09-11, 14:20–14:25 (Africa/Johannesburg), Omega
Constraint-based modelling and genome scale models (GSM's) are ubiquitous in Systems Biology with applications ranging from agriculture to human health (1). Fundamental to this methodology is the ability to create and exchange models, a process facilitated through the use of the Systems Biology Markup Language (SBML) (2) and its Flux Balance Constraints Package (FBC) extension.
Released in September 2015, FBC version 2 has become the de facto standard for encoding GSM's and is widely used in model repositories (BioModels, BiGG), software (e.g. COBRAPy, CBMPy) and curation pipelines (MEMOTE, FROG). It extends SBML by adding the components necessary for building typical GSM, including a linear objective function, reaction flux bounds and gene-protein-reaction associations (3). However, more recent model types, such as community and macromolecular expression (ME) models, could not be fully encoded in FBC version 2.
To address these shortcomings a working group, including members of both the SBML and constraint-based modelling community, have been working towards a new version of FBC. Recently finalised, the FBC version 3 specification (4) builds on FBC version 2 by allowing the definition of:
- objective functions with mixed quadratic and linear terms, that allows the definition of QP based models,
- user-defined (UD) constraints that are not defined as part of the stoichiometric matrix,
- UD constraints can contain quadratic terms that allow the definition of quadratic constraint (QC) models,
- UD constraint can also contain "artificial" variables that are defined as non-constant parameters,
- species that have chemical formulas with generic terms (e.g. R, X) and non-integer charges,
- KeyValuePairs, a simple, flexible annotation type that supplements the existing SBML annotations.
The FAIR (findable, accessible, interoperable, reusable) data principles form the basis of data management practices that are focussed on the reuse of research data (5). In this context models are also considered research data that should be reusable by yourself and others thus enabling good and reproducible research practices. While much of the focus on FAIR data is on the findability and accessibility, SBML provides a structured data format with built-in support for metadata that is primarily focussed on interoperability. The FBC 3 KeyValuePair annotations introduce support for less metadata that allows for a wider range of information to be stored as model annotation, and documentation, potentially leading to enhanced model reusability.
