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
What is UniProt Knowledgebase (UniProtKB)?
The UniProt Knowledgebase (UniProtKB) combines reviewed UniProtKB/Swiss-Prot entries, to which data have been added by our expert biocuration team, with the unreviewed UniProtKB/TrEMBL entries that are annotated by automated systems.
How do I access previous versions of a UniProtKB entry?
Archived versions of a UniProtKB entry are accessible through the Previous versions link located at the bottom of the entry view's left-hand navigation bar.
Where are the protein sequences provided by UniProtKB derived?
More than 95 % of the protein sequences provided by UniProtKB are derived from the translation of the coding sequences (CDS) which have been submitted to the public nucleic acid databases, the EMBL-Bank/GenBank/DDBJ databases ( INSDC ).
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 ).
What is UniProtKB used for?
The UniProt Knowledgebase (UniProtKB) is an expertly curated database, a central access point for integrated protein information with cross-references to multiple sources. The UniProt Archive (UniParc) is a comprehensive sequence repository, reflecting the history of all protein sequences (1).
What is UniProtKB database?
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.
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.
Who maintains Swiss-Prot?
1. Swiss-Prot and TrEMBL. SWISS-PROT is a protein sequence database containing detailed annotations. It was established in 1986 and jointly maintained by the department of medical biochemistry of the University of Geneva and the EMBL data library (now EBI) since 1987.
What is PDB used for?
The PDB distributes coordinate data, structure factor files and NMR constraint files. In addition it provides documentation and derived data. The coordinate data are distributed in PDB and mmCIF formats.
What is Cath in bioinformatics?
The CATH database[3,4] is a classification of protein domains (sub-sequences of proteins that may fold, evolve and function independently of the rest of the protein), based not only on sequence information, but also on structural and functional properties.
Who created Swiss-Prot?
SWISS-PROT (1) is an annotated protein sequence database, which was created at the Department of Medical Biochemistry of the University of Geneva and has been a collaborative effort of the Department and the European Molecular Biology Laboratory (EMBL), since 1987.
Why does UniProtKB have two parts?
These UniProtKB/TrEMBL unreviewed entries are kept separated from the UniProtKB/Swiss-Prot manually reviewed entries so that the high quality data of the latter is not diluted in any way. Automatic processing of the data enables the records to be made available to the public quickly.
What is UniRef50?
UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.
What is the difference between SWISS-PROT and TrEMBL?
TrEMBL consists of entries in a SWISS-PROT format that are derived from the translation of all coding sequences in the EMBL nucleotide sequence database, that are not in SWISS-PROT. Unlike SWISS-PROT entries those in TrEMBL are awaiting manual annotation.
Is SWISS-PROT a secondary database?
Complete answer: SWISS PROT is a protein sequence database. Annotations in the database provide all the information regarding the structure and function of a particular protein along with its functions and modifications if any. The data is all primary and easily accessible.
When was SWISS-PROT established?
SWISS-PROT ( 1 ) is an annotated protein sequence database established in 1986 and maintained collaboratively, since 1987, by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library (now the EMBL Outstation-The European Bioinformatics Institute; 2 ).
When was Uniprot created?
The consortium members pooled their overlapping resources and expertise, and launched UniProt in December 2003.
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 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 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.
What is a trEMBL?
UniProtKB/TrEMBL contains high-quality computationally analyzed records, which are enriched with automatic annotation. It was introduced in response to increased dataflow resulting from genome projects, as the time- and labour-consuming manual annotation process of UniProtKB/Swiss-Prot could not be broadened to include all available protein sequences. The translations of annotated coding sequences in the EMBL-Bank/GenBank/DDBJ nucleotide sequence database are automatically processed and entered in UniProtKB/TrEMBL. UniProtKB/TrEMBL also contains sequences from PDB, and from gene prediction, including Ensembl, RefSeq and CCDS.
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.
What is Swiss Prot?
