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. Author manuscript; available in PMC: 2017 May 31.
Published in final edited form as: J Integr Bioinform. 2016 Dec 18;13(3):290. doi: 10.2390/biecoll-jib-2016-290
General rules about this package
groups-10101 graphic file with name nihms859555ig4.jpg To conform to the Groups package specification for SBML Level 3 Version 1, an SBML document must declare “http://www.sbml.org/sbml/level3/version1/groups/version1” as the XMLNamespaceto use for elements of this package. (Reference: SBML Level 3 Package specification for Groups, Version 1 Section 3.1 on page 5.)
groups-10102 graphic file with name nihms859555ig4.jpg Wherever they appear in an SBML document, elements and attributes from the Groups package must use the “http://www.sbml.org/sbml/level3/version1/groups/version1” names-pace, declaring so either explicitly or implicitly. (Reference: SBML Level 3 Package specification for Groups, Version 1 Section 3.1 on page 5.)
General rules about identifiers
groups-10301 graphic file with name nihms859555ig4.jpg (Extends validation rule #10301 in the SBML Level 3 Version 1 Core specification.) Within a Model object, the values of the attributes id and groups:id on every instance of the following classes of objects must be unique across the set of all id and groups:id attribute values of all such objects in a model: the Model itself, plus all contained FunctionDefinition, Compartment, Species, Reaction, SpeciesReference, ModifierSpeciesReference, Event, and Parameter objects, plus the Group, ListOfMembers, and Member objects defined by the Groups package, plus any objects defined by any other package with package:id attributes defined as falling in the ’SId’ namespace. (References: SBML Level 3 Package Specification for Groups, Version 1, Section 3.3 on page 5.)
groups-10302 graphic file with name nihms859555ig4.jpg The value of a groups:id must conform to the syntax of the SBML data type SId (Reference: SBML Level 3 Package specification for Groups, Version 1 Section 3.3.1 on page 6.)
Rules for the extended SBML class
groups-20101 graphic file with name nihms859555ig4.jpg In all SBML documents using the Groups package, the SBML object must have the groups:-required attribute. (Reference: SBML Level 3 Version 1 Core, Section 4.1.2.)
groups-20102 graphic file with name nihms859555ig4.jpg The value of attribute groups:required on the SBML object must be of data type boolean. (Reference: SBML Level 3 Version 1 Core, Section 4.1.2.)
groups-20103 graphic file with name nihms859555ig4.jpg The value of attribute groups:required on the SBML object must be set to “ false”. (Reference: SBML Level 3 Package specification for Groups, Version 1 Section 3.1 on page 5.)
Rules for extended Model object
groups-20201 graphic file with name nihms859555ig4.jpg A Model object may contain one and only one instance of the ListOfGroups element. No other elements from the SBML Level 3 Groups namespaces are permitted on a Model object. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.6 on page 10.)
groups-20202 graphic file with name nihms859555ig4.jpg The ListOfGroups subobject on a Model object is optional, but if present, this container object must not be empty. (Reference: SBML Level 3 Specification for Groups Version 1, Section 3.6 on page 10.)
groups-20203 graphic file with name nihms859555ig4.jpg Apart from the general notes and annotations subobjects permitted on all SBML objects, a ListOfGroups container object may only contain Group objects. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.6 on page 10.)
groups-20204 graphic file with name nihms859555ig4.jpg A ListOfGroups object may have the optional SBML Level 3 Core attributes metaid and sboTerm. No other attributes from the SBML Level 3 Core namespaces are permitted on a ListOfGroups object. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.6 on page 10.)
Rules for Group object
groups-20301 graphic file with name nihms859555ig4.jpg A Group object may have the optional SBML Level 3 Core attributes metaid and sboTerm. No other attributes from the SBML Level 3 Core namespaces are permitted on a Group. (Reference: SBML Level 3 Version 1 Core, Section 3.2.)
groups-20302 graphic file with name nihms859555ig4.jpg A Group object may have the optional SBML Level 3 Core subobjects for notes and annotations. No other elements from the SBML Level 3 Core namespaces are permitted on a Group. (Reference: SBML Level 3 Version 1 Core, Section 3.2.)
groups-20303 graphic file with name nihms859555ig4.jpg A Group object must have the required attribute groups:kind, and may have the optional attributes groups:id and groups:name. No other attributes from the SBML Level 3 Groups namespaces are permitted on a Group object. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.3 on page 5.)
groups-20304 graphic file with name nihms859555ig4.jpg A Group object may contain one and only one instance of the ListOfMembers element. No other elements from the SBML Level 3 Groups namespaces are permitted on a Group object. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.3 on page 5.)
