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UniProt [the Universal Protein Resource] UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. UniProt is comprised of three components, each optimised for different uses. The UniProt Archive (UniParc) is a comprehensive repository, reflecting the history of all protein sequences. www.ebi.ac.uk /uniprot/index.html   (164 words)

ISMB 2006: Fortaleza, Brazil, August 6-10   (Site not responding. Last check: 2007-10-20) UniProt is comprised of three major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase and the UniProt Reference Clusters. The UniProt Archive (UniParc) is the main sequence storehouse and is a comprehensive repository that reflects the history of all protein sequences. UniProt Knowledgebase entries are subject to change in both sequence and annotation, but only the most recent versions are currently preserved in the database. ismb2006.cbi.cnptia.embrapa.br /tester/poster_abstract.php?id=B-5   (987 words)

Genomining - Décrypthon Genomining congratulates the Uniprot Consortium for the release of the new database, and informs its clients that the Uniprot Knowledgebase is utilizable via GetDB. Scientists expect UniProt, which brings together three separate world-class databases, to become the primary information resource for proteomic data. UniProt went on line on December 15, 2003, is the result of work undertaken by the UniProt consortium (the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR)). www.genomining.com /uniprot.en.html   (486 words)

Introduction to Sequence Databases Installed at Tel Aviv Unversity Bioinformatics Unit UniProt is comprised of three components, each optimized for different uses. The consortium members — all dedicated to the same goal of providing expansive and meaningful protein annotation, and all with solid foundations stemming from decades of activity — decided to pool their overlapping (and, importantly, their complementary) resources, efforts, and expertise. The UniProt Knowledgebase (UniProt) is the central database of protein sequences with accurate, consistent, and rich sequence and functional annotation. bioinfo.tau.ac.il /databases/intro_databases.html   (2268 words)

A Search Facility for the UniProt (Universal Protein Resource) Resource Before outlining the main features of The UniProt Search Facility, it is necessary to introduce one of the underlying concepts.Nearly all search facilities provide the ability to create complex queries using simple operators such as AND, OR, etc. There is however an implicit limitation of this, that is in understanding how these affect the result. The UniProt Knowledgebase and UniParc components of UniProt have these power search facilities, where users are able to narrow their searches by specifying the entry line type they are interested in. The two UniProt formats are HTML based formats, the Extended format shows automated annotation of the entries by RuleBase, Spearmint and Xanthippe, where as the Basic format does not. www.iscb.org /ismb2004/posters/spatientATebi.ac.uk_245.html   (990 words)

Experiments with Uniprot RDF and RDF Gateway   (Site not responding. Last check: 2007-10-20) The goal of this effort is to demonstrate the ability of RDF Gateway to efficiently store and query massive amounts of RDF data in its native RDF repository. The Uniprot RDF project provides all UniProt protein sequence and annotation data in RDF format and is an excellent large source of data. The uniprot data is delivered in a number of rdf/xml files ranging in size from 4kB to 11.4GB. labs.intellidimension.com /uniprot   (773 words)

XML Format of the UniProt Knowledgbase UniProt, the Universal Protein Resource, is a comprehensive catalogue of data on protein sequence and function maintained by the UniProt Consortium, a collaboration of the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI), and the Protein Information Resource (PIR) (Apweiler et al., 2004). UniProt consists of three layers: the Knowledgebase (UniProt), the Archive (UniParc), and the non-redundant databases (UniRef). The corresponding section in UniProt XML is marked by tags that contain subelements for each domain name and its synonyms. www.iscb.org /ismb2004/posters/allysonATebi.ac.uk_797.html   (815 words)

Configuring, Customizing and using the GoMiner Database The UniProt (Swiss-Prot, TrEMBL and PIR) Data Source in the GO Consortium database does not include gene names, but uses UniProt entry names instead, and the entry names are tedious to associate with gene names. In short though, if you are using the UniProt data source, and your input is in the form of gene names, you may want to consider using this option. UniProt used to be known in GoMiner as SPTR. discover.nci.nih.gov /gominer/database.jsp   (925 words)

Welcome to UniProt - UniProt [the Universal Protein Resource] UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. UniProt has three components, each optimized for different uses. The UniProt Knowledgebase (UniProtKB) is the central access point for extensive curated protein information, including function, classification, and cross-reference. www.expasy.uniprot.org   (120 words)