UniProtKB/Swiss-Prot contains high-quality expertly curated and non-redundant protein sequence records. Expert curation consists of a critical review of experimental and predicted data for each protein by a team of biologists, as well as manual verification of each protein sequence. UniProt curators extract biological information from the literature and perform numerous computational analyses. UniProtKB/Swiss-Prot aims to provide all known relevant information about a particular protein. Data captured from the scientific literature includes information on protein and gene names, function, catalytic activity, cofactors, subcellular location, protein-protein interactions and much more.
What is a trEMBL?
UniProtKB/TrEMBL contains high-quality computationally analysed records enriched with automatic annotation and classification . Records are selected for full manual curation and integration into UniProtKB/Swiss-Prot according to defined priorities. You can find more information about UniProt curation priorities and processes on the UniProt website.
How does UniProtKB work?
UniProtKB integrates large-scale datasets, mapping these data onto the appropriate protein sequence records and displaying the mappings via the ProtVista visualisation tool ( 28) and downloadable via FTP and APIs ( 29 ). Clinically relevant sources of variation (e.g. 100K genomes, gnomAD and ClinVar SNPs) are mapped to protein features and variants using a pre-calculated mapping of the genomic coordinates for the amino acids at the beginning and end of each exon and the conversion of UniProt position annotations to their genomic coordinates ( 30 ). Functional positional annotations from the UniProt human reference proteome are now being mapped to the corresponding genomic coordinates on the GRCh38 version of the human genome for each release of UniProt. These mappings are also available as BED files or as part of a UniProt genomic track hub and can be downloaded from the UniProt FTP site ( www.uniprot.org/downloads ). Aligning variants to protein features, such as functional domains and active sites, ligand binding sites and PTMs in the UniProt record, can provide mechanistic insights into how specific variants can lead to disease or resistance to a drug or to a pathogen.
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 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 2020?
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.
How is Uniprot evolving?
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. In our last update published in this journal in 2019 ( 3 ), we described how we are responding to the growth in microbial protein sequence records, largely derived from high-quality metagenomic assembled genomes. These will increasingly be added to by large-scale eukaryotic sequencing programs, such as the Darwin Tree of Life ( www.darwintreeoflife.org) and Earth Biogenome ( www.earthbiogenome.org) projects. Collectively, these have already resulted in the number of entries contained in UniProtKB growing by >65 million records, an increase of >50% in just 2 years. As the volume of sequence data continues to grow, we will continue to explore different ways to ensure database sustainability and scalability whilst still providing the best possible service to our user community.
What is an ARBA annotation?
To complement the expert guided process of creating UniRules, we have recently (release 2020_04) introduced the Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins ( 3 ). This replaces the previous rule-based SAAS system. ARBA is trained on UniProtKB/Swiss-Prot, then uses rule mining techniques to generate concise annotation models with the highest representativeness and coverage based on the properties of InterPro group membership and taxonomy. ARBA employs a data exclusion set that censors data not suitable for computational annotation (such as specific biophysical or chemical properties) and generates human-readable rules for each release which are made available at https://www.uniprot.org/arba/. 22 894 ARBA rules were used to annotate 87 325 890 proteins in release 2020_04, increasing the combined coverage of the rule-based annotation systems from 35% to 49% in UniProtKB/TrEMBL. Sequence feature predictions are currently excluded from annotation by ARBA. Additionally, in release 2020_04, more than 15 million uncharacterized protein names have been improved using InterPro member database signatures, updating their name to ‘domain X containing protein’ following the International Protein Nomenclature Guidelines ( https://www.uniprot.org/docs/International_Protein_Nomenclature_Guidelines.pdf ). For example, the uncharacterized Western lowland gorilla protein UniProtKB:G3RLC3 has now been renamed ‘SH2 domain-containing protein’ giving biological information to the user. This system includes adding names based on domains of unknown function (e.g. UniProtKB:A0A009EMH9 DUF4372 domain-containing protein) as, although not immediately informative, it enables protein grouping thus improving the chances of eventually assigning a function to that domain. All automatic annotations are labelled with their evidence/source.
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.
Overview
- The UniProt Knowledgebase consists of two sections: a section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis, and a section with computationally analyzed records that await full manual annotation. For the s…
Organization of UniProt databases
The UniProt consortium
The roots of UniProt databases
Funding
External links