Author | dc.contributor.author | Loira, Nicolás | |
Author | dc.contributor.author | Zhukova, Anna | |
Author | dc.contributor.author | Sherman, David James | |
Admission date | dc.date.accessioned | 2016-05-09T19:47:43Z | |
Available date | dc.date.available | 2016-05-09T19:47:43Z | |
Publication date | dc.date.issued | 2015 | |
Cita de ítem | dc.identifier.citation | Journal of Bioinformatics and Computational Biology Volumen: 13 Número: 2 Apr 2015 | en_US |
Identifier | dc.identifier.other | DOI: 10.1142/S0219720015500067 | |
Identifier | dc.identifier.uri | https://repositorio.uchile.cl/handle/2250/138212 | |
General note | dc.description | Artículo de publicación ISI | en_US |
General note | dc.description | Sin acceso a texto completo | |
Abstract | dc.description.abstract | Genome-scale metabolic models are a powerful tool to study the inner workings of biological
systems and to guide applications. The advent of cheap sequencing has brought the opportunity to
create metabolic maps of biotechnologically interesting organisms. While this drives the
development of new methods and automatic tools, network reconstruction remains a timeconsuming
process where extensive manual curation is required. This curation introduces specific
knowledge about the modeled organism, either explicitly in the form of molecular processes, or
indirectly in the form of annotations of the model elements. Paradoxically, this knowledge is usually
lost when reconstruction of a different organism is started. We introduce the Pantograph method for
metabolic model reconstruction. This method combines a template reaction knowledge base,
orthology mappings between two organisms, and experimental phenotypic evidence, to build a
genome-scale metabolic model for a target organism. Our method infers implicit knowledge from
annotations in the template, and rewrites these inferences to include them in the resulting model of
the target organism. The generated model is well suited for manual curation. Scripts for evaluating
the model with respect to experimental data are automatically generated, to aid curators in iterative
improvement. We present an implementation of the Pantograph method, as a toolbox for genomescale
model reconstruction, curation and validation. This open source package can be obtained
from: pathtastic. gforge.inria.fr. | en_US |
Patrocinador | dc.description.sponsorship | Fondap 15090007
Fondecyt 3140480
Basal Grant CMM (UMI-CNRS) 2807 | en_US |
Lenguage | dc.language.iso | en | en_US |
Publisher | dc.publisher | Imperial College Press | en_US |
Keywords | dc.subject | Metabolic modeling | en_US |
Keywords | dc.subject | Genome-scale reconstruction | en_US |
Keywords | dc.subject | Model validation | en_US |
Título | dc.title | Pantograph: A template-based method for genome-scale metabolic model reconstruction | en_US |
Document type | dc.type | Artículo de revista | |