EMBL - About Us - News and Communication - Press Releases - 2003 - UniProt consortium goes on-line   (Site not responding. Last check: 2007-10-20) UniProt will provide a 'one-stop shop,' allowing easy access to all the publicly available information on proteins. The UniProt databases launched today are the result of a hectic but immensely productive year of collaboration among the three institutions that make up the UniProt Consortium. Underpinning the entire project is the UniProt Archive [UniParc] – the most comprehensive publicly accessible non-redundant protein sequence database available. www.embl.org /aboutus/news/press/2003/press15dec03.html   (894 words)

Genomics, Proteomics, and Bioinformatics: NCSU Libraries PIR is one of the co-founders of the UniProt consortium. Swiss-Prot is part of the UniProt consortiumand its contents have been incorporated into the UniProt KnowledgeBase. TrEMBL is part of the UniProt consortium and its contents have been incorporated into the UniProt KnowledgeBase. www.lib.ncsu.edu /data/biogenomics/proteins/seqandstruct.html   (696 words)

[No title] The primary mission of the consortium is to support biological research by maintaining a high quality database that serves as a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. Except for initiator N-terminal methionine residues, which are not included in a sequence when their absence from the mature sequence has been proven, the sequence data correspond to the precursor form of a protein before posttranslational modifications and processing. A description of the format differences between the UniProt knowledgebase and EMBL databases is given in Appendix C of this document. web.utk.edu /~eperez3/IS520/docs/text_search_retrieval_controlled_full_text_controlled_vocabulary_Ernest_Perez_04.27.03.50.39/Sources/www.expasy.org_sprot_userman.html   (9458 words)

STLQ: UniProt - The Universal Protein Resource The UniProt Consortium is comprised of the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information... The UniProt Consortium is comprised of the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). The UniProt databases (UniPARC, UniProtKB, UniREF) are built upon the pooled overlapping and complementary resources, efforts and expertise of these pioneereing efforts; UniProt FAQ stlq.info /2006/02/uniprot_1.html   (209 words)

UniProt: the Universal Protein knowledgebase -- Apweiler et al. 32 (Supplement 1): D115 -- Nucleic Acids Research UniProt: the Universal Protein knowledgebase -- Apweiler et al. The UniProt knowledgebase is the centrepiece of the consortium The UniProt consortium emphasizes the use of an evidence attribution nar.oxfordjournals.org /cgi/content/full/32/suppl_1/D115   (3632 words)

*BioCreAtIvE II - Protein Interaction Pairs Sub-task 2 (IPS)* The individual proteins of a given interaction pair should be uniquely identified by their corresponding UniProt ID. In principle, any of the data files from the IntAct and the MINT ftp servers would be usable to derive protein interactions pairs (with their corresponding UniProt IDs or protein accession number of UniProt), but for this sub-task, files released in 2005 and 2006 are used. Note that the interacting proteins are not restricted to a single organism source, so in principle for the linking step to the UniProt database entry, inter-species protein name ambiguity may have to be taken into account. biocreative.sourceforge.net /bc2_ppi_ips.html   (1229 words)

Genomining's GetDB gives users immediate access to UniProt, the new protein knowledgebase launched this week It lets them do what they do best - concentrate on their core research without worrying about whether the data is up to date." "The availability of UniProt is a major event in the integration of proteomics data - and GetDB customers will be among the first to benefit from the increased productivity UniProt brings to life science research," said William Saurin, chairman and chief technology officer of Genomining. Genomining offers its clients a unique combination of access to large scale biological databases and extremely high performance computing as demonstrated by the Decrypthon project a proteome mapping project completed in 2002. www.bioportfolio.com /news/genomining_1.htm   (635 words)

