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<div class="breadcrumb"><a href="/">Home</a> › Standards covered by or related to COMBINE activities </div> <h1 class="title">Standards covered by or related to COMBINE activities </h1>
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<p>One of the major goals of COMBINE is to improve the interoperability of existing standards, and to foster or support fledging efforts aimed at filling gaps or new needs. Below are listed some of the major community standard representation formats covered by or related to COMBINE activity. </p> <h1><span class="mw-headline" id="COMBINE_standards">COMBINE standards</span></h1> <p>The following standardization activities are open community efforts. The standards are described in freely available specifications, and associated tools (XML schemas, UML diagrams etc.). They are piloted by democratically elected editorial boards, sometimes assisted by scientific committees. A decent software support exist, including API implementations. The development is supported by central teams and/or funding sources. The different formats try to avoid overlapping but rather strive to interoperate, via interconversion, cross-linking, use of common metadata layers etc. </p><p>A <a class="freelinking external" href="http://old_co.mbine.org/standards/specifications"> comprehensive list of specification documents</a> is also available, following the COMBINE <a href="/standards/specification-infrastructure" class="freelinking"> specification infrastructure</a>. </p> <table cellpadding="10"> <tr> <td style="background-color:#1D636A;color:white;font-size:x-large;font-weight:bold;"> BioPAX </td></tr> <tr> <td style="background-color:#EFEFEF;color:black;"> <a rel="nofollow" class="external text" href="http://www.biopax.org">BioPAX</a> is a standard language that aims to enable integration, exchange and analysis of biological pathway data. It is expressed in <a rel="nofollow" class="external text" href="http://www.w3.org/2004/OWL/">OWL</a>. <p>The last specification is <a rel="nofollow" class="external text" href="http://www.biopax.org/release/biopax-level3-documentation.pdf">BioPAX Level 3</a>. </p><p>BioPAX development is <a rel="nofollow" class="external text" href="http://www.biopax.org/mediawiki/index.php/BioPAX_Governance">coordinated</a> by an elected editorial board and a Scientific Advisory Board. </p><p>BioPAX is supported by <a rel="nofollow" class="external text" href="http://biopax.sourceforge.net/mediawiki/index.php?title=Category:SOFTWARE">many pathway database or processing tools</a>. An API is available to help implementing support: <a rel="nofollow" class="external text" href="http://www.biopax.org/mediawiki/index.php/Paxtools">Paxtools</a> </p><p><a class="freelinking external" href="http://old_co.mbine.org/standards/biopax">More information</a> </p> </td></tr></table> <table cellpadding="10"> <tr> <td style="background-color:#1D636A;color:white;"> <img src="/system/files/LogoWhiteBackBlackLetters-75.png" alt="SBGN" height="40"/> </td></tr> <tr> <td style="background-color:#EFEFEF;color:black;"> The <a rel="nofollow" class="external text" href="http://sbgn.org/">Systems Biology Graphical Notation (SBGN)</a>, 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. <p>The <a rel="nofollow" class="external text" href="http://sbgn.github.io/sbgn/specifications">last specifications</a> are SBGN PD Level 1 Version 2.0, SBGN ER Level 1 Version 2 and SBGN AF Level 1 Version 1.2. </p><p>SBGN development is <a rel="nofollow" class="external text" href="http://sbgn.github.io/sbgn/about">coordinated</a> by an elected editorial board and a Scientific Committee. </p><p>Several <a rel="nofollow" class="external text" href="https://sbgn.github.io/software">data resources and software claim support for SBGN</a>. An API is available