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. Author manuscript; available in PMC: 2017 May 31.
Published in final edited form as: J Integr Bioinform. 2015 Sep 4;12(2):268. doi: 10.2390/biecoll-jib-2015-268
General rules about this package
comp-10101 graphic file with name nihms859652ig3.jpg To conform to Version 1 of the Hierarchical Model Composition package specification for SBML Level 3, an SBML document must declare the use of the following XML Namespace: “http://www.sbml.org/sbml/level3/version1/comp/version1”. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.1 on page 11.)
comp-10102 graphic file with name nihms859652ig3.jpg Wherever they appear in an SBML document, elements and attributes from the Hierarchical Model Composition package must be declared either implicitly or explicitly to be in the XML namespace “http://www.sbml.org/sbml/level3/version1/comp/version1”. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.1 on page 11.)
General rules about identifiers
comp-10301 graphic file with name nihms859652ig3.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 comp:id on every instance of the following classes of objects must be unique across the set of all id and comp: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 Submodel and Deletion objects defined by the Hierarchical Model Composition 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 Hierarchical Model Composition, Version 1, Section 3.9 on page 32.)
comp-10302 graphic file with name nihms859652ig3.jpg The values of the attributes id and comp:id on every instance of all Model and ExternalModelDefinition objects must be unique across the set of all id and comp:id attribute values of such objects in the SBML document to which they belong. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.9 on page 32.)
comp-10303 graphic file with name nihms859652ig3.jpg Within a Model object inside an SBML document, the value of the attribute comp:id on every instance of a Port object must be unique across the set of all comp:id attribute values of all such objects in the model. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.9 on page 32.)
comp-10304 graphic file with name nihms859652ig3.jpg The value of a comp:id attribute must always conform to the syntax of the SBML data type SId. (References: SBML Level 3 Version 1 Core, Section 3.1.7.)
comp-10308 graphic file with name nihms859652ig3.jpg The value of a comp:submodelRef attribute on ReplacedElement and ReplacedBy objects must always conform to the syntax of the SBML data type SId. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.2 on page 23.)
comp-10309 graphic file with name nihms859652ig3.jpg The value of a comp:deletion attribute on a ReplacedElement object must always conform to the syntax of the SBML data type SId. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.2 on page 23.)
comp-10310 graphic file with name nihms859652ig3.jpg The value of a comp:conversionFactor attribute on a ReplacedElement object must always conform to the syntax of the SBML data type SId. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.2 on page 23.)
comp-10311 graphic file with name nihms859652ig3.jpg The value of a comp:name attribute must always conform to the syntax of type string. (References: SBML Level 3 Version 1 Core, Section 3.1.1.)
General Rules for Units
comp-10501 graphic file with name nihms859652ig4.jpg If one element replaces another, whether it is the target of a ReplacedBy element, or whether it has a child ReplacedElement, the units of the replaced element, multiplied by the units of any applicable conversion factor, should equal the units of the replacement element. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.5 on page 24.)
Rules for the extended SBase abstract class
comp-20101 graphic file with name nihms859652ig3.jpg Any object derived from the extended SBase class (defined in the Hierarchical Model Composition package) may contain at most one instance of a ListOfReplacedElements subobject. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6 on page 20.)
comp-20102 graphic file with name nihms859652ig3.jpg Apart from the general notes and annotation subobjects permitted on all SBML objects, a ListOfReplacedElements container object may only contain ReplacedElement objects. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6 on page 20.)
comp-20103 graphic file with name nihms859652ig3.jpg A ListOfReplacedElements object may have the optional attributes metaid and sboTerm defined by SBML Level 3 Core. No other attributes from the SBML Level 3 Core namespace or the Hierarchical Model Composition namespace are permitted on a ListOfReplacedElements object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6 on page 20.)
comp-20104 graphic file with name nihms859652ig3.jpg The ListOfReplacedElements in an SBase object is optional, but if present, must not be empty. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6 on page 20.)
comp-20105 graphic file with name nihms859652ig3.jpg Any object derived from the extended SBase class (defined in the Hierarchical Model Composition package) may contain at most one instance of a ReplacedBy subobject. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6 on page 20.)
