Organelle DB


17130152	Organelle DB: an updated resource of eukaryotic protein localization and function. [PMID: 17130152] Wiwatwattana N, Landau CM, Cope GJ, Harp GA, Kumar A. Abstract Organelle DB (http://organelledb.lsi.umich.edu) is a web-accessible relational database presenting a supplemented catalog of organelle-localized proteins and major protein complexes. Since its release in 2004, Organelle DB has grown by 20% to encompass over 30,000 proteins from 138 eukaryotic organisms. Each protein in Organelle DB is presented with its subcellular localization, primary sequence and a detailed description of its function, as available. All records in Organelle DB have been annotated using controlled vocabulary from the Gene Ontology consortium. Protein localization data are inherently visual, and Organelle DB is a significant repository of biological images, housing 1500 micrographs of yeast cells carrying stained proteins. Furthermore, we report here the development of Organelle View, an extension of Organelle DB for the interactive visualization of organelles and subcellular structures in the budding yeast Saccharomyces cerevisiae. Organelle View offers a dimensional representation of a yeast cell; users can search Organelle View for proteins of interest, and the organelles housing these proteins will be highlighted in the cell image. Among other applications, Organelle View may serve as an educational aid engaging introductory biology students through a visually 'fun' interface. Organelle View can be accessed from the Organelle DB home page or directly at http://organelleview.lsi.umich.edu. Nucleic Acids Res. 2007:35(Database issue) \| 23 Citations (from Europe PMC, 2025-03-29)
15608270	Organelle DB: a cross-species database of protein localization and function. [PMID: 15608270] Wiwatwattana N, Kumar A. Abstract To efficiently utilize the growing body of available protein localization data, we have developed Organelle DB, a web-accessible database cataloging more than 25,000 proteins from nearly 60 organelles, subcellular structures and protein complexes in 154 organisms spanning the eukaryotic kingdom. Organelle DB is the first on-line resource devoted to the identification and presentation of eukaryotic proteins localized to organelles and subcellular structures. As such, Organelle DB is a strong resource of data from the human proteome as well as from the major model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans and Mus musculus. In particular, Organelle DB is a central repository of yeast data, incorporating results--and actual fluorescent imagesfrom ongoing large-scale studies of protein localization in S.cerevisiae. Each protein in Organelle DB is presented with its sequence and, as available, a detailed description of its function; functions were extracted from relevant model organism databases, and links to these databases are provided within Organelle DB. To facilitate data interoperability, we have annotated all protein localizations using vocabulary from the Gene Ontology consortium. We also welcome new data for inclusion in Organelle DB, which may be freely accessed at http://organelledb.lsi.umich.edu. Nucleic Acids Res. 2005:33(Database issue) \| 23 Citations (from Europe PMC, 2025-03-29)

Organelle DB: an updated resource of eukaryotic protein localization and function. [PMID: 17130152]

Wiwatwattana N, Landau CM, Cope GJ, Harp GA, Kumar A.

Organelle DB (http://organelledb.lsi.umich.edu) is a web-accessible relational database presenting a supplemented catalog of organelle-localized proteins and major protein complexes. Since its release in 2004, Organelle DB has grown by 20% to encompass over 30,000 proteins from 138 eukaryotic organisms. Each protein in Organelle DB is presented with its subcellular localization, primary sequence and a detailed description of its function, as available. All records in Organelle DB have been annotated using controlled vocabulary from the Gene Ontology consortium. Protein localization data are inherently visual, and Organelle DB is a significant repository of biological images, housing 1500 micrographs of yeast cells carrying stained proteins. Furthermore, we report here the development of Organelle View, an extension of Organelle DB for the interactive visualization of organelles and subcellular structures in the budding yeast Saccharomyces cerevisiae. Organelle View offers a dimensional representation of a yeast cell; users can search Organelle View for proteins of interest, and the organelles housing these proteins will be highlighted in the cell image. Among other applications, Organelle View may serve as an educational aid engaging introductory biology students through a visually 'fun' interface. Organelle View can be accessed from the Organelle DB home page or directly at http://organelleview.lsi.umich.edu.

Nucleic Acids Res. 2007:35(Database issue) | 23 Citations (from Europe PMC, 2025-03-29)

Organelle DB: a cross-species database of protein localization and function. [PMID: 15608270]

Wiwatwattana N, Kumar A.

Abstract

To efficiently utilize the growing body of available protein localization data, we have developed Organelle DB, a web-accessible database cataloging more than 25,000 proteins from nearly 60 organelles, subcellular structures and protein complexes in 154 organisms spanning the eukaryotic kingdom. Organelle DB is the first on-line resource devoted to the identification and presentation of eukaryotic proteins localized to organelles and subcellular structures. As such, Organelle DB is a strong resource of data from the human proteome as well as from the major model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans and Mus musculus. In particular, Organelle DB is a central repository of yeast data, incorporating results--and actual fluorescent imagesfrom ongoing large-scale studies of protein localization in S.cerevisiae. Each protein in Organelle DB is presented with its sequence and, as available, a detailed description of its function; functions were extracted from relevant model organism databases, and links to these databases are provided within Organelle DB. To facilitate data interoperability, we have annotated all protein localizations using vocabulary from the Gene Ontology consortium. We also welcome new data for inclusion in Organelle DB, which may be freely accessed at http://organelledb.lsi.umich.edu.

Nucleic Acids Res. 2005:33(Database issue) | 23 Citations (from Europe PMC, 2025-03-29)

URL:	http://organelledb.lsi.umich.edu
Full name:
Description:	a web-accessible relational database presenting a supplemented catalog of organelle-localized proteins and major protein complexes.
Year founded:	2005
Last update:
Version:
Accessibility:	Accessible
Country/Region:	United States

Data type:	Protein
Data object:	Fungi
Database category:	Interaction
Major species:	Saccharomyces cerevisiae
Keywords:	eukaryotic protein localization function

University/Institution:	University of Michigan
Address:
City:
Province/State:
Country/Region:	United States
Contact name (PI/Team):	Anuj Kumar
Contact email (PI/Helpdesk):	anujk@umich.edu

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Database Commons a catalog of worldwide biological databases