File Entry: ONDEX Graph from the Yeast Jamboree SBML

Created: 2009-02-10 10:51:58      Last updated: 2009-02-10 12:48:52
Information Version 1 (of 1)

Version created on: 2009-02-10 10:51:58

Last edited on: 2009-02-10 12:48:52


Information Description

<dl class="AbstractPlusReport">
The oxl file represents in ONDEX the SBML reconstruction of yeast metabolism produced in the "Jamboree", as described in the following paper.
 

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.

Nature Biotechnology. 2008 Oct;26(10):1155-60.

Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412, USA.

Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.

</dl>

Information Download

Information Uploader

Information License

All versions of this File are licensed under:

Information Credits (1)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (8)

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

3158 viewings

765 downloads

[ see breakdown ]

 

Version History

In chronological order:



Comments Comments (0)

No comments yet

Log in to make a comment


What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/files/177


Alternative Formats

HTML
RDF
XML