Rules for the extended SBML class
comp-20201 graphic file with name nihms859652ig3.jpg In all SBML documents using the Hierarchical Model Composition package, the SBML object must include a value for the attribute comp:required attribute. (References: SBML Level 3 Version 1 Core, Section 4.1.2.)
comp-20202 graphic file with name nihms859652ig3.jpg The value of attribute comp:required on the SBML object must be of the data type boolean. (References: SBML Level 3 Version 1 Core, Section 4.1.2.)
comp-20203 graphic file with name nihms859652ig3.jpg (Rule removed because of a change in the interpretation of the required attribute by the SBML Editors.)
comp-20204 graphic file with name nihms859652ig3.jpg (Rule removed because of a change in the interpretation of the required attribute by the SBML Editors.)
comp-20205 graphic file with name nihms859652ig3.jpg There may be at most one instance of the ListOfModelDefinitions within an SBML object that uses the SBML Level 3 Hierarchical Model Composition package. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3 on page 12.)
comp-20206 graphic file with name nihms859652ig3.jpg The various ListOf subobjects within an SBML object are optional, but if present, these container objects must not be empty. Specifically, if any of the following classes of objects is present within the SBML object, it must not be empty: ListOfModelDefinitions and ListOfExternalModelDefinitions. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3 on page 12.)
comp-20207 graphic file with name nihms859652ig3.jpg Apart from the general notes and annotation subobjects permitted on all SBML objects, a ListOfModelDefinitions container may only contain extended Model class objects. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3 on page 12.)
comp-20208 graphic file with name nihms859652ig3.jpg Apart from the general notes and annotation subobjects permitted on all SBML objects, a ListOfExternalModelDefinitions container may only contain ExternalModelDefinition objects. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3 on page 12.)
comp-20209 graphic file with name nihms859652ig3.jpg A ListOfModelDefinitions object may have the optional attributes metaid and sboTerm. No other attributes from the SBML Level 3 Core namespace or the Hierarchical Model Composition namespace are permitted on a ListOfModelDefinitions object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3 on page 12.)
comp-20210 graphic file with name nihms859652ig3.jpg A ListOfExternalModelDefinitions object may have the optional SBML core attributes metaid and sboTerm. No other attributes from the SBML Level 3 Core namespace or the Hierarchical Model Composition namespace are permitted on a ListOfExternalModelDefinitions object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3 on page 12.)
comp-20211 graphic file with name nihms859652ig3.jpg There may be at most one instance of the ListOfExternalModelDefinitions within an SBML object that uses the Hierarchical Model Composition package. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3 on page 12.)
comp-20212 graphic file with name nihms859652ig3.jpg The value of attribute comp:required on the SBML object must be set to “ true“”. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.1 on page 11.)
Rules for ExternalModelDefinition objects
comp-20301 graphic file with name nihms859652ig3.jpg An ExternalModelDefinition object may have the optional SBML Level 3 Core attributes metaid and sboTerm. No other attributes from the SBML Level 3 Core namespace are permitted on an ExternalModelDefinition. (References: SBML Level 3 Version 1 Core, Section 3.2.)
comp-20302 graphic file with name nihms859652ig3.jpg An ExternalModelDefinition object may have the optional SBML Level 3 Core subobjects for notes and annotation. No other subobjects from the SBML Level 3 Core namespace or the Hierarchical Model Composition namespace are permitted in an ExternalModelDefinition. (References: SBML Level 3 Version 1 Core, Section 3.2.)
comp-20303 graphic file with name nihms859652ig3.jpg An ExternalModelDefinition object must have the attributes comp:id and comp:source because they are required, and may have the optional attributes comp:name, comp:modelRef, and comp:md5. No other attributes from the Hierarchical Model Composition namespace are permitted on an ExternalModelDefinition object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3.2 on page 14.)
comp-20304 graphic file with name nihms859652ig3.jpg The value of the comp:source attribute on an ExternalModelDefinition object must reference an SBML Level 3 Version 1 document. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3.2 on page 14.)
comp-20305 graphic file with name nihms859652ig3.jpg The value of the comp:modelRef attribute on an ExternalModelDefinition object must be the value of an id attribute on a Model or ExternalModelDefinition object in the SBML document referenced by the comp:source attribute. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3.2 on page 14.)