groups-20305 graphic file with name nihms859555ig4.jpg The value of the attribute groups:kind of a Group object must conform to the syntax of SBML data type groupKind and may only take on the allowed values of groupKind defined in SBML; that is, the value must be one of the following: ’classification’, ’partonomy’ or ’collection’. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.3 on page 5.)
groups-20306 graphic file with name nihms859555ig4.jpg The attribute groups:name on a Group must have a value of data type string. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.3 on page 5.)
groups-20307 graphic file with name nihms859555ig4.jpg The ListOfMembers subobject on a Group object is optional, but if present, this container object must not be empty. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.3 on page 5.)
groups-20308 graphic file with name nihms859555ig4.jpg Apart from the general notes and annotations subobjects permitted on all SBML objects, a ListOfMembers container object may only contain Member objects. (Reference: SBML Level 3 Version 1 Core, Section 3.2.)
groups-20309 graphic file with name nihms859555ig4.jpg A ListOfMembers object may have the optional SBML Level 3 Core attributes metaid and sboTerm. No other attributes from the SBML Level 3 Core namespaces are permitted on a ListOfMembers object. (Reference: SBML Level 3 Version 1 Core, Section 3.2.)
groups-20310 graphic file with name nihms859555ig4.jpg A ListOfMembers object may have the optional attributes groups:id and groups:name. No other attributes from the SBML Level 3 Groups namespaces are permitted on a ListOfMembers object. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.4 on page 7.)
groups-20311 graphic file with name nihms859555ig4.jpg The attribute groups:name on a ListOfMembers must have a value of data type string. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.4 on page 7.)
groups-20312 graphic file with name nihms859555ig5.jpg If ListOfMembers objects from different Group objects contain Member elements that reference the same SBase object, the sboterm and any child Notes or Annotation elements set for those ListOfMembers should be consistent, as they all should apply to the same referenced object. (References: SBML Level 3 Package Specification for Groups, Version 1, Section 3.4 on page 7.)
groups-20313 graphic file with name nihms859555ig4.jpg Member references may not be circular: no Member’s idRef or metaIdRef may reference itself, its parent ListOfMembers, nor its parent Group. If a Member references a Group or a ListOfMembers, the same restrictions apply to that subgroup’s children: they may not reference the Member, its parent ListOfMembers, nor its parent Group, and if any of those children reference a Group, the same restrictions apply to them, etc. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.5.4 on page 8.)
Rules for Member object
groups-20401 graphic file with name nihms859555ig4.jpg A Member object may have the optional SBML Level 3 Core attributes metaid and sboTerm. No other attributes from the SBML Level 3 Core namespaces are permitted on a Member. (Reference: SBML Level 3 Version 1 Core, Section 3.2.)
groups-20402 graphic file with name nihms859555ig4.jpg A Member object may have the optional SBML Level 3 Core subobjects for notes and annotations. No other elements from the SBML Level 3 Core namespaces are permitted on a Member. (Reference: SBML Level 3 Version 1 Core, Section 3.2.)
groups-20403 graphic file with name nihms859555ig4.jpg A Member object may have the optional attributes groups:id and groups:name and must have a value for one (and exactly one) of the attributes groups:idRef and groups:metaIdRef. No other attributes from the SBML Level 3 Groups namespaces are permitted on a Member object. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.5 on page 7.)
groups-20404 graphic file with name nihms859555ig4.jpg The attribute groups:name on a Member must have a value of data type string. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.5 on page 7.)
groups-20405 graphic file with name nihms859555ig4.jpg The value of the attribute groups:idRef of a Member object must be the identifier of an existing SBase object defined in the enclosing Model object. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.5 on page 7.)
groups-20406 graphic file with name nihms859555ig4.jpg The value of the attribute groups:metaIdRef of a Member object must be the metaid of an existing SBase object defined in the enclosing Model object. (Reference: SBML Level 3 Package specification for Groups, Version 1, Section 3.5 on page 7.)
groups-20407 graphic file with name nihms859555ig4.jpg The value of a groups:idRef attribute on Member objects must conform to the syntax of the SBML data type SIdRef. (References: SBML Level 3 Package Specification for Groups, Version 1, Section 3.5 on page 7.)
groups-20408 graphic file with name nihms859555ig4.jpg The value of a groups:metaIdRef attribute on Member objects must conform to the syntax of the SBML data type IDREF. (References:SBML Level 3 Package Specification for Groups, Version 1, Section 3.5 on page 7.)