Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY

The use of computational modelling in the description and analysis of biological systems is at the heart of Systems Biology. Besides the information stored in a core model, there is increasingly a need to provide additional semantic information: to identify model components, to assist in biological interpretation of models, to define simulation conditions and to describe simulation results. This information deficit can be addressed through the use of ontologies. We describe here three ontologies created specifically to address the needs of the Systems Biology community in each sub-division, and illustrate their practical use with the 'Repressilator' model (Elowitz and Leibler, 2000)

Toward community standards and software for whole-cell modeling

Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate, comprehensive models of complex cells. Methods: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in SBML. Results: Our analysis revealed several challenges to representing WC models using the current standards. Conclusion: We, therefore, propose several new WC modeling standards, software, and databases. Significance:We anticipate that these new standards and software will enable more comprehensive models

SBML Level 3 Package Proposal: Annotation

The annotation of Systems Biology Markup Language (SBML) models with semantic terms has been supported for a number of years. The prevalence of such annotated models is growing, with repositories such as Biomodels.net and an increasing number of software tools supporting and encouraging their use and development.

With the increasing use of semantic annotations in the context of systems biology modeling has come the realization that the current Core SBML specification defining their use contains limitations that reduce the scope of metadata that can be captured in such models.

SBML Level 3 provides the facility to propose and develop optional extensions to the Core specification. One such extension is described here, with an initial proposal of an Annotation package.

This proposal extends the current Core annotation specification to provide support for a richer set of semantic annotations while adhering more closely to the existing specification of Resource Description Framework (RDF)

SBML Level 3 Package Proposal: Annotation

The annotation of Systems Biology Markup Language (SBML) models with semantic terms has been supported for a number of years. The prevalence of such annotated models is growing, with repositories such as Biomodels.net and an increasing number of software tools supporting and encouraging their use and development.With the increasing use of semantic annotations in the context of systems biology modeling has come the realization that the current Core SBML specification defining their use contains limitations that reduce the scope of metadata that can be captured in such models.SBML Level 3 provides the facility to propose and develop optional extensions to the Core specification. One such extension is described here, with an initial proposal of an Annotation package.This proposal extends the current Core annotation specification to provide support for a richer set of semantic annotations while adhering more closely to the existing specification of Resource Description Framework (RDF)

Research briefings: the 'Effects of transfusion thresholds on neurocognitive outcome of extremely low birth-weight infants (ETTNO)' study: background, aims, and study protocol

Background: Infants with extremely low birth weight uniformly develop anemia of prematurity and frequently require red blood cell transfusions (RBCTs). Although RBCT is widely practiced, the indications remain controversial in the absence of conclusive data on the long-term effects of RBCT. Objectives: To summarize the current equipoise and to outline the study protocol of the 'Effects of Transfusion Thresholds on Neurocognitive Outcome of extremely low birth-weight infants (ETTNO)' study. Methods: Review of the literature and design of a large pragmatic randomized controlled trial of restrictive versus liberal RBCT guidelines enrolling 920 infants with birth weights of 400-999 g with long-term neurodevelopmental follow-up. Results and Conclusions: The results of ETTNO will provide definite data about the efficacy and safety of restrictive versus liberal RBCT guidelines in very preterm infants