to help implementing support: <a rel="nofollow" class="external text" href="https://github.com/sbgn/sbgn/wiki/LibSBGN">libSBGN</a> </p><p><a class="freelinking external" href="http://old_co.mbine.org/standards/sbgn">More information</a> </p> </td></tr></table> <table cellpadding="10"> <tr> <td style="background-color:#1D636A;color:white;font-size:x-large;font-weight:bold;"> <img src="/system/files/Official-sbml-supported-70.png" alt="SBML" height="40"/> </td></tr> <tr> <td style="background-color:#EFEFEF;color:black;"> The <a rel="nofollow" class="external text" href="http://sbml.org">Systems Biology Markup Language (SBML)</a> is a computer-readable <a rel="nofollow" class="external text" href="http://www.w3.org/XML/">XML format</a> for representing models of biological processes. SBML is suitable for, but not limited to, models using a process description approach. <p>The latest stable specification is <a rel="nofollow" class="external text" href="http://sbml.org/Documents/Specifications">Level 3 Version 2 Core</a>. </p><p>SBML development is <a rel="nofollow" class="external text" href="http://sbml.org/About">coordinated</a> by an elected editorial board and central developer team. </p><p>Over 250 software systems known to support SBML can be found in the <a rel="nofollow" class="external text" href="http://sbml.org/SBML_Software_Guide">SBML software guide</a>. APIs are available to help implementing support: <a rel="nofollow" class="external text" href="http://sbml.org/Software/libSBML">libSBML</a> in C++ and <a rel="nofollow" class="external text" href="http://sbml.org/Software/JSBML">JSBML</a> in Java. </p><p><a class="freelinking external" href="http://old_co.mbine.org/standards/sbml">More information</a> </p> </td></tr></table> <table cellpadding="10"> <tr> <td style="background-color:#1D636A;color:white;font-size:x-large;font-weight:bold;"> <img src="/system/files/SED-ML-border_1.png" alt="SED-ML" height="40"/> </td></tr> <tr> <td style="background-color:#EFEFEF;color:black;"> <p>The <a rel="nofollow" class="external text" href="http://sed-ml.org">Simulation Experiment Description Markup Language (SED-ML)</a> 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. </p><p>The latest stable specification is <a rel="nofollow" class="external text" href="http://old_co.mbine.org/specifications/sed-ml.level-1.version-3.pdf">Level 1 Version 3</a>. </p><p>SED-ML development is coordinated by an <a rel="nofollow" class="external text" href="http://sed-ml.org/about.html">elected editorial board</a>. </p><p>APIs are available to help implementing support: <a rel="nofollow" class="external text" href="http://libsedml.sourceforge.net/libSedML/Welcome.html">libSedML</a> in C#, <a rel="nofollow" class="external text" href="https://github.com/fbergmann/libSEDML">libSEDML</a> in C++ with swig bindings for python, java, perl, R and ruby, and <a rel="nofollow" class="external text" href="http://sourceforge.net/projects/jlibsedml/">jlibsedml</a> in Java. </p><p><a class="freelinking external" href="http://old_co.mbine.org/standards/sed-ml">More information</a> </p> </td></tr></table> <table cellpadding="10"> <tr> <td style="background-color:#1D636A;color:white;font-size:x-large;font-weight:bold;"> <img src="/system/files/logo-cellml.png" alt="CellML" height="40"/> </td></tr> <tr> <td style="background-color:#EFEFEF;color:black;"> <p>The <a rel="nofollow" class="external text" href="http://www.cellml.org">CellML language</a> 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. </p><p>The latest stable specification is <a rel="nofollow" class="external text" href="http://www.cellml.org/specifications/cellml_1.1">Version 1.1</a>. </p><p>CellML development is coordinated by an <a rel="nofollow" class="external text" href="http://www.cellml.org/community/editorial_board">elected editorial board</a>. </p><p>APIs