Computational Science Seminar Series Abstract: A tour through the functionality of UniProt 2.0 will be provided with particular reference to annotation of members of the Protein Kinase family, one of the largest, and arguably best conserved protein families – members of which can be found in species as diverse as man and bacteria. The Swiss-Prot, TrEMBL and PIR protein databaseactivities have united to form the Universal Protein Knowledgebase(UniProt) consortium, to provide a comprehensive,fully classified, richly and accurately annotated protein sequenceknowledgebase, with extensive cross-references and query interfaces.The central database will has two sections, corresponding tothe familiar Swiss-Prot (fully manually curated entries) andTrEMBL (enriched with automated classification, annotation andextensive cross-references). A tour through the functionality of UniProt 2.0 will be provided with particular reference to annotation of members of the Protein Kinase family, one of the largest, and arguably best conserved protein families – members of which can be found in species as diverse as man and bacteria. www.sdsc.edu /CSSS/forthcoming/orchard_03_2004.html   (297 words)

Biotechnology Information Center News: UniProt is now Freely Available to All -Katie - UniProt http://www.pir.uniprot.org/> (Universal Protein Resource), the "the world's most comprehensive catalog of information on proteins", now uses a Creative Commons license http://www.pir.uniprot.org/terms/ and is freely available to all. We spent a lot of time talking to the Uniprot folks over the last year. Congratulations to the Uniprot consortium and to Eric Jain www.library.uiuc.edu /blog/bicnews/archives/2006/02/uniprot_is_now.html   (318 words)

KU Libraries: Information Gateway: Web Sites by Subject Provides access to Swiss-Prot, 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 domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. UniProt (Universal Protein Resource) is a comprehensive catalog of information on proteins. Search for compounds and bioassay information by description, name, or keywords or by structure search. www.lib.ku.edu /infogateway/index.cfm?type=wrs&sid=90   (728 words)

Available DAS services The UniProt DAS Reference Server serves both sequence and feature data from UniProt/Swiss-Prot and UniProt/TrEMBL. Read more >rot are provided, including basic information (position, id and a brief description) and internet addresses to the relevant data source. Served from the Sanger installation of the MSD oracle database. servlet.sanger.ac.uk /dasregistry/listServices.jsp   (107 words)

EBI Databases EMBL Nucleotide Database - Europe’s primary collection of nucleotide sequences is maintained in collaboration with Genbank (USA) and DDBJ (Japan) UniProt Knowledgebase - a complete annotated protein sequence database CluSTr is an automatic classification of UniProt protein entries. www.embl-ebi.ac.uk /Databases/index.html   (375 words)

Databases maintained locally by ACHS UniProt is a combination of the information previously contained Since UniProt is wholly redudant with PIR, eventually (ie. Version 80 will remain available, but users should access UniProt for the most recent, and accurate protein sequences. www.itc.virginia.edu /achs/molbio/databases/database.html   (694 words)

The Universal Protein Resource (UniProt) -- The UniProt Consortium 35 (Supplement 1): D193 -- Nucleic Acids Research UniProt is updated and distributed on a bi-weekly basis and UniProt is freely available for both commercial and non-commercial The UniProt Consortium: Amos Bairoch, Lydie Bougueleret, Severine nar.oxfordjournals.org /cgi/content/full/35/suppl_1/D193   (2333 words)

uniprot RDF :: Migration Guide The original flat text format is described in the UniProt user manual. Reduced the amount of data that is duplicated from the UniProt data set. All data is distributed in a single file rather than one file per similarity level. dev.isb-sib.ch /projects/uniprot-rdf/migration.html   (2721 words)

DasProt - CBS DAS protein viewer The proteins are identified by their UniProt identifiers or accession numbers. The reference server for this DAS viewer is the UniProt DAS server at EBI. PDB structure aligned to UniProt proteins www.sanger.ac.uk, www.ebi.ac.uk www.cbs.dtu.dk /cgi-bin/das   (136 words)

uniprot - OneLook Dictionary Search   (Site not responding. Last check: 2007-10-20) We found 2 dictionaries with English definitions that include the word uniprot: Tip: Click on the first link on a line below to go directly to a page where "uniprot" is defined. UniProt : ACRONYMS FOR HEALTH INFORMATION RESOURCES [home, info] www.onelook.com /?w=uniprot   (77 words)

Plant Protein Annotation in the UniProt Knowledgebase -- Schneider et al. 138 (1): 59 -- PLANT PHYSIOLOGY Plant Protein Annotation in the UniProt Knowledgebase -- Schneider et al. UniProt, described in detail in Apweiler et al. The main distribution format of UniProt is as an ASCII flat www.plantphysiol.org /cgi/content/full/138/1/59   (4262 words)

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