Background: The KEGG PATHWAY database provides a plethora of pathways
for a diversity of organisms. All pathway components are directly
linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION.
Therefore, the pathways can be extended with an enormous amount of
information and provide a foundation for initial structural modeling
approaches. As a drawback, KGML-formatted KEGG pathways are primarily
designed for visualization purposes and often omit important details
for the sake of a clear arrangement of its entries. Thus, a direct
conversion into systems biology models would produce incomplete and
erroneous models.
Results: Here, we present a precise method for processing and converting
KEGG pathways into initial metabolic and signaling models encoded in the
standardized community pathway formats SBML (Levels 2 and 3) and BioPAX
(Levels 2 and 3). This method involves correcting invalid or incomplete KGML
content, creating complete and valid stoichiometric reactions, translating
relations to signaling models and augmenting the pathway content with
various information, such as cross-references to Entrez Gene, OMIM, UniProt
ChEBI, and many more. Finally, we compare several existing conversion tools
for KEGG pathways and show that the conversion from KEGG to BioPAX
does not involve a loss of information, whilst lossless translations
to SBML can only be performed using SBML Level 3, including its recently
proposed qualitative models and groups extension packages.
Conclusions: Building correct BioPAX and SBML signaling models from the KEGG
database is a unique characteristic of the proposed method. Further, there
is no other approach that is able to appropriately construct metabolic
models from KEGG pathways, including correct reactions with stoichiometry.
The resulting initial models, which contain valid and comprehensive
SBML or BioPAX code and a multitude of cross-references, lay the
foundation to facilitate further modeling steps.
@article{Wrzodek2013a,
author = {Wrzodek, Clemens and B\"uchel, Finja and Ruff, Manuel and Dr\"ager,
Andreas and Zell, Andreas},
title = {Precise generation of systems biology models from {KEGG} pathways.},
journal = {BMC Systems Biology},
year = {2013},
volume = {7},
pages = {15},
number = {1},
month = jan,
abstract = {Background: The KEGG PATHWAY database provides a plethora of pathways
for a diversity of organisms. All pathway components are directly
linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION.
Therefore, the pathways can be extended with an enormous amount of
information and provide a foundation for initial structural modeling
approaches. As a drawback, KGML-formatted KEGG pathways are primarily
designed for visualization purposes and often omit important details
for the sake of a clear arrangement of its entries. Thus, a direct
conversion into systems biology models would produce incomplete and
erroneous models.
Results: Here, we present a precise method for processing and converting
KEGG pathways into initial metabolic and signaling models encoded in the
standardized community pathway formats SBML (Levels 2 and 3) and BioPAX
(Levels 2 and 3). This method involves correcting invalid or incomplete KGML
content, creating complete and valid stoichiometric reactions, translating
relations to signaling models and augmenting the pathway content with
various information, such as cross-references to Entrez Gene, OMIM, UniProt
ChEBI, and many more. Finally, we compare several existing conversion tools
for KEGG pathways and show that the conversion from KEGG to BioPAX
does not involve a loss of information, whilst lossless translations
to SBML can only be performed using SBML Level 3, including its recently
proposed qualitative models and groups extension packages.
Conclusions: Building correct BioPAX and SBML signaling models from the KEGG
database is a unique characteristic of the proposed method. Further, there
is no other approach that is able to appropriately construct metabolic
models from KEGG pathways, including correct reactions with stoichiometry.
The resulting initial models, which contain valid and comprehensive
SBML or BioPAX code and a multitude of cross-references, lay the
foundation to facilitate further modeling steps.},
doi = {10.1186/1752-0509-7-15},
issn = {1752-0509},
keywords = {KEGG, KGML, SBML, BioPAX, modeling, systems biology, qualitative modeling,
quantitative modeling, converter, comparison},
pdf = {http://www.biomedcentral.com/content/pdf/1752-0509-7-15.pdf},
url = {http://www.biomedcentral.com/1752-0509/7/15}
}