are available to help implementing support: <a rel="nofollow" class="external text" href="http://cellml-api.sourceforge.net/">CellML API</a> in C. </p><p><a class="freelinking external" href="http://old_co.mbine.org/standards/CellML">More information</a> </p> </td></tr></table> <table cellpadding="10"> <tr> <td style="background-color:#1D636A;color:white;font-size:x-large;font-weight:bold;"> <img src="/system/files/sbol2017_1.png" alt="SBOLData" height="40"/> </td></tr> <tr> <td style="background-color:#EFEFEF;color:black;"> <p>The <a rel="nofollow" class="external text" href="http://www.sbolstandard.org/">Synthetic Biology Open Language Data (SBOL Data)</a> is a language for the description and the exchange of synthetic biological parts, devices and systems. </p><p>The latest stable specification of SBOL Data is <a rel="nofollow" class="external text" href="http://old_co.mbine.org/specifications/sbol.version-2.2.0.pdf">2.2.0</a>. </p><p>SBOL Data is developed by the <a rel="nofollow" class="external text" href="http://sbolstandard.org/developers/">SBOL Developers Group</a>. The development is coordinated by an <a rel="nofollow" class="external text" href="http://sbolstandard.org/gov/">editorial board and the SBOL Chair</a>. </p><p>SBOL data is supported by many software tools. <a rel="nofollow" class="external text" href="http://sbolstandard.org/software/libraries/">APIs</a> are available to help implement the support of this data standard. </p><p><a class="freelinking external" href="http://old_co.mbine.org/standards/sbol">More information</a> </p> </td></tr></table> <table cellpadding="10"> <tr> <td style="background-color:#1D636A;color:white;font-size:x-large;font-weight:bold;"> <img src="/system/files/sbol_visual_0.png" alt="SBOLVisual" height="40"/> </td></tr> <tr> <td style="background-color:#EFEFEF;color:black;"> <p>The <a rel="nofollow" class="external text" href="http://sbolstandard.org/visual/">Synthetic Open Language Visual (SBOL Visual) </a> is an open-source graphical notation that uses schematic “glyphs” to specify genetic parts, devices, modules, and systems. </p><p>The latest stable specification of SBOL Visual is <a rel="nofollow" class="external text" href="http://sbolstandard.org/wp-content/uploads/2017/10/SBOLVisual_Specification_2_0_0.pdf">2.0.0</a>. </p><p>SBOL is developed by the <a rel="nofollow" class="external text" href="http://sbolstandard.org/developers/">SBOL Developers Group</a> and <a rel="nofollow" class="external text" href="http://sbolstandard.org/visual-2/">SBOL Visual Group</a>. The development is coordinated by an <a rel="nofollow" class="external text" href="http://sbolstandard.org/gov/">editorial board and the SBOL Chair</a>. </p><p>SBOL Visual is supported by many <a rel="nofollow" class="external text" href="http://sbolstandard.org/software/tools/">software tools</a>. </p><p><a class="freelinking external" href="http://old_co.mbine.org/standards/sbolVisual">More information</a> </p> </td></tr></table> <p><br /> </p> <table cellpadding="10"> <tr> <td style="background-color:#1D636A;color:white;font-size:x-large;font-weight:bold;"> <img src="/system/files/neuroml.png" alt="NeuroML" height="40"/> </td></tr> <tr> <td style="background-color:#EFEFEF;color:black;"> <p>The <a rel="nofollow" class="external text" href="http://www.neuroml.org/">NeuroML</a> 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. </p><p>The latest stable specification of NeuroML is <a rel="nofollow" class="external text" href="https://www.neuroml.org/getneuroml">version 2 beta 4</a>. </p><p>NeuroML development is coordinated by the <a rel="nofollow" class="external text" href="https://www.neuroml.org/editors">NeuroML Editorial Board</a>. </p><p>NeuroML is supported by many software tools and databases, see <a rel="nofollow" class="external text" href="https://www.neuroml.org/tool_support">here</a>. </p><p><a