RT Journal Article
A1 O. Ruebenacker
A1 I.I. Moraru
A1 J.C. Schaff
A1 M.L. Blinov

PB iet
T1 Integrating BioPAX pathway knowledge with SBML models
JN IET Systems Biology
VO 3
IS 5
SP 317
OP 328
AB Online databases store thousands of molecular interactions and pathways, and numerous modelling software tools provide users with an interface to create and simulate mathematical models of such interactions. However, the two most widespread used standards for storing pathway data (biological pathway exchange; BioPAX) and for exchanging mathematical models of pathways (systems biology markup language; SBML) are structurally and semantically different. Conversion between formats (making data present in one format available in another format) based on simple one-to-one mappings may lead to loss or distortion of data, is difficult to automate, and often impractical and/or erroneous. This seriously limits the integration of knowledge data and models. In this paper we introduce an approach for such integration based on a bridging format that we named systems biology pathway exchange (SBPAX) alluding to SBML and BioPAX. It facilitates conversion between data in different formats by a combination of one-to-one mappings to and from SBPAX and operations within the SBPAX data. The concept of SBPAX is to provide a flexible description expanding around essential pathway data – basically the common subset of all formats describing processes, the substances participating in these processes and their locations. SBPAX can act as a repository for molecular interaction data from a variety of sources in different formats, and the information about their relative relationships, thus providing a platform for converting between formats and documenting assumptions used during conversion, gluing (identifying related elements across different formats) and merging (creating a coherent set of data from multiple sources) data.
K1 SBPAX data
K1 SBML models
K1 online databases
K1 bridging format
K1 one-to-one mappings
K1 BioPAX pathway knowledge
K1 molecular interactions
DO https://doi.org/10.1049/iet-syb.2009.0007
UL https://digital-library.theiet.org/;jsessionid=e57gfts98r01.x-iet-live-01content/journals/10.1049/iet-syb.2009.0007
LA English
SN 1751-8849
YR 2009
OL EN