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The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

B. Boeckmann
2003 Nucleic Acids Research  
The SWISS-PROT protein knowledgebase  ...  All statistical information given in this article is retrieved from SWISS-PROT release 40.27 (August 2002) and TrEMBL release 21.10 (September 2002), respectively.  ...  ACKNOWLEDGEMENTS We wish to thank Andrea Auchincloss, Livia Famiglietti and Michele Magrane for helpful discussions, and Vivienne Baillie Gerritsen for the correction of the manuscript.  ... 
doi:10.1093/nar/gkg095 pmid:12520024 pmcid:PMC165542 fatcat:qdooywnignc6vlqqpyylvfvqae

Protein sequence databases [chapter]

Rolf Apweiler
2000 Advances in Protein Chemistry  
databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record.  ...  Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium.  ...  Swiss-Prot activities at the SIB are supported by the Swiss Federal Government through the Federal Office of Education and Science.  ... 
doi:10.1016/s0065-3233(00)54002-9 pmid:10829224 fatcat:wfukhw4wl5fa7dlclssofxa6ei

Protein Sequence Databases [chapter]

Michele Magrane, Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler
2005 The Proteomics Protocols Handbook  
databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record.  ...  Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium.  ...  Swiss-Prot activities at the SIB are supported by the Swiss Federal Government through the Federal Office of Education and Science.  ... 
doi:10.1385/1-59259-890-0:609 fatcat:6s6rbabhovgybeeay7hui35joi

Protein sequence databases

Rolf Apweiler, Amos Bairoch, Cathy H Wu
2004 Current Opinion in Chemical Biology  
databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record.  ...  Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium.  ...  Swiss-Prot activities at the SIB are supported by the Swiss Federal Government through the Federal Office of Education and Science.  ... 
doi:10.1016/j.cbpa.2003.12.004 pmid:15036160 fatcat:mq2wzitgvvhexnzz5otzf7b3a4

NEWT, a new taxonomy portal

I. Q. H. Phan
2003 Nucleic Acids Research  
NEWT is a new taxonomy portal to the SWISS-PROT protein sequence knowledgebase.  ...  Users can navigate through the taxonomy tree and access corresponding SWISS-PROT protein entries.  ...  NEWT LINKS Integration with SWISS-PROT For every taxon stored in NEWT where protein sequence data in SWISS-PROT or TrEMBL (the computer-annotated supplement of SWISS-PROT) is found, the total number  ... 
doi:10.1093/nar/gkg516 pmid:12824428 pmcid:PMC168923 fatcat:ejk3dmnd5jceba35thciwjdly4

The Gene Ontology Annotation (GOA) Project—Application of GO in SWISS-PROT, TrEMBL and InterPro

Evelyn Camon, Daniel Barrell, Catherine Brooksbank, Michele Magrane, Rolf Apweiler
2003 Comparative and Functional Genomics  
Acknowledgements GOA is supported by the European Commission and the US National Institutes of Health.  ...  Many new gene products, from a wide range of species, are being added to the SWISS-PROT Protein Knowledgebase -the world's most highly annotated protein sequence database -and its supplement, TrEMBL [  ...  proteins in SWISS-PROT and TrEMBL.  ... 
doi:10.1002/cfg.235 pmid:18629103 pmcid:PMC2447390 fatcat:ans3bf5ewfcytdlejdkhc6lbya

Plant Protein Annotation in the UniProt Knowledgebase

M. Schneider
2005 Plant Physiology  
ACKNOWLEDGMENTS We would like to thank Alan Bridge, Michael Tognolli, and Sylvain Poux for critical reading of the manuscript.  ...  Swiss-Prot and TrEMBL In 1996, Swiss-Prot already contained 83,000 entries.  ...  With its two sections, UniProtKB/ Swiss-Prot and UniProtKB/TrEMBL, the UniProtKB contains all known proteins, without species restriction.  ... 
doi:10.1104/pp.104.058933 pmid:15888679 fatcat:khnmftwseraablpqrqqxansis4

The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro

E. Camon
2003 Genome Research  
Article and publication are at  ...  Continual advancement in proteome research has led to an increase in sequences from a wide range of species requiring addition to the SWISS-PROT Protein Knowledgebase and its supplement, TrEMBL (Bairoch  ...  The dataset was created by combining all human protein sequences in the SWISS-PROT database and supplementing these with a nonredundant selection of human proteins from the TrEMBL and Ensembl (Hubbard  ... 
doi:10.1101/gr.461403 pmid:12654719 pmcid:PMC430163 fatcat:y33clngkn5g2pb7eegoclhgbvq