class="freelinking external" href="http://old_co.mbine.org/standards/neuroml">More information</a> </p> </td></tr></table> <p><br /> </p> <h1><span class="mw-headline" id="Associated_standardization_efforts">Associated standardization efforts</span></h1> <p>The standardisation efforts described below are not community-developed representation formats. However, they are tools to add a layer of semantics that facilitate the use, the interoperability or enhance the usefulness of COMBINE representation formats. </p> <h2><span class="mw-headline" id=".5B.5BFile:COMBINEArchive.png.7C_alt.3D.22COMBINE_Archive.22_height.3D.2240.22.5D.5D_COMBINE_Archive"><img src="/system/files/COMBINEArchive.png" alt="COMBINE Archive" height="40"/> COMBINE Archive</span></h2> <p>A <a rel="nofollow" class="external text" href="http://old_co.mbine.org/standards/omex">COMBINE archive</a> 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 <a rel="nofollow" class="external text" href="http://old_co.mbine.org/standards/omex">Open Modeling EXchange format (OMEX)</a>. </p> <h2><span class="mw-headline" id=".5B.5BFile:OMEXmetadataIconMetaBracketsVerySmall.png.7C_alt.3D.22COMBINE_Archive_Metadata.22_height.3D.2240.22.5D.5D_COMBINE_Archive_Metadata"><img src="/system/files/OMEXmetadataIconMetaBracketsVerySmall.png" alt="COMBINE Archive Metadata" height="40"/> COMBINE Archive Metadata</span></h2> <p><a rel="nofollow" class="external text" href="http://old_co.mbine.org/standards/omex-metadata">COMBINE archive metadata</a> provides a harmonized, community-driven approach for annotating a variety of standardized model and data representation formats within a COMBINE archive. </p> <h2><span class="mw-headline" id=".5B.5BFile:identifiers-org_logo-new-whiteBg.png_.7C_alt.3D.22Identifiers.org.22_height.3D.2240.22.5D.5D_Identifiers.org_URIs"><img src="/system/files/identifiers-org_logo-new-whiteBg.png" alt="Identifiers.org" height="40"/> Identifiers.org URIs</span></h2> <p><a rel="nofollow" class="external text" href="http://old_co.mbine.org/standards/miriam_uris">MIRIAM Unique Resource Identifiers</a> allow one to uniquely and unambiguously identify an entity in a stable and perennial manner. <a rel="nofollow" class="external text" href="http://old_co.mbine.org/standards/miriam#MIRIAM_Registry_and_Identifiers.org">MIRIAM Registry</a> is a set of services and resources that provide support for generating, interpreting and resolving MIRIAM URIs. Through the <a rel="nofollow" class="external text" href="http://identifiers.org/">Identifiers.org</a> technology, MIRIAM URIs can be dereferenced in a flexible and robust way. </p><p>MIRIAM URIs are used by SBML, SED-ML, CellML and BioPAX controlled annotation schemes. </p> <h2><span class="mw-headline" id=".5B.5BFile:sbo150x100.png_.7C_alt.3D.22SBO.22_height.3D.2240.22.5D.5D_Systems_Biology_Ontology"><img src="/system/files/sbo150x100.png" alt="SBO" height="40"/> Systems Biology Ontology</span></h2> <p>The <a rel="nofollow" class="external text" href="http://old_co.mbine.org/standards/sbo">Systems Biology Ontology (SBO)</a> is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. </p><p>Each element of an SBML file carries an optional attribute sboTerm which value must be a term from SBO. </p><p>Each symbol of SBGN is associated with an SBO term. </p> <h2><span class="mw-headline" id="Kinetic_Simulation_Algorithm_Ontology">Kinetic Simulation Algorithm Ontology</span></h2> <p>The <a rel="nofollow" class="external text" href="http://old_co.mbine.org/standards/kisao">Kinetic Simulation Algorithm Ontology (KiSAO)</a> describes existing algorithms and their inter-relationships through their characteristics and parameters. </p><p>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. </p> <h2><span class="mw-headline" id="BioModels.net_qualifiers">BioModels.net