BioPAX
Biological Pathway Exchange
BioPAX is a standard language that aims to enable integration, exchange and analysis of biological pathway data. It is expressed in OWL. The last specification is BioPAX Level 3. BioPAX development is coordinated by an elected editorial board and a Scientific Advisory Board. BioPAX is supported by many pathway database or processing tools. An API is available to help implementing support: Paxtools
CellML
CellML
The CellML language is an XML markup language to store and exchange computer-based mathematical models. CellML is being developed by the Auckland Bioengineering Institute at the University of Auckland and affiliated research groups.
The latest stable specification is Version 2.0.
CellML development is coordinated by an elected editorial board.
APIs are available to help implementing support: libCellML in C++, with Python and Javascript bindings available.
SBOL
Synthetic Biology Open Language
The Synthetic Biology Open Language Data (SBOL Data) is a language for the description and the exchange of synthetic biological parts, devices and systems.
The latest stable specification of SBOL Data is 3.1.0.
SBOL Data is developed by the SBOL Developers Group. The development is coordinated by an editorial board and the SBOL Chair.
SBOL data is supported by many software tools. APIs are available to help implement the support of this data standard.
NeuroML
NeuroML
The NeuroML project focuses on the development of an XML based description language that provides a common data format for defining and exchanging descriptions of neuronal cell and network models.
The latest stable specification is Version 2.2.
NeuroML development is coordinated by an elected editorial board.
SBGN
SBGN
The Systems Biology Graphical Notation (SBGN), is a set standard graphical languages to describe visually biological knowledge. It is currently made up of three languages describing Process Descriptions, Entity Relationships and Activity Flows.
The last specifications are SBGN PD Level 1 Version 2.0, SBGN ER Level 1 Version 2 and SBGN AF Level 1 Version 1.2.
SBGN development is coordinated by an elected editorial board and a Scientific Committee.
Several data resources and software claim support for SBGN. An API is available to help implementing support: libSBGN
SBML
SBML
The Systems Biology Markup Language (SBML) is a computer-readable XML format for representing models of biological processes. SBML is suitable for, but not limited to, models using a process description approach.
The latest stable specification is Level 3 Version 2 Core.
SBML development is coordinated by an elected editorial board and central developer team.
Over 250 software systems known to support SBML can be found in the SBML software documentation. APIs are available to help implementing support: libSBML in C++ and JSBML in Java.
SBOL Visual
SBOL Visual
The Synthetic Open Language Visual (SBOL Visual) is an open-source graphical notation that uses schematic “glyphs” to specify genetic parts, devices, modules, and systems.
The latest stable specification of SBOL Visual is 3.0.0.
SBOL is developed by the SBOL Developers Group and SBOL Visual Group. The development is coordinated by an editorial board and the SBOL Chair.
SBOL Visual is supported by many software tools.
SED-ML
SED-ML
The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments. SED-ML allows to define the models to use, the experimental tasks to run and which results to produce.is a computer-readable format for representing the models of biological processes. SED-ML can be used with models encoded in several languages, as far as they are in XML.
The latest stable specification is Level 1 Version 5.
SED-ML development is coordinated by an elected editorial board.
APIs are available to help implementing support: libSedML in C#, libSEDML in C++ with swig bindings for python, java, perl, R and ruby, and jlibsedml in Java.
Associated Standards
BioModels.net qualifiers
BioModels.net qualifiers are standardized relationships (predicates) that specify the relation between an object represented in a description language and the external resource used to annotate it. The relationship is rarely one-to-one, and the information content of an annotation is greatly increased if one knows what it represents, rather than only know it is “related to” the model component.
COMBINE Archive
A COMBINE archive is a single file bundling the various documents necessary for a modelling and simulation project, and all relevant information. The archive is encoded using the Open Modeling EXchange format (OMEX).
COMBINE Archive Metadata
COMBINE archive metadata provides a harmonized, community-driven approach for annotating a variety of standardized model and data representation formats within a COMBINE archive.
Identifiers.org
The identifiers.org web site uses MIRIAM Unique Resource Identifiers to allow one to uniquely and unambiguously identify an entity in a stable and perennial manner. Identifiers.org URIs can be dereferenced in a flexible and robust way, and are used by SBML, SED-ML, CellML and BioPAX controlled annotation schemes.
