific mammalian systems Plos One (2011) Burmester A, Shelest E, Glockner G, Heddergott C, Schindler S, Staib P, Heidel A, Felder M, Petzold A, Szafranski K, Feuermann M, Pedruzzi I, Priebe S, Groth M, Winkler R, Li W, Kniemeyer O, Schroeckh …
Overview
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, United States.
The UniProt consortium
The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation (NBRF) at the Ge…
The roots of UniProt databases
Each consortium member is heavily involved in protein database maintenance and annotation. Until recently, EBI and SIB together produced the Swiss-Prot and TrEMBL databases, while PIR produced the Protein Sequence Database (PIR-PSD). These databases coexisted with differing protein sequence coverage and annotation priorities.
Swiss-Prot was created in 1986 by Amos Bairoch during his PhD and developed by the Swiss Institute of Bioinfor…
Organization of UniProt databases
UniProt provides four core databases: UniProtKB (with sub-parts Swiss-Prot and TrEMBL), UniParc, UniRef.
UniProt Knowledgebase (UniProtKB) is a protein database partially curated by experts, consisting of two sections: UniProtKB/Swiss-Prot (containing reviewed, manually annotated entries) and UniProtKB/TrEMBL (containing unreviewed, automatically annotated entries). As of 19 March 2014 , release "2014_03" of UniProtKB/Swiss-Prot contains 542,782 sequence entries (comprising 193,019,802 amino acids abstracted from 226,896 references) a…
Funding
UniProt is funded by grants from the National Human Genome Research Institute, the National Institutes of Health (NIH), the European Commission, the Swiss Federal Government through the Federal Office of Education and Science, NCI-caBIG, and the US Department of Defense.
External links
• UniProt
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 entries, to which data have been added by our expert biocuration team, with the unreviewe…
Progress and New Developments
- Growth of sequence records 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.unip… - Expert curation
The evaluation of experimental data published in the scientific literature, and summarizing key points of biological relevance in the appropriate reviewed UniProtKB/Swiss-Prot record, is fundamental to the operation of the UniProt database. The functional information extracted from the literature is added both in the form of human readable …
Data Availability
- 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 proces…
Conclusions
- 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 s…
Acknowledgements
- The UniProt publication has been prepared by Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan Da Silva, Paul Denny, Tunca Dogan, ThankGod Ebenezer, Jun Fan, Leyla Garcia Castro, Penelope Garmiri, George Georghiou, Leonardo Gonzales, Emma Hatton …
Funding
- National Eye Institute, National Human Genome Research Institute, National Heart, Lung, and Blood Institute, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of General Medical Sciences, National Cancer Institute, National Institute On Aging, and National Institute of Mental Health of the National Institutes of Health [U24HG007822]; National Human Gen…