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
Preview |
PDF (Paper)
ParameciumDB a community resource.pdf - Published Version Download (2MB) | Preview |
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: | https://repository.cshl.edu/id/eprint/22961 |
Actions (login required)
 |
Administrator's edit/view item |