How does UniProtKB integrate with external databases?
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.
What is the UniProt KnowledgeBase?
The UniProt Knowledgebase is a central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (expert-curated records) and UniProtKB/TrEMBL (computationally annotated records). UniProtKB is produced by the UniProt consortium.
Why UniProt for data integration?
The UniProt approach to data integration ensures that information is captured in the most appropriate resource for subsequent integration with other databases and also ensures maximum curation efficiency by preventing duplication of efforts across multiple resources.
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 UniProtKB database?
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 in bioinformatics?
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 are the differences between UniProtKB Swiss-Prot and UniProtKB TrEMBL?
UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator, while the records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification.
Why is UniProtKB composed of 2 sections?
The centrepiece of the UniProt databases is the UniProt knowledge base (UniProtKB), which comprises 2 sections: manually annotated UniProtKB/Swiss-Prot and automatically annotated UniProtKB/TrEMBL. Taken together, these 2 sections give access to all publicly available protein sequences.
How UniProtKB database is useful in identifying the function of a protein?
The UniProt database has cross-references to over 150 databases and acts as a central hub to organize protein information. Its accession numbers are a primary mechanism for accurate and sustainable tagging of proteins in informatics applications.
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 UniProtKB Swiss-Prot what is its purpose?
UniProtKB/Swiss-Prot is the expertly curated component of UniProtKB (produced by the UniProt consortium). It contains hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants.
How are data from Swiss-Prot and TrEMBL different?
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 primary database?
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.
What are the important features of UniProt?
UniProt provides cross-references to external data collections such as the underlying DNA sequence entries in the DDBJ/EMBL/GenBank nucleotide sequence databases, 2D PAGE and 3D protein structure databases, various protein domain and family characterization databases, PTM databases, species-specific data collections, ...
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.
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.
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 PDB in bioinformatics?
Protein Data Bank (PDB) is the single worldwide archive of structural data of biological macromolecules. It includes data obtained by X-ray crystallography and nuclear magnetic resonance (NMR) spectrometry submitted by biologists and biochemists from all over the world.
What is a bioinformatic?
Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology (fig 1).
What is UniRef?
The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.
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.
How are sequences analysed?
Sequences are analysed using a range of analysis tools for prediction of sequence features. The various tools have been integrated into an interactive sequence analysis platform that runs the programs simultaneously and displays the results in an interface that allows curators to review and select relevant results for inclusion. The predicted features include domains, repeats, transmembrane domains, secretory and organelle targeting sequences, coiled coils, regions of compositional bias, glycosylation sites, N-terminal myristoylation, GPI lipid anchor modification, and tyrosine sulfation. All predictions are manually reviewed and considered in the context of experimental data, and only relevant results are selected for integration. The full list of prediction methods used is described in Table 2.