A Systems Biology Results Markup Language — SBRML
By Joseph O. Dada, Irena Spasic, Norman W. Paton and Pedro Mendes
Systems Biology has benefited tremendously from the development and use of SBML
, which is a markup language to specify models composed of molecular species, and their interactions (including reactions). SBML is a common format that many systems biology software understand and thus it has become the way in which models are shared and communicated.
Despite the popularity of SBML, that has resulted in many models being available in electronic format, there is currently no standard way of communicating the results of the operations carried out with such models (e.g. simulations). Here we propose a new markup language which is complementary to SBML and which is intended to specify results from operations carried out on models — SBRML. In fact, this markup language is useful also to communicate experimental data as long as it is possible to express the data in terms of a reference SBML model. Thus SBRML is a means of specifying quantitative results in the context of a systems biology model.
We are pleased to release the SBRML level 1 version 1 specification
and the XML schema for SBRML
. A draft of the specification was first presented at the 13th SBML Forum in Gothenburg (Aug. 27–28, 2008)
. Feedback and comments are welcome and should be directed to <pedro.mendes/joseph.dada at manchester.ac.uk>.
SBRML example files
We thank the BBSRC and EPSRC for funding this project as an integral part of the Manchester Centre for Integrative Systems Biology. We thank several colleagues in the SBML community who provided feedback about the specification (both online and in the 13th SBML Forum Meeting).