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Resource:Organelle DB

Name: Resource:Organelle DB
Description: Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed.

The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures.

When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization.

Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light.
Other Name(s): Organelle DB: A Database of Organelles and Protein Complexes
Abbreviation: Organelle DB
Parent Organization: University of Michigan; Michigan; USA
Supporting Agency: NSF, Resource:American Cancer Society, March of Dimes, (Basil O'Connor Starter Scholar Research Award)
Grant: DBI-0543017, RSG-06-179-01-MBC, 5-FY05-1224
Resource Type(s): Database, 3D spatial image, Image collection, Data repository
Resource: Resource
URL: http://organelledb.lsi.umich.edu/
*Id: nif-0000-03226
PMID: PMID 17130152, 15608270
Publication link: http://nar.oxfordjournals.org/content/35/suppl_1/D810.long
Related to: Resource:GO
Availability: Free; please cite.
Address: Kumar Lab, Life Sciences Institute, The University of Michigan, 210 Washtenaw Avenue Ann Arbor, MI 48109-2216
Keywords: gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, K-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, Data analysis service
Organism: Eukaryote, Human, Mouse, Plant, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Other
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.

Facts about Resource:Organelle DBRDF feed
AbbrevOrganelle DB  +
AddressKumar Lab  +, Life Sciences Institute  +, The University of Michigan  +, 210 Washtenaw Avenue Ann Arbor  +, and MI 48109-2216  +
AvailabilityFree  +, and Acknowledgement requested  +
CurationStatusuncurated  +
DefiningCitationhttp://organelledb.lsi.umich.edu/  +
DefinitionDatabase of organelle proteins, and subcel Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed.

The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures.

When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization.

Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light.
t kinds of information will come to light.
ExampleImageOrganelle DB.PNG  +
GrantCategory:DBI-0543017   +, Category:RSG-06-179-01-MBC   +, and Category:5-FY05-1224   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +, 3D spatial image  +, Image collection  +, and Data repository  +
Idnif-0000-03226  +
Is part ofUniversity of Michigan; Michigan; USA  +
KeywordsGene  +, Fly  +, Vertebrate  +, Human  +, Mouse  +, Plant  +, Worm  +, Yeast  +, Protein  +, K-12  +, Organelle  +, Protein localization  +, Function  +, Subcellular Parts Table  +, Protein complex  +, Sequence  +, Annotation  +, Micrograph  +, Visualization  +, and Data analysis service  +
LabelResource:Organelle DB  +
ModifiedDate14 April 2014  +
PMID17130152, 15608270  +
Page has default formThis property is a special property in this wiki.Resource  +
PublicationLinkhttp://nar.oxfordjournals.org/content/35/suppl_1/D810.long  +
RelatedToResource:GO  +
SpeciesHuman  +, Mouse  +, Plant  +, Arabidopsis thaliana  +, Drosophila melanogaster  +, Caenorhabditis elegans  +, Saccharomyces cerevisiae  +, Other  +, and Eukaryota  +
SuperCategoryResource  +
Supporting AgencyResource:American Cancer Society  +, March of Dimes  +, and (Basil O'Connor Starter Scholar Research Award)  +
SynonymOrganelle DB: A Database of Organelles and Protein Complexes  +