SBtab - Conventions for structured data tables in Systems Biology

TL;DR

SBtab is a standardized, flexible table format designed to improve data structuring and annotation in Systems Biology, facilitating model building and data sharing.

Contribution

It introduces a structured, extendable table format with syntax rules and predefined types to enhance data consistency and usability in Systems Biology.

Findings

Defines SBtab as a flexible, structured table format

Includes syntax rules for naming and annotation

Supports biochemical network modeling

Abstract

Data tables in the form of spreadsheets or delimited text files are the most utilised data format in Systems Biology. However, they are often not sufficiently structured and lack clear naming conventions that would be required for modelling. We propose the SBtab format as an attempt to establish an easy-to-use table format that is both flexible and clearly structured. It comprises defined table types for different kinds of data; syntax rules for usage of names, shortnames, and database identifiers used for annotation; and standardised formulae for reaction stoichiometries. Predefined table types can be used to define biochemical network models and the biochemical constants therein. The user can also define own table types, adjusting SBtab to other types of data. Software code, tools, and further information can be found at www.sbtab.net.