Full Answer
What is UniProtKB?
The UniProt Consortium is committed to using and promoting common data exchange formats and technologies, and UniProtKB data is made freely available in a range of formats to facilitate integration with other databases.
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.
What is the'basket'in the UniProt KnowledgeBase?
When browsing through different UniProt proteins, you can use the 'basket' to save them, so that you can back to find or analyse them later. More... The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.
What is UniProtKB database?
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.
What is UniProtKB in bioinformatics?
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.02-Feb-2021
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.23-Nov-2021
What are the components of UniProtKB?
UniProt is comprised of four major components, each optimized for different uses: the UniProt Knowledgebase, the UniProt Reference Clusters, the UniProt Archive and the UniProt Metagenomic and Environmental Sequences database.
Is Swiss-Prot a primary database?
Hint: A primary database is one that makes information available to the public. The secondary databases take this information on sequences to then add layers to the existing DNA sequence and protein sequence data. Complete answer: SWISS PROT is a protein sequence database.
Why do we need UniProt?
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 saves researchers countless hours of work in monitoring and collecting this information themselves.
How do I use UniProtKB?
10:0127:56A guide to UniProt for students - YouTubeYouTubeStart of suggested clipEnd of suggested clipSimply input your sequence of interest into it or any uniprot identified into the search box thenMoreSimply input your sequence of interest into it or any uniprot identified into the search box then click blast.
Is Swiss-Prot manually annotated?
The Swiss-Prot section of the UniProt KnowledgeBase (UniProtKB/Swiss-Prot) contains publicly available expertly manually annotated protein sequences obtained from a broad spectrum of organisms.
What is Expasy in bioinformatics?
It is an extensible and integrative portal which provides access to over 160 databases and software tools, developed by SIB Groups and supporting a range of life science and clinical research domains, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry.
What is Swiss-Prot used for?
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc), a minimal level of redundancy and a high level of integration with other databases.
How many proteins are 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:// ...25-Nov-2020
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.
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.
What is a UniProtKB?
UniProtKB is a protein sequence database which aims to offer a complete collection of all publicly available sequences. To achieve this, it integrates sequences from a range of resources as summarized in Table 1. More than 99% of the sequences in UniProtKB are derived from translations of the coding regions in the International Nucleotide Sequence Database Collaboration (INSDC) which is composed of the European Nucleotide Archive ( 1 ), the DNA Data Bank of Japan ( 2) and GenBank ( 3 ). UniProtKB also accepts submissions of directly sequenced protein sequences through the web-based SPIN submission tool ( 4) which allows researchers to submit directly sequenced proteins and associated biological data. In addition, the published literature is searched on a monthly basis using literature databases such as CiteXplore ( 5) and UK PubMed Central ( 6) to identify papers reporting unsubmitted peptide sequence data for incorporation into the database. As part of an ongoing collaboration with PDBe ( 7 ), novel protein sequences are imported from the resource to ensure that all appropriate sequences in the worldwide Protein Data Bank (wwPDB) are represented in UniProtKB.
How does UniProtKB work?
UniProtKB adds value to each protein sequence record by including a wealth of information related to the role of the protein such as its function, structure, subcellular location, interactions with other proteins and domain composition, as well as a wide range of sequence features such as active sites and post-translational modifications. The information which is added directly to the database by the UniProt group comes from two main sources, manual curation and automatic annotation. Manual curation provides high-quality information for experimentally characterized proteins using data from the scientific literature as well as manual verification of results from sequence analysis programs. While manual curation is essential in providing accurate data, it is a time-consuming and labour intensive process which cannot keep up with the ever-increasing amounts of sequence data being generated. In addition, for many species, only the genome sequence has been determined with no functional experimental information available for the encoded proteins. To address these issues, automated methods have been developed which use information from known proteins to annotate uncharacterized proteins. Using both manual and automated curation approaches, as much information as possible is added to each UniProtKB record.
What is manual curation in UniprotKB?
Manual curation will continue to provide high-quality UniProtKB data, ensuring that users have access to accurate and consistently annotated experimental information coupled with manually verified sequence analysis predictions. In addition, the automatic annotation systems will be improved and expanded to increase the depth and breadth of predicted data while ensuring the continued quality of the predicted annotations. Existing cross-references will continue to be maintained and regularly updated with each release and new cross-references will be added to the collection as appropriate.
What is a UniProt Knowledgebase?
The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialized data collections. UniProtKB also integrates a range of data from other resources. All information is attributed to its original source, allowing users to trace the provenance of all data. The UniProt Consortium is committed to using and promoting common data exchange formats and technologies, and UniProtKB data is made freely available in a range of formats to facilitate integration with other databases.
Why is information added to an entry during the manual annotation process linked to its original source?
All information added to an entry during the manual annotation process is linked to its original source so that users can trace the origin of each piece of information and evaluate it. The evidence attribution system and its use in both manual and automatic annotation procedures is described in more detail in a later section.
Exploring the UniProt protein knowledgebase with AWS Open Data and Amazon Neptune
The Universal Protein Resource (UniProt) is a widely used resource of protein data that is now available through the Registry of Open Data on AWS. Its centerpiece is the UniProt Knowledgebase (UniProtKB), a central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.
Registry of Open Data on AWS
The Registry of Open Data on AWS makes it easy to find datasets made publicly available through AWS services. UniProt is made available through the Registry of Open Data via the Open Data Sponsorship Program, which covers the cost of storage for publicly available high-value cloud-optimized datasets.
Amazon Neptune
Amazon Neptune is a fast, reliable, fully managed graph database service that makes it easy to build and run applications that work with highly connected datasets. The core of Neptune is a purpose-built, high-performance graph database engine.
Creating a custom UniProtKB
In this example, we select a list of UniProt RDF files that we are interested in exploring. Then we ingest the RDF files from the Open Data Registry on AWS into Amazon Neptune DB. Once the data is ingested, we demonstrate how to query relationships and attributes.
Taxonomy, Gene Ontology (GO) and other reference data
UniProt uses several supporting reference datasets that contain related information and metadata. Among these are the NCBI taxonomy, for the hierarchical classification of organisms, and the Gene Ontology (GO), used to describe the current scientific knowledge about the functions of proteins.
UniProt Knowledgebase (UniProtKB)
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.
UniProt Sequence archive (UniParc)
The UniProt Archive (UniParc) is a comprehensive and non-redundant database that contains most of the publicly available protein sequences in the world. Data is partitioned into files of around 1 Gigabyte in size depending on the size of the protein sequence. For more information on this archive, see the UniParc documentation.