comp-20306 graphic file with name nihms859652ig4.jpg The value of the comp:md5 attribute, if present on an ExternalModelDefinition object, should match the calculated MD5 checksum of the SBML document referenced by the comp:source attribute. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3.2 on page 14.)
comp-20307 graphic file with name nihms859652ig3.jpg The value of a comp:source attribute on an ExternalModelDefinition object must always conform to the syntax of the XML Schema 1.0 data type anyURI. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3.2 on page 14.)
comp-20308 graphic file with name nihms859652ig3.jpg The value of a comp:modelRef attribute on an ExternalModelDefinition object must always conform to the syntax of the SBML data type SId. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3.2 on page 14.)
comp-20309 graphic file with name nihms859652ig3.jpg The value of a comp:md5 attribute on an ExternalModelDefinition object must always conform to the syntax of type string. (References: SBML Level 3 Package Specification for Hierarchical Model Composition Package Version 1 Section 3.3.2 on page 14.)
comp-20310 graphic file with name nihms859652ig3.jpg An ExternalModelDefinition object must not reference an ExternalModelDefinition in a different SBML document that, in turn, refers back to the original ExternalModelDefinition object, whether directly or indirectly through a chain of ExternalModelDefinition objects. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.3.2 on page 14.)
Rules for extended Model objects
comp-20501 graphic file with name nihms859652ig3.jpg There may be at most one instance of each of the following kinds of objects within a Model object using Hierarchical Model Composition: ListOfSubmodels and ListOfPorts. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4 on page 15.)
comp-20502 graphic file with name nihms859652ig3.jpg The various ListOf subobjects with an Model object are optional, but if present, these container object must not be empty. Specifically, if any of the following classes of objects are present on the Model, it must not be empty: ListOfSubmodels and ListOfPorts. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4 on page 15.)
comp-20503 graphic file with name nihms859652ig3.jpg Apart from the general notes and annotation subobjects permitted on all SBML objects, a ListOfSubmodels container object may only contain Submodel objects. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4 on page 15.)
comp-20504 graphic file with name nihms859652ig3.jpg Apart from the general notes and annotation subobjects permitted on all SBML objects, a ListOfPorts container object may only contain Port objects. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4 on page 15.)
comp-20505 graphic file with name nihms859652ig3.jpg A ListOfSubmodels object may have the optional attributes metaid and sboTerm defined by SBML Level 3 Core. No other attributes from the SBML Level 3 Core namespace or the Hierarchical Model Composition namespace are permitted on a ListOfSubmodels object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4 on page 15.)
comp-20506 graphic file with name nihms859652ig3.jpg A ListOfPorts object may have the optional attributes metaid and sboTerm defined by SBML Level 3 Core. No other attributes from the SBML Level 3 Core namespace or the Hierarchical Model Composition namespace are permitted on a ListOfPorts object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4 on page 15.)
Rules for Submodel objects
comp-20601 graphic file with name nihms859652ig3.jpg A Submodel object may have the optional SBML Level 3 Core attributes metaid and sboTerm. No other attributes from the SBML Level 3 Core namespace are permitted on an Submodel object. (References: SBML Level 3 Version 1 Core, Section 3.2.)
comp-20602 graphic file with name nihms859652ig3.jpg An Submodel object may have the optional SBML Level 3 Core subobjects for notes and annotation. No other elements from the SBML Level 3 Core namespace are permitted on an Submodel object. (References: SBML Level 3 Version 1 Core, Section 3.2.)
comp-20603 graphic file with name nihms859652ig3.jpg There may be at most one ListOfDeletions container object within a Submodel object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5 on page 17.)
comp-20604 graphic file with name nihms859652ig3.jpg A ListOfDeletions container object within a Submodel object is optional, but if present, must not be empty. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5 on page 17.)
comp-20605 graphic file with name nihms859652ig3.jpg Apart from the general notes and annotation subobjects permitted on all SBML objects, a ListOfDeletions container object may only contain Deletion objects. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5 on page 17.)
comp-20606 graphic file with name nihms859652ig3.jpg A ListOfDeletions object may have the optional SBML core attributes metaid and sboTerm. No other attributes from the SBML Level 3 Core namespace or the comp namespace are permitted on a ListOfDeletions object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5 on page 17.)