qualifiers</span></h2> <p><a href="/standards/qualifiers" class="freelinking"> BioModels.net qualifiers</a> 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. </p> <h1><span class="mw-headline" id="Related_standardization_efforts">Related standardization efforts</span></h1> <p>The following standardization efforts are of interest for COMBINE, either as candidate standards, or similar efforts in different domains. </p> <h2><span class="mw-headline" id="Computational_Neuroscience_Ontology">Computational Neuroscience Ontology</span></h2> <p>The <a rel="nofollow" class="external text" href="https://github.com/INCF/Computational-Neurosciences-Ontology--C.N.O.-">Computational Neuroscience Ontology (CNO)</a> is a controlled vocabulary composed of classes representing general concepts related to computational neuroscience. <a rel="nofollow" class="external text" href="http://www.biomedcentral.com/1471-2202/13/S1/P149">More ...</a> </p> <h2><span class="mw-headline" id="FieldML">FieldML</span></h2> <p><a rel="nofollow" class="external text" href="http://www.fieldml.org/">FieldML</a>'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. </p> <h2><span class="mw-headline" id=".5B.5BFile:fROG_analysis_200x95.png.7C_alt.3D.22FROG.22_height.3D.2240.22.5D.5D_FROG"><img src="/system/files/FROG_analysis_200x95_0.png" alt="FROG" height="40"/> FROG</span></h2> <p><a rel="nofollow" class="external text" href="https://www.ebi.ac.uk/biomodels/curation/fbc">FROG</a> analysis - a community standard to foster reproducibility and curation of constraint-based models. FROG provides guidelines, best practices, and a set of standardized FBA analyses to assess reproducibility and curation efforts. </p> <h2><span class="mw-headline" id="FSK-ML">FSK-ML</span></h2> <p><a rel="nofollow" class="external text" href="https://foodrisklabs.bfr.bund.de/fsk-ml-food-safety-knowledge-markup-language/">FSK-ML</a>'s (Food Safety Knowledge Markup Language) aims at encoding experimental data and mathematical models from the domain of predictive microbial modelling (and beyond) in a software independent manner. An FSK-ML file is an <a rel="nofollow" class="external text" href="http://old_co.mbine.org/standards/omex">OMEX</a> container, as the COMBINE Archive, and re-use other COMBINE standards to store models and simulations. A former version of the standard was the <a rel="nofollow" class="external text" href="https://sourceforge.net/projects/microbialmodelingexchange/">PMF-ML</a>, and OpenML for Predictive Modelling in Food. </p> <h2><span class="mw-headline" id="GPML">GPML</span></h2> <p><a rel="nofollow" class="external text" href="http://www.pathvisio.org/wiki/EverythingGpml">GPML</a> (GenMAPP Pathway Markup Language) is an XML-based format to define a pathway consisting of purely graphical elements (such as lines and shapes) or graphical elements with added biological information (such as genes, proteins and datanodes). </p> <h2><span class="mw-headline" id="MAMO">MAMO</span></h2> <p>The <a href="/standards/MAMO" class="freelinking"> mathematical modelling ontology</a> (MAMO) is an ontology describing and classifying the mathematical models used in the life sciences (for the time being). MAMO provides the types of models, the variables they use, the readout to expect and other relevant features. </p><p><br /> </p> <h2><span class="mw-headline" id="NineML">NineML</span></h2> <p>The <a rel="nofollow" class="external text" href="http://software.incf.org/software/nineml">Network Interchange for Neuroscience Modeling Language (NineML)</a> - is a language developed by the <a rel="nofollow" class="external text" href="http://www.incf.org/">International Neuroinformatics Coordinating Facility (INCF)</a> and designed for the description of large networks of spiking neurons. </p> <h2><span class="mw-headline" id="NuML">NuML</span></h2> <p>The <a rel="nofollow" class="external text" href="http://code.google.com/p/numl/">Numerical Markup Language (NuML)</a> (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 <a rel="nofollow" class="external text" href="http://www.comp-sys-bio.org/tiki-index.php?page=SBRML">Systems Biology Results Markup Language (SBRML)</a>. </p> <h2><span class="mw-headline" id=".5B.5BFile:PEtab2.png.7C_alt.3D.22PEtab.22_height.3D.2240.22.5D.5D"><img src="/system/files/PEtab2.png" alt="PEtab" height="40"/></span></h2> <p><a rel="nofollow" class="external text" href="https://github.com/PEtab-dev/PEtab">PEtab</a> is an SBML and TSV based data format for parameter estimation problems in systems biology. </p><p><br /> </p> <h2><span class="mw-headline" id=".5B.5BFile:PharmML.gif_.7C_alt.3D.22PharmML.22_height.3D.2240.22.5D.5D"><img src="/system/files/PharmML.gif" alt="PharmML" height="40"/></span></h2> <p>The <a rel="nofollow" class="external text" href="http://pharmml.org">Pharmacometrics Markup Language</a> is an exchange format for encoding of models, associated tasks and their annotation as used in pharmacometrics. PharmML is developed by the <a rel="nofollow" class="external text" href="http://ddmore.eu">DDMoRe consortium</a>, an <a rel="nofollow" class="external text" href="http://www.imi.europa.eu/">European Innovative Medicines Initiative (IMI)</a> project. </p> <h2><span class="mw-headline" id="PSI-MI">PSI-MI</span></h2> <p>The <a rel="nofollow" class="external text" href="http://www.psidev.info/index.php?q=node/60">Proteomics Standards Initiative Molecular Interaction XML Format</a> is a a data exchange format for molecular interactions developed by the <a rel="nofollow" class="external text" href="http://www.psidev.info/">the HUPO Proteomics Standards Initiative</a> </p> <h2><span class="mw-headline" id=".5B.5BFile:Spineml_logo_large.png_.7C_alt.3D.22SpineML.22_height.3D.2240.22.5D.5D"><img src="/system/files/Spineml_logo_large.png" alt="SpineML" height="40"/></span></h2> <p>The <a rel="nofollow" class="external text" href="http://bimpa.group.shef.ac.uk/SpineML/index.php/Home">Spiking Neural Mark-up Language (SpineML)</a> is a declarative XML based model description language for large scale neural network models. It is partially based upon on the <a rel="nofollow" class="external text" href="http://software.incf.org/software/nineml">INCF NineML</a>. </p> <h2><span class="mw-headline" id=".5B.5BFile:teddy150x100.png_.7C_alt.3D.22TEDDY.22_height.3D.2240.22.5D.5D"><img src="/system/files/teddy150x100_0.png" alt="TEDDY" height="40"/></span></h2> <p>The <a href="/standards/TEDDY" class="freelinking"> Terminology for the Description of Dynamics</a> 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. </p> <hr /> <p><img src="/system/files/FAIRsharing-sdp_7.png" alt="FAIRsharing" height="80"/> </p><p>More information about standards used to share data in life sciences can be found at <a rel="nofollow" class="external text" href="https://fairsharing.org/">FAIRsharing</a>. 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 <a rel="nofollow" class="external text" href="https://fairsharing.org/search/?q=systems+biology&selected_facets=expanded_onto_disciplines_exact:Systems%20Biology">many Systems Biology resources</a>. </p> <!-- NewPP limit report Cached time: 20220802140938 Cache expiry: 86400 Dynamic content: false CPU time usage: 0.060 seconds Real time usage: 0.060 seconds Preprocessor visited node count: 323/1000000 Preprocessor generated node count: 692/1000000 Post‐expand include size: 0/2097152 bytes Template argument size: 0/2097152 bytes Highest expansion depth: 3/40 Expensive parser function count: 0/100 --> <!-- Transclusion expansion time report (%,ms,calls,template) 100.00% 0.000 1 - -total --> <table id="attachments" class="sticky-enabled">
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