Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

Abstract

This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.

The long journey towards standards for engineering biosystems

“…The question remains, however, whether the wider community of potential users will see the value of adopting standards in their daily practice. Today, SynBio and systems biology practitioners are widely using the Synthetic Biology Open Language SBOL and SBOL visual for describing vectors and constructs , and there is a great consensus on the need to go beyond the state of the art and further advance towards the standardisation of biological systems .…”

Towards standardization guidelines for in silico approaches in personalized medicine

“…These three ingredients need to be well-documented and each component must be tested for correctness. Reproducibility then requires standard formats to represent the data, detailed descriptions following the Good Scientific Practices described in Minimum Information Guidelines, and semantic annotations [ 8 ], [ 9 ]. The computational biology community has already developed standards for all parts of a typical virtual study and the authors are convinced that these well-established COMBINE standards [ 9 ] shall be thoroughly evaluated for use in predictive in silico models in personalized medicine.…”

Specifications of standards in systems and synthetic biology: status and developments in 2021

“…This editorial will present the latest specifications of all COMBINE standards, and this special issue highlights updates over the last year, namely the releases of the following specifications: OMEX Metadata Version 1.2, SED-ML Level 1 Version 4, SBOL Visual 2.3 and 3.0. Special issues on COMBINE standards have been published since 2016, and earlier editions [ 3 ], [ 4 ], [ 5 ], [ 6 ], [ 7 ] provide updates for the years 2015–2020.…”