ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network . Issue 2 (25th April 2017)
- Record Type:
- Journal Article
- Title:
- ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network . Issue 2 (25th April 2017)
- Main Title:
- ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network
- Authors:
- Gloaguen, Pauline
Bournais, Sylvain
Alban, Claude
Ravanel, Stéphane
Seigneurin-Berny, Daphné
Matringe, Michel
Tardif, Marianne
Kuntz, Marcel
Ferro, Myriam
Bruley, Christophe
Rolland, Norbert
Vandenbrouck, Yves
Curien, Gilles - Abstract:
- Abstract : ChloroKB, a Web-based application that enables the user to explore the chloroplast metabolic network in Arabidopsis. Abstract: Higher plants, as autotrophic organisms, are effective sources of molecules. They hold great promise for metabolic engineering, but the behavior of plant metabolism at the network level is still incompletely described. Although structural models (stoichiometry matrices) and pathway databases are extremely useful, they cannot describe the complexity of the metabolic context, and new tools are required to visually represent integrated biocurated knowledge for use by both humans and computers. Here, we describe ChloroKB, a Web application (http://chlorokb.fr/ ) for visual exploration and analysis of the Arabidopsis ( Arabidopsis thaliana ) metabolic network in the chloroplast and related cellular pathways. The network was manually reconstructed through extensive biocuration to provide transparent traceability of experimental data. Proteins and metabolites were placed in their biological context (spatial distribution within cells, connectivity in the network, participation in supramolecular complexes, and regulatory interactions) using CellDesigner software. The network contains 1, 147 reviewed proteins (559 localized exclusively in plastids, 68 in at least one additional compartment, and 520 outside the plastid), 122 proteins awaiting biochemical/genetic characterization, and 228 proteins for which genes have not yet been identified. TheAbstract : ChloroKB, a Web-based application that enables the user to explore the chloroplast metabolic network in Arabidopsis. Abstract: Higher plants, as autotrophic organisms, are effective sources of molecules. They hold great promise for metabolic engineering, but the behavior of plant metabolism at the network level is still incompletely described. Although structural models (stoichiometry matrices) and pathway databases are extremely useful, they cannot describe the complexity of the metabolic context, and new tools are required to visually represent integrated biocurated knowledge for use by both humans and computers. Here, we describe ChloroKB, a Web application (http://chlorokb.fr/ ) for visual exploration and analysis of the Arabidopsis ( Arabidopsis thaliana ) metabolic network in the chloroplast and related cellular pathways. The network was manually reconstructed through extensive biocuration to provide transparent traceability of experimental data. Proteins and metabolites were placed in their biological context (spatial distribution within cells, connectivity in the network, participation in supramolecular complexes, and regulatory interactions) using CellDesigner software. The network contains 1, 147 reviewed proteins (559 localized exclusively in plastids, 68 in at least one additional compartment, and 520 outside the plastid), 122 proteins awaiting biochemical/genetic characterization, and 228 proteins for which genes have not yet been identified. The visual presentation is intuitive and browsing is fluid, providing instant access to the graphical representation of integrated processes and to a wealth of refined qualitative and quantitative data. ChloroKB will be a significant support for structural and quantitative kinetic modeling, for biological reasoning, when comparing novel data with established knowledge, for computer analyses, and for educational purposes. ChloroKB will be enhanced by continuous updates following contributions from plant researchers. … (more)
- Is Part Of:
- Plant physiology. Volume 174:Issue 2(2017)
- Journal:
- Plant physiology
- Issue:
- Volume 174:Issue 2(2017)
- Issue Display:
- Volume 174, Issue 2 (2017)
- Year:
- 2017
- Volume:
- 174
- Issue:
- 2
- Issue Sort Value:
- 2017-0174-0002-0000
- Page Start:
- 922
- Page End:
- 934
- Publication Date:
- 2017-04-25
- Subjects:
- Plant physiology -- Periodicals
Botany -- Periodicals
Periodicals
Electronic journals
571.2 - Journal URLs:
- https://academic.oup.com/plphys/issue ↗
http://www.plantphysiol.org/ ↗
http://www.jstor.org/journals/00320889.html ↗
http://www.pubmedcentral.nih.gov/tocrender.fcgi?journal=69 ↗
http://www-us.ebsco.com/online/direct.asp?JournalID=101725 ↗
http://www.oxfordjournals.org/ ↗ - DOI:
- 10.1104/pp.17.00242 ↗
- Languages:
- English
- ISSNs:
- 0032-0889
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - BLDSS-3PM
British Library HMNTS - ELD Digital store - Ingest File:
- 22687.xml