The Universal Protein Resource (UniProt)

@article{Bairoch2005TheUP,
  title={The Universal Protein Resource (UniProt)},
  author={Amos Bairoch and Rolf Apweiler and Cathy H. Wu and Winona C. Barker and Brigitte Boeckmann and Serenella Ferro and Elisabeth Gasteiger and Hongzhan Huang and Rodrigo Lopez and Michele Magrane and Maria Jesus Martin and Darren A. Natale and Claire O’Donovan and Nicole Redaschi and Lai-Su L. Yeh},
  journal={Nucleic Acids Research},
  year={2005},
  volume={33},
  pages={D154 - D159}
}
The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully… Expand
UniProtKB/Swiss-Prot.
TLDR
The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry, paying particular attention to the specificities of plant protein annotation, and some of the tools and databases that are linked to each entry. Expand
Plant Protein Annotation in the UniProt Knowledgebase1
TLDR
The Swiss-Prot, TrEMBL, Protein Information Resource (PIR), and DNA Data Bank of Japan (DDBJ) protein database activities have united to form the Universal Protein Resource (UniProt) Consortium, providing the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Expand
UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View.
TLDR
The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry, and some of the tools and databases that are linked to each entry. Expand
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program.
TLDR
The UniProt knowledgebase, UniProt KB, is the main product of the UniProt consortium, and UniProtKB/TrEMBL, the computer translation of the EMBL/GenBank/DDBJ nucleotide sequence database, and the Plant Proteome Annotation Program, which focuses on the manual annotation of plant-specific proteins and protein families. Expand
Annotating single amino acid polymorphisms in the UniProt/Swiss‐Prot knowledgebase
TLDR
Information on single amino acid polymorphisms recorded in UniProtKB/Swiss‐Prot complements nicely those existing in genomic and phenotypic databases, and is valuable for the understanding of SAPs and diseases. Expand
UniProtKB/Swiss-Prot: New and Future Developments
TLDR
The Swiss-Prot knowledgebase is the cornerstone of the UniProt consortium efforts that aims to provide to life scientists a wide range of information concerning proteins, including their function, domain structure, post-translational modifications and variants. Expand
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
TLDR
A semi-automated system, HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes), that uses manually built annotation templates for protein families to propagate annotation to all members of manually defined protein families, using very strict criteria. Expand
SSMap: A new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase
TLDR
The systematic comparison conducted in this study allows the further identification of general problems in UniProt-PDB mappings so that both the coverage and the quality of the mappings can be systematically improved for the benefit of the scientific community. Expand
ProGMap: an integrated annotation resource for protein orthology
TLDR
ProGMap is a web-tool designed to help researchers and database annotators to assess the coherence of protein groups defined in various databases and thereby facilitate the annotation of newly sequenced proteins. Expand
InterPro: the integrative protein signature database
TLDR
The InterPro database integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 35 REFERENCES
UniProt: the Universal Protein knowledgebase
TLDR
The Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt), which is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. Expand
The Protein Information Resource
TLDR
The Protein Information Resource is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery and has developed a bibliography system for literature searching, mapping, and user submission. Expand
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
TLDR
The SWISS-PROT protein knowledgebase connects amino acid sequences with the current knowledge in the Life Sciences by providing an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Expand
A novel method for automatic functional annotation of proteins
TLDR
A method of automatic annotation that produces highly reliable functional prediction using the language and the syntax of SWISS-PROT is developed and successfully used for the automatic annotation of a testset of unknown proteins. Expand
UniProt archive
TLDR
UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available and contains only protein sequences and database cross-references; all other information must be retrieved from the source databases. Expand
Protein family classification and functional annotation
TLDR
The approach to protein functional annotation with case studies and examines common identification errors is described and it is illustrated that data integration in PIR supports exploration of protein relationships and may reveal protein functional associations beyond sequence homology. Expand
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
TLDR
The Gene Ontology Annotation database aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of theGene Ontology (GO). Expand
The InterPro Database, 2003 brings increased coverage and new features
TLDR
The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications, an increase of nearly 15% since the inception of Inter pro. Expand
Filtering erroneous protein annotation
TLDR
Xanthippe is a contradictive application that can be combined seamlessly with predictive systems and can be used either to improve the precision of automated annotation at a constant level of recall or increase the recall at a Constant level of precision. Expand
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT
TLDR
The statistical evaluation of the generated rules by cross-validation suggests that by applying them on arbitrary proteins 33% of their keyword annotation can be generated with an error rate of 1.5%, and the coverage rate can be increased to 60% by tolerating a higher error rate. Expand
...
1
2
3
4
...