Dataset Information

Qualitative translation of relations from BioPAX to SBML qual.

ABSTRACT:

Motivation

The biological pathway exchange language (BioPAX) and the systems biology markup language (SBML) belong to the most popular modeling and data exchange languages in systems biology. The focus of SBML is quantitative modeling and dynamic simulation of models, whereas the BioPAX specification concentrates mainly on visualization and qualitative analysis of pathway maps. BioPAX describes reactions and relations. In contrast, SBML core exclusively describes quantitative processes such as reactions. With the SBML qualitative models extension (qual), it has recently also become possible to describe relations in SBML. Before the development of SBML qual, relations could not be properly translated into SBML. Until now, there exists no BioPAX to SBML converter that is fully capable of translating both reactions and relations.

Results

The entire nature pathway interaction database has been converted from BioPAX (Level 2 and Level 3) into SBML (Level 3 Version 1) including both reactions and relations by using the new qual extension package. Additionally, we present the new webtool BioPAX2SBML for further BioPAX to SBML conversions. Compared with previous conversion tools, BioPAX2SBML is more comprehensive, more robust and more exact.

Availability

BioPAX2SBML is freely available at http://webservices.cs.uni-tuebingen.de/ and the complete collection of the PID models is available at http://www.cogsys.cs.uni-tuebingen.de/downloads/Qualitative-Models/.

SUBMITTER: Buchel F

PROVIDER: S-EPMC3467751 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Qualitative translation of relations from BioPAX to SBML qual.

Büchel Finja F Wrzodek Clemens C Wrzodek Clemens C Mittag Florian F Dräger Andreas A Eichner Johannes J Rodriguez Nicolas N Le Novère Nicolas N Zell Andreas A

Bioinformatics (Oxford, England) 20120824 20

<h4>Motivation</h4>The biological pathway exchange language (BioPAX) and the systems biology markup language (SBML) belong to the most popular modeling and data exchange languages in systems biology. The focus of SBML is quantitative modeling and dynamic simulation of models, whereas the BioPAX specification concentrates mainly on visualization and qualitative analysis of pathway maps. BioPAX describes reactions and relations. In contrast, SBML core exclusively describes quantitative processes s ...[more]

PMID: 22923304

Similar Datasets

Project description:The SBML standard is used in a number of online repositories for storing systems biology models, yet there is currently no Web-capable JavaScript library that can read and write the SBML format. This is a severe limitation since the Web has become a universal means of software distribution, and the graphical capabilities of modern web browsers offer a powerful means for building rich, interactive applications. Also, there is a growing developer population specialized in web technologies that is poised to take advantage of the universality of the web to build the next generation of tools in systems biology and other fields. However, current solutions require server-side processing in order to support existing standards in modeling. We present libsbmljs, a JavaScript/WebAssembly library for Node.js and the Web with full support for all SBML extensions. Our library is an enabling technology for online SBML editors, model-building tools, and web-based simulators, and runs entirely in the browser without the need for any dedicated server resources. We provide NPM packages, an extensive set of examples, JavaScript API documentation, and an online demo that allows users to read and validate the SBML content of any model in the BioModels and BiGG databases. We also provide instructions and scripts to allow users to build a copy of libsbmljs against any libSBML version. Although our library supports all existing SBML extensions, we cover how to add additional extensions to the wrapper, should any arise in the future. To demonstrate the utility of this implementation, we also provide a demo at https://libsbmljsdemo.github.io/ with a proof-of-concept SBML simulator that supports ODE and stochastic simulations for SBML core models. Our project is hosted at https://libsbmljs.github.io/, which contains links to examples, API documentation, and all source code files and build scripts used to create libsbmljs. Our source code is licensed under the Apache 2.0 open source license.

Dataset Information

Qualitative translation of relations from BioPAX to SBML qual.

Motivation

Results

Availability

Publications

Qualitative translation of relations from BioPAX to SBML qual.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets