COMBINE Standards

BioPAX

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

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.

More information.

SBOL

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 3.0.0.

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.

More information

NeuroML

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.

More information.

SBGN

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

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 guide. APIs are available to help implementing support: libSBML in C++ and JSBML in Java.

SBOL Visual

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 2.0.0.

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

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 3.

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.

More information

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.

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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).

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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.

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Identifiers.org

MIRIAM Unique Resource Identifiers allow one to uniquely and unambiguously identify an entity in a stable and perennial manner. MIRIAM Registry is 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.

KiSAO

The Kinetic Simulation Algorithm Ontology (KiSAO) describes existing algorithms and their inter-relationships through their characteristics and parameters., 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.

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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

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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.