comp-20607 graphic file with name nihms859652ig3.jpg A Submodel object must have the attributes comp:id and comp:modelRef because they are required, and may also have the optional attributes comp:name, comp:timeConversionFactor, and/or comp:extentConversionFactor. No other attributes from the Hierarchical Model Composition namespace are permitted on a Submodel object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5 on page 17.)
comp-20608 graphic file with name nihms859652ig3.jpg The value of a comp:modelRef attribute on a Submodel object must always conform to the syntax of the SBML data type SId. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.1 on page 18.)
comp-20613 graphic file with name nihms859652ig3.jpg The value of a comp:timeConversionFactorattribute on a Submodel object must always conform to the syntax of the SBML data type SId. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.1 on page 19.)
comp-20614 graphic file with name nihms859652ig3.jpg The value of a comp:extentConversionFactor attribute on a Submodel object must always conform to the syntax of the SBML data type SId. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.1 on page 19.)
comp-20615 graphic file with name nihms859652ig3.jpg The value of a comp:modelRef attribute on a Submodel must be the identifier of a Model or ExternalModelDefinition object in the same SBML object as the Submodel. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.1 on page 18.)
comp-20616 graphic file with name nihms859652ig3.jpg A Model object must not contain a Submodel which references that Model object itself. That is, the value of a comp:modelRef attribute on a Submodel must not be the value of the parent Model object’s id attribute. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.1 on page 18.)
comp-20617 graphic file with name nihms859652ig3.jpg A Model object must not contain a Submodel which references that Model indirectly. That is, the comp:modelRef attribute of a Submodel may not point to the id of a Model containing a Submodel object that references the original Model directly or indirectly through a chain of Model/Submodel pairs. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.1 on page 18.)
comp-20622 graphic file with name nihms859652ig3.jpg The value of a comp:timeConversionFactor attribute on a given Submodel object must be the identifier of a Parameter object defined in the same Model containing the Submodel. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.1 on page 19.)
comp-20623 graphic file with name nihms859652ig3.jpg The value of a comp:extentConversionFactor attribute on a given Submodel object must be the identifier of a Parameter object defined in the same Model containing the Submodel. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.1 on page 19.)
Rules for the SBaseRef object
comp-20701 graphic file with name nihms859652ig3.jpg The value of a comp:portRef attribute on an SBaseRef object must be the identifier of a Port object in the Model referenced by that SBaseRef. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.1 on page 27.)
comp-20702 graphic file with name nihms859652ig3.jpg The value of a comp:idRef attribute on an SBaseRef object must be the identifier of an object contained in (that is, within the SId namespace of ) the Model referenced by that SBaseRef. This includes objects with id attributes defined in packages other than SBML Level 3 Core or the Hierarchical Model Composition package. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.1 on page 27.)
comp-20703 graphic file with name nihms859652ig3.jpg The value of a comp:unitRef attribute on an SBaseRef object must be the identifier of a UnitDefinition object contained in the Model referenced by that SBaseRef. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.1 on page 27.)
comp-20704 graphic file with name nihms859652ig3.jpg The value of a comp:metaIdRef attribute on an SBaseRef object must be the value of a comp:metaid attribute on an element contained in the Model referenced by that SBaseRef. This includes elements with metaid attributes defined in packages other than SBML Level 3 Core or the Hierarchical Model Composition package. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.1 on page 27.)
comp-20705 graphic file with name nihms859652ig3.jpg If an SBaseRef object contains an SBaseRef child, the parent SBaseRef must point to a Submodel object, or a Port that itself points to a Submodel object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.2 on page 28.)
comp-20706 graphic file with name nihms859652ig3.jpg The value of a comp:portRef attribute on an SBaseRef object must always conform to the syntax of the SBML data type SId. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.1 on page 27.)
comp-20707 graphic file with name nihms859652ig3.jpg The value of a comp:idRef attribute on an SBaseRef object must always conform to the syntax of the SBML data type SId. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.1 on page 27.)
comp-20708 graphic file with name nihms859652ig3.jpg The value of a comp:unitRef attribute on an SBaseRef object must always conform to the syntax of the SBML data type UnitSId. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.1 on page 27.)
comp-20709 graphic file with name nihms859652ig3.jpg The value of a comp:metaIdRef attribute on an SBaseRef object must always conform to the syntax of the XML data type ID. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.1 on page 27.)