UniProtKB amid the turmoil of plant proteomics research

Michel Schneider, the UniProt Consortium, Sylvain Poux
2012 Frontiers in Plant Science  
Manual annotation is one of the landmarks of the Swiss-Prot section of UniProtKB. Besides adding functional annotation, curators are checking, and often correcting, gene model predictions.  ...  The UniProt KnowledgeBase (UniProtKB) provides a single, centralized, authoritative resource for protein sequences and functional information.  ...  To solve with this problem, TrEMBL, a computerannotated supplement to Swiss-Prot, was launched.  ... 
doi:10.3389/fpls.2012.00270 pmid:23230445 pmcid:PMC3515866 fatcat:77u6uwcod5ggtarheel6gqcrce

ExPASy: the proteomics server for in-depth protein knowledge and analysis

E. Gasteiger
2003 Nucleic Acids Research  
The ExPASy (  ...  ACKNOWLEDGEMENTS Finally, we want to thank all the users of ExPASy who, over the years, have sent us feedback that has led to the improvement of existing services and to the development of new ones.  ...  SWISS-PROT is supplemented by TrEMBL, which contains computer-annotated entries for all sequences not yet integrated in SWISS-PROT.  ... 
doi:10.1093/nar/gkg563 pmid:12824418 pmcid:PMC168970 fatcat:mmswhmjr3vespn43t2phzjz2zi

The International Protein Index: An integrated database for proteomics experiments

Paul J. Kersey, Jorge Duarte, Allyson Williams, Youla Karavidopoulou, Ewan Birney, Rolf Apweiler
2004 Proteomics  
IPI (the International Protein Index) has been developed to address these issues and offers complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL  ...  Information about proteins identified by different experimental and computational methods is stored in different databases, meaning that no single resource offers full coverage of known and predicted proteins  ...  This work has in part been funded by EU grant number QLRI-CT-2001-00015 under the RTD program "Quality of Life and Management of Living Resources".  ... 
doi:10.1002/pmic.200300721 pmid:15221759 fatcat:ma43xexok5cmffncasqxn3izdm

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology

E. Camon
2004 Nucleic Acids Research  
The GOA project is grateful for the support of Grants QRLT-2001-00015 and QLRI-2000-00981 of the European Commission and a supplementary NIH grant, 1R01HGO2273-01.  ...  ACKNOWLEDGEMENTS We especially thank all colleagues worldwide who have contributed to the information content of the GOA data set and to the development of annotation and retrieval tools.  ...  INTRODUCTION The UniProt Knowledgebase (1) [which includes Swiss-Prot (2) , TrEMBL (2) and PIR-PSD (3) ] is the world's most highly annotated protein sequence database, having archived and annotated  ... 
doi:10.1093/nar/gkh021 pmid:14681408 pmcid:PMC308756 fatcat:aqclkomfwrgdfeeaq6ik2tqabe

Automated annotation of microbial proteomes in SWISS-PROT

Alexandre Gattiker, Karine Michoud, Catherine Rivoire, Andrea H Auchincloss, Elisabeth Coudert, Tania Lima, Paul Kersey, Marco Pagni, Christian J.A Sigrist, Corinne Lachaize, Anne-Lise Veuthey, Elisabeth Gasteiger (+1 others)
2003 Computational biology and chemistry  
Large-scale sequencing of prokaryotic genomes demands the automation of certain annotation tasks currently manually performed in the production of the SWISS-PROT protein knowledgebase.  ...  The results of this annotation are integrated in SWISS-PROT, and a website is provided at http://www.expasy.org/ sprot/hamap/. #  ...  The specific value of SWISS-PROT compared with its supplements lies in the extent and quality of the annotation attached to protein sequences.  ... 
doi:10.1016/s1476-9271(02)00094-4 pmid:12798039 fatcat:prchx2b565dlpfdy5elx2mec4e

The European Bioinformatics Institute's data resources

C. Brooksbank
2003 Nucleic Acids Research  
The European Bioinformatics Institute (EBI) hosts six core databases, which store information on DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), protein structure (MSD), whole genomes  ...  As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner.  ...  the proteins in SWISS-PROT and TrEMBL that match the Table 2 .  ... 
doi:10.1093/nar/gkg066 pmid:12519944 pmcid:PMC165513 fatcat:46gy4lg2v5ak7mdns47kaelgpu

Integrating biological data through the genome

Gabrielle A. Reeves, Janet M. Thornton
2006 Human Molecular Genetics  
Owing to the ongoing success of the genome sequencing and structural genomics projects, the increase in both sequence and structural data is rapid.  ...  The development of tools for the annotation of sequence and structural data has become more important in the hope of keeping up with this data explosion.  ...  ACKNOWLEDGEMENT This work was funded through the BioSapiens Network of Excellence, by the European Commission within its FP6 Programme, under the thematic area 'Life Sciences, Genomics and Biotechnology  ... 
doi:10.1093/hmg/ddl086 pmid:16651373 fatcat:i6wzv4myyfbbloxrpunoglucam
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