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| Nicole Redaschi; UniProt Consortium. |
| The UniProt knowledgebase (UniProtKB) is a comprehensive repository of protein sequence and annotation data. We collect information from the scientific literature and other databases and provide links to over one hundred biological resources. Such links between different databases are an important basis for data integration, but the lack of a common standard to represent and link information makes data integration an expensive business. At UniProt we have started to tackle this problem by using the Resource Description Framework ("http://www.w3.org/RDF/":http://www.w3.org/RDF/) to represent our data. RDF is a core technology for the World Wide Web Consortium's Semantic Web activities... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3193/version/1 |
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| Michele Magrane; UniProt Consortium. |
| UniProtKB provides the scientific community with a comprehensive collection of protein sequence records containing extensive curated information including functional and sequence annotation. This information is derived from a variety of sources such as scientific literature and sequence analysis programs as well as data imported from automatic annotation systems and external databases. To allow users to ascertain the origin of each data item in a UniProtKB record, an evidence attribution system is being introduced which links each piece of information to its original source. This system allows users to trace the origin of all information, to differentiate easily between experimental and computational data, and to assess data reliability. The current system... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3129/version/1 |
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| Duncan J. Legge; UniProt Consortium. |
| The nematode worm, _Caenorhabditis elegans_, was the first multicellular organism to be sequenced. Its genome was published in 1998, providing an impetus for gene and protein annotation. Recently, the genome of _C. briggsae_ has been sequenced. This has given bioinformaticans the opportunity to study comparative genomics between two highly similar organisms. Currently, there are 12 species of _Caenorhabditis_ in UniProtKB and over 700 nematode species, including some of interest to parasitology. Functional and sequence annotation from literature and sequence analysis tools are included in each curated record. _C. elegans_ has a relatively small genome size, short life span and a transparent body, making it ideal for knock-out/RNAi studies. Thus many _C.... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3157/version/1 |
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| Rebecca E. Foulger; UniProt Consortium. |
| The African clawed frog Xenopus laevis and the zebrafish Danio rerio have both proved to be good model organisms for studying early vertebrate cellular and developmental biology. More recently, the related western clawed frog Xenopus tropicalis has become a popular choice in the laboratory, since its shorter life style and diploid genome make it more amenable to genetic analysis. Ongoing sequencing of the X. tropicalis and D. rerio genomes, together with the growing number of EST/cDNA projects, is generating large amounts of sequence data and revealing many human developmental and disease genes that have counterparts in fish and frog.

UniProtKB/Swiss-Prot curates Xenopus and zebrafish proteins with functional and sequence... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3153/version/1 |
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| Serenella Ferro Rojas; Anne Morgat; UniProt Consortium. |
| Within the UniProt consortium, the UniProtKB/Swiss-Prot knowledge base provides the international community with a stable, comprehensive, fully classified, richly and accurately annotated protein sequence database that is fully operable with other databases. Annotation relates to function(s) of the protein (their catalytic activity and the corresponding metabolic pathway(s) in which the protein may be involved), their cellular location, their interactions with other cellular components, etc. 

It is challenging to unify the way we annotate proteins, to ensure consistency and to describe data unambiguously. It is also highly valuable both for querying the database and for analyzing high-throughput data (expression data for... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3214/version/1 |
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| Michele Magrane; UniProt Consortium. |
| Data integration plays an increasingly important role in bringing together the large amounts of diverse information spread across disparate resources and presenting a comprehensive overview of these data to the scientific community. 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 specialised data collections. UniProtKB also integrates data such as protein sequences, protein-protein interactions, Gene Ontology terms and official gene... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5092/version/1 |
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| The HAPMAP Team; The PROSITE Team; Edouard de Castro; Alan Bridge; UniProt Consortium. |
| The development of next generation sequencing technologies promises a massive increase in the rate of submission of new protein sequences to sequence databases such as the Universal Protein Resource Knowledge Base, UniProtKB. At UniProtKB/Swiss-Prot we propose to meet this challenge by continuing to expand and develop systems for the automatic propagation of existing annotation to newly submitted protein sequences. These developments will promote the standardization of ortholog annotation both across and within kingdoms and significantly enhance our ability to accurately annotate new protein sequences which are being produced at an ever increasing rate.
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| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3215/version/1 |
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