comp-20710 graphic file with name nihms859652ig3.jpg Apart from the general notes and annotation subobjects permitted on all SBML objects, an SBaseRef object may only contain a single SBaseRef child. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.2 on page 28.)
comp-20711 graphic file with name nihms859652ig4.jpg The ‘sbaseRef’ spelling of an SBaseRef child of an SBaseRef object is considered deprecated, and ‘sBaseRef’ should be used instead. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7.2 on page 29.)
comp-20712 graphic file with name nihms859652ig3.jpg An SBaseRef object must point to another object; that is, a SBaseRef object must always have a value for one of the attributes comp:portRef, comp:idRef, comp:unitRef, or comp:metaIdRef. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.7 on page 26.)
comp-20713 graphic file with name nihms859652ig3.jpg An SBaseRef object can only point to one other object; that is, a given SBaseRef object can only have a value for one of the attributes comp:portRef, comp:idRef, comp:unitRef, or comp:metaIdRef. No other attributes from the Hierarchical Model Composition namespace are permitted on an SBaseRef object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4.3 on page 16.)
comp-20714 graphic file with name nihms859652ig3.jpg Any one SBML object may only be referenced in one of the following ways: referenced by a single Port object; referenced by a single Deletion object; referenced by a single ReplacedElement; be the parent of a single ReplacedBy child; be referenced by one or more ReplacedBy objects; or be referenced by one or more ReplacedElement objects all using the deletion attribute. Essentially, once an object has been referenced in one of these ways it cannot be referenced again. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.5 on page 24.)
Rules for Port objects
comp-20801 graphic file with name nihms859652ig3.jpg A Port object must point to another object; that is, a Port object must always have a value for one of the attributes comp:idRef, comp:unitRef, or comp:metaIdRef. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4.3 on page 16.)
comp-20802 graphic file with name nihms859652ig3.jpg A Port object can only point to one other object; that is, a given Port object can only have a value for one of the attributes comp:idRef, comp:unitRef, or comp:metaIdRef. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4.3 on page 16.)
comp-20803 graphic file with name nihms859652ig3.jpg A Port object must have a value for the required attribute comp:id, and one, and only one, of the attributes comp:idRef, comp:unitRef, or comp:metaIdRef. It may also have the optional attribute comp:name. No other attributes from the Hierarchical Model Composition namespace are permitted on a Port object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4.3 on page 16.)
comp-20804 graphic file with name nihms859652ig3.jpg Port definitions must be unique; that is, no two Port objects in a given Model may reference the same object in that Model. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.4.3 on page 16.)
Rules for Deletion objects
comp-20901 graphic file with name nihms859652ig3.jpg A Deletion object must point to another object; that is, a Deletion object must have a value for one of the attributes comp:portRef, comp:idRef, comp:unitRef, or comp:metaIdRef. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.3 on page 20.)
comp-20902 graphic file with name nihms859652ig3.jpg A Deletion object can only point to one other object; that is, a given Deletion object can only have a value for one of the attributes comp:portRef, comp:idRef, comp:unitRef, or comp:metaIdRef. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.3 on page 20.)
comp-20903 graphic file with name nihms859652ig3.jpg A Deletion object must have a value for one, and only one, of the attributes comp:portRef, comp:idRef, comp:unitRef, or comp:metaIdRef. It may also have the optional attributes comp:id and comp:name. No other attributes from the Hierarchical Model Composition namespace are permitted on a Deletion object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.5.3 on page 20.)
Rules for ReplacedElement objects
comp-21001 graphic file with name nihms859652ig3.jpg A ReplacedElement object must point to another object; that is, a given ReplacedElement object must have a value for one of the following attributes: comp:portRef, comp:idRef, comp:unitRef, comp:metaIdRef, or comp:deletion. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.2 on page 21.)
comp-21002 graphic file with name nihms859652ig3.jpg A ReplacedElement object can only point to one target object; that is, a given ReplacedElement can only have a value for one of the following attributes: comp:portRef, comp:idRef, comp:unitRef, comp:metaIdRef, or comp:deletion. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.2 on page 21.)
