ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data

Arnaiz, Olivier, Cain, Scott, Cohen, Jean, Sperling, Linda (January 2007) ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res, 35. D439-D444. ISSN 0305-1048

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URL: https://www.ncbi.nlm.nih.gov/pubmed/17142227
DOI: 10.1093/nar/gkl777

Abstract

ParameciumDB (http://paramecium.cgm.cnrs-gif.fr) is a new model organism database associated with the genome sequencing project of the unicellular eukaryote Paramecium tetraurelia. Built with the core components of the Generic Model Organism Database (GMOD) project, ParameciumDB currently contains the genome sequence and annotations, linked to available genetic data including the Gif Paramecium stock collection. It is thus possible to navigate between sequences and stocks via the genes and alleles. Phenotypes, of mutant strains and of knockdowns obtained by RNA interference, are captured using controlled vocabularies according to the Entity-Attribute-Value model. ParameciumDB currently supports browsing of phenotypes, alleles and stocks as well as querying of sequence features (genes, UniProt matches, InterPro domains, Gene Ontology terms) and of genetic data (phenotypes, stocks, RNA interference experiments). Forms allow submission of RNA interference data and some bioinformatics services are available. Future ParameciumDB development plans include coordination of human curation of the near 40 000 gene models by members of the research community.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > databases > database construction
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
bioinformatics > genomics and proteomics > databases > databases
organism description > animal > paramecium
CSHL Authors:
Communities: CSHL labs > Stein lab
Depositing User: CSHL Librarian
Date: January 2007
Date Deposited: 02 Dec 2011 16:37
Last Modified: 21 Mar 2018 13:44
PMCID: PMC1669747
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22961

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