KiSAO
The Kinetic Simulation Algorithm Ontology (KiSAO) describes existing algorithms and their inter-relationships through their characteristics and parameters. It is updated from its github repository., KiSAO is used in SED-ML, which allows simulation software to automatically choose the best algorithm available to perform a simulation and unambiguously refer to it.
MIRIAM
MIRIAM Unique Resource Identifiers allow one to uniquely and unambiguously identify an entity in a stable and perennial manner. Identifiers.org contains a set of services and resources that provide support for generating, interpreting and resolving MIRIAM URIs. Through the Identifiers.org technology, MIRIAM URIs can be dereferenced in a flexible and robust way., MIRIAM URIs are used by SBML, SED-ML, CellML and BioPAX controlled annotation schemes.
SBO
The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling., Each element of an SBML file carries an optional attribute sboTerm which value must be a term from SBO., Each symbol of SBGN is associated with an SBO term.
Related Standardization Efforts
FieldML
FieldML’s (Field Modelling/Markup Language) goal is to be a declarative language for building hierarchical models represented by generalized mathematical fields. Its primary use will be to represent the dynamic geometry and solution fields from computational models of cells, tissues and organs.
CNO
The Computational Neurosciences Ontology aims to be a domain specific ontology, describing Computational Neurosciences models. CNO was created to add semantic information to NineML, a simulator independent language developed by the INCF Multi-Scale modeling Program. NineML aims to provide an unambiguous description of neuronal network models for efficient model sharing and reusability.
FAIRsharing.org
More information about standards used to share data in life sciences can be found at FAIRsharing. The FAIRsharing team manually curates data and metadata standards, databases and data policies across all scientific research areas. FAIRsharing provides links among these standards and databases as well as to journal and funder data policies that recommend or endorse their use. For example, FAIRsharing contains a collection of the COMBINE standards as well as many Systems Biology resources.
FROG
The FROG standard is designed to faithfully reproduce the analysis results of a flux balance model. Flux values are commonly reported as results in manuscripts with flux balance analysis of constraint-based models. These values cannot be used to test the reproducibility as often multiple solutions exist for the same. Hence, numerically reproducible results of the analysis are required to verify the reproducibility of the models. Following the discussion in the HARMONY2020 and COMBINE2020 meetings, we recognized the several outputs/results of the FBA analysis that are numerically reproducible and can be used for curation.
FSKX
The FAIR Scientific Knowledge eXchange (FSKX) Format is an open, standardized file format designed to facilitate the efficient sharing of scientific models and datasets in a Findable, Accessible, Interoperable, and Reusable (FAIR) manner. Originally developed as the Food Safety Knowledge Exchange (FSKX) Format within the Risk Assessment Knowledge Integration Platform (RAKIP) Initiative, FSKX has evolved into a general-purpose format for exchanging models across multiple scientific domains, including Life Sciences, Food Safety, One Health, and Artificial Intelligence (AI).
HUPO-PSI
The Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) is a global collaborative effort aimed at creating and maintaining community-driven standards, data formats, and controlled vocabularies for proteomics and mass spectrometry-based research. Through its working groups and annual workshops, HUPO-PSI encourages collaboration and ensures thorough public review of proposals before their adoption as standards. By advocating for open data sharing, the initiative accelerates advancements in proteomics and related scientific fields.
MAMO
The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.
NuML
The Numerical Markup Language (NuML) (pronounce “neumeul” and not “new em el”, that sounds like NewML) is a simple XML format to exchange multidimensional arrays of numbers to be used with model and simulation descriptions. NuML was initially developed as part of the Systems Biology Results Markup Language (SBRML).
SpineML
The Spiking Neural Mark-up Language (SpineML) is a declarative XML based model description language for large scale neural network models. It is partially based upon on the INCF NineML syntax utilising the LEMS (Low Entropy Model Specification) common model specification syntax which is proposed to unite a range of INCF supported simulators including NeuroML v2.0 and PyNN.
TEDDY
The Terminology for the Description of Dynamics is a project to build an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.