  Background: Systems biology projects and omics technologies have led to a
growing number of biochemical pathway reconstructions. However, mathematical
models are still most often created de novo, based on reading the literature
and processing pathway data manually. Results: To increase the efficiency with
which such models can be created, we automatically generated mathematical
models from pathway representations using a suite of freely available software.
We produced models that combine data from KEGG PATHWAY, BioCarta, MetaCyc and
SABIO-RK; According to the source data, three types of models are provided:
kinetic, logical and constraint-based. All models are encoded using SBML Core
and Qual packages, and available through BioModels Database. Each model
contains the list of participants, the interactions, and the relevant
mathematical constructs, but, in most cases, no meaningful parameter values.
Most models are also available as easy to understand graphical SBGN maps.
Conclusions: to date, the project has resulted in more than 140000 models
freely available. We believe this resource can tremendously accelerate the
development of mathematical models by providing initial starting points ready
for parametrization.
