Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX

@article{Stromback2005, abstract = {MOTIVATION: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed. RESULTS: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data.}, author = {Str\"{o}mb\"{a}ck, Lena and Lambrix, Patrick }, citeulike-article-id = {435359}, doi = {http://dx.doi.org/10.1093/bioinformatics/bti718}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {biopax, data, dt, format, pathway, psi-mi, representation, sbml}, month = {December}, number = {24}, pages = {4401--4407}, posted-at = {2007-10-17 19:19:55}, priority = {2}, publisher = {Oxford University Press}, title = {Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX}, url = {http://dx.doi.org/10.1093/bioinformatics/bti718}, volume = {21}, year = {2005} }

TY - JOUR ID - Stromback2005 L3 - citeulike-article-id:435359 N2 - MOTIVATION: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed. RESULTS: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data. IS - 24 JF - Bioinformatics SN - 1367-4803 EP - 4407 TI - Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX PB - Oxford University Press VL - 21 SP - 4401 KW - biopax KW - data KW - dt KW - format KW - pathway KW - psi-mi KW - representation KW - sbml AU - Strömbäck, Lena AU - Lambrix, Patrick PY - 2005/12/15/ UR - http://dx.doi.org/10.1093/bioinformatics/bti718 ER -