http://precedings.nature.com/tags/uniprot Recently posted documents tagged with 'uniprot' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3193.1 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/) to represent our data. RDF is a core technology for the World Wide Web Consortium’s Semantic Web activities (http://www.w3.org/2001/sw/) and is therefore well suited to work in a distributed and decentralized environment. The RDF data model represents arbitrary information as a set of simple statements of the form subject-predicate-object. To enable the linking of data on the Web, RDF requires that each resource must have a (globally) unique identifier. These identifiers allow everybody to make statements about a given resource and, together with the simple structure of the RDF data model, make it easy to combine the statements made by different people (or databases) to allow queries across different datasets. RDF is thus an industry standard that can make a major contribution to solve two important problems of bioinformatics: distributed annotation and data integration. http://dx.doi.org/10.1038/npre.2009.3193.1 Tue, 28 Apr 2009 18:42:07 UTC UniProt in RDF: Tackling Data Integration and Distributed Annotation with the Semantic Web doi:10.1038/npre.2009.3193.1 2009-04-28 Nicole Redaschi Nature Precedings 2009-04-28T18:42:07Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3157.1 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. elegans UniProtKB entries have characterization details in the newly introduced DISRUPTION PHENOTYPE comment. Many more worm genome sequencing projects are underway, three of which involve species from the Caenorhabditis genus (C. brenneri, C. japonica and C.remanei). We look forward to working with this influx of data and continuing our close collaboration with WormBase. http://dx.doi.org/10.1038/npre.2009.3157.1 Thu, 23 Apr 2009 17:20:07 UTC Worm Annotation in the UniProt Knowledgebase (UniProtKB) doi:10.1038/npre.2009.3157.1 2009-04-23 Duncan J. Legge Nature Precedings 2009-04-23T17:20:07Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3153.1 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 annotation from the literature and sequence analysis tools, using both controlled vocabularies (including GO terms) and free text. The tetraploid nature of the X. laevis and D. rerio genomes complicates annotation since the protein copies need to be identified and curated as separate UniProtKB/Swiss-Prot entries. The recent addition of Xenbase cross-references in Xenopus UniProtKB entries has been the result of cross-talk with Xenbase, and we continue to collaborate with ZFIN to ensure consistency between databases. UniProt is mainly supported by the NIH, European Commission FELICS, Swiss Federal Government, PATRIC BRC and NSF grants. http://dx.doi.org/10.1038/npre.2009.3153.1 Thu, 23 Apr 2009 17:20:01 UTC Xenopus and Zebrafish Annotation in the UniProt Knowledgebase (UniProtKB) doi:10.1038/npre.2009.3153.1 2009-04-23 Rebecca E. Foulger Nature Precedings 2009-04-23T17:20:01Z Poster Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3122.1 Manual curation of biomedical data is highly accurate but time consuming, and does not scale with the ever increasing growth of biomedical literature. Text mining as a high-throughput computational technique scales well but requires human expertise to produce highly accurate results. Ontologies can help organizing large quantities of unstructured information. Here we present three systems, namely GoGene, GoPubMed and GoWeb, employing biomedical ontologies and show how they can assist manual curation of biomedical data.GoGene associates all genes from different model organisms to concepts of the Gene Ontology (GO) and the Medical Subject Headings (MeSH). The hierarchical structures of both terminologies support clustering and summarizing long lists of genes. Through the integration of known gene annotations from UniProt and EntrezGene with text-mined annotations from all abstracts in PubMed, GoGene currently contains up to 4,000,000 associations between genes and concepts from GO and MeSH for ten model organisms. The quality of all associations can be verified by following the links to their origin, that is, literature or database entries.GoPubMed aims at reducing the limitations of classical keyword search. It handles inconsistent vocabulary such as synonyms and specialized terminology. It shows the most relevant concepts in GO and MeSH for a search and thus reveals information which otherwise remains buried in the masses of text. This feature as well as the entire bibliography of all authors in PubMed facilitate comprehensive literature search. GoWeb translates these ideas to the World Wide Web and is thus not only limited to PubMed abstracts. GoWeb uses a standard web-search service and organizes search results based on GO, MeSH, and other concepts such as companies and institutions. http://dx.doi.org/10.1038/npre.2009.3122.1 Wed, 22 Apr 2009 21:14:18 UTC Ontology-based Assisted Curation of Biomedical Data doi:10.1038/npre.2009.3122.1 2009-04-22 Conrad Plake Nature Precedings 2009-04-22T21:14:18Z Presentation Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3129.1 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 and plans for its future development and enhancement will be presented. http://dx.doi.org/10.1038/npre.2009.3129.1 Wed, 22 Apr 2009 13:12:51 UTC Evidence attribution in the UniProt Knowledgebase doi:10.1038/npre.2009.3129.1 2009-04-22 Michele Magrane Nature Precedings 2009-04-22T13:12:51Z Poster Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2611/version/1 The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access. http://precedings.nature.com/documents/2611/version/1 Mon, 08 Dec 2008 18:34:03 UTC Design and Implementation of the UniProt Website hdl:10101/npre.2008.2611.1 2008-12-08 Eric Jain Nature Precedings 2008-12-08T18:34:03Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/