comp-21003 graphic file with name nihms859652ig3.jpg A ReplacedElement object must have a value for the required attribute comp:submodelRef, and a value for one, and only one, of the following attributes: comp:portRef, comp:idRef, comp:unitRef, comp:metaIdRef, or comp:deletion. It may also have a value for the optional attribute comp:conversionFactor. No other attributes from the Hierarchical Model Composition namespace are permitted on a ReplacedElement object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.2 on page 21.)
comp-21004 graphic file with name nihms859652ig3.jpg The value of a comp:submodelRef attribute on a ReplacedElement object must be the identifier of a Submodel present in the ReplacedElement object’s parent Model. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.2 on page 23.)
comp-21005 graphic file with name nihms859652ig3.jpg The value of a comp:deletion attribute on a ReplacedElement object must be the identifier of a Deletion present in the ReplacedElement object’s parent Model. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.2 on page 23.)
comp-21006 graphic file with name nihms859652ig3.jpg The value of a comp:conversionFactor attribute on a ReplacedElement object must be the identifier of a Parameter present in the ReplacedElement object’s parent Model. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.2 on page 23.)
comp-21007 graphic file with name nihms859652ig3.jpg (Rule removed because it was a duplicate of 10308.)
comp-21008 graphic file with name nihms859652ig3.jpg (Rule removed because it was a duplicate of 10309.)
comp-21009 graphic file with name nihms859652ig3.jpg (Rule removed because it was a duplicate of 10310.)
comp-21010 graphic file with name nihms859652ig3.jpg No two ReplacedElement objects in the same Model may reference the same object unless that object is a Deletion. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.2 on page 21.)
Rules for ReplacedBy objects
comp-21101 graphic file with name nihms859652ig3.jpg A ReplacedBy object must point to another object; that is, a given ReplacedBy object must have a value for one of the following attributes: comp:portRef, comp:idRef, comp:unitRef, or comp:metaIdRef. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.4 on page 23.)
comp-21102 graphic file with name nihms859652ig3.jpg A ReplacedBy object can only point to one target object; that is, a given ReplacedBy can only have a value for one of the following attributes: comp:portRef, comp:idRef, comp:unitRef, or comp:metaIdRef. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.4 on page 23.)
comp-21103 graphic file with name nihms859652ig3.jpg A ReplacedBy object must have a value for the required attribute comp:submodelRef, and a value for one, and only one, of the following other attributes: comp:portRef, comp:idRef, comp:unitRef, or comp:metaIdRef. No other attributes from the Hierarchical Model Composition namespace are permitted on a ReplacedBy object. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.4 on page 23.)
comp-21104 graphic file with name nihms859652ig3.jpg The value of a comp:submodelRef attribute on a ReplacedBy object must be the identifier of a Submodel present in ReplacedBy object’s parent Model. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.4 on page 24.)
comp-21105 graphic file with name nihms859652ig3.jpg (Rule removed because it was a duplicate of 10308.)
General Rules for Replacements
comp-21201 graphic file with name nihms859652ig3.jpg If one element replaces another, whether it is the target of a ReplacedBy element, or whether it has a child ReplacedElement, the SBML class of the replacement element must match the SBML class of the replaced element, with two exceptions: an element of a derived class may replace an object of its base class (for base classes other than SBase), and any SBML class with mathematical meaning may replace a Parameter. A base class may not replace a derived class, however, nor may a Parameter replace some other SBML element with mathematical meaning. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.5 on page 24.)
comp-21202 graphic file with name nihms859652ig3.jpg If one element replaces another, whether it is the target of a ReplacedBy element, or whether it has a child ReplacedElement, if the replaced element has the id attribute set, the replacement element must also have the id attribute set. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.5 on page 24.)
comp-21203 graphic file with name nihms859652ig3.jpg If one element replaces another, whether it is the target of a ReplacedBy element, or whether it has a child ReplacedElement, if the replaced element has the metaid attribute set, the replacement element must also have the metaid attribute set. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.5 on page 24.)
comp-21204 graphic file with name nihms859652ig3.jpg If one element replaces another, whether it is the target of a ReplacedBy element, or whether it has a child ReplacedElement, if the replaced element has an identifier attribute from some other SBML package set, the replacement element must also have that same identifier attribute set. (References: SBML Level 3 Package Specification for Hierarchical Model Composition, Version 1, Section 3.6.5 on page 24.)