Link kinds¶
An element of a report references other elements, and is referenced by others. The inspector groups both directions by kind under "References" and "Referenced by", the tables link the referenced element directly.
compartment¶
The compartment a species or a qualitative species is located in, or a reaction takes place in.
Every species and every qualitative species names the compartment it is located in, and a reaction may name the compartment it takes place in.
The link is shown under "References" of the species, of the qualitative species or of the reaction, and under "Referenced by" of the compartment, which is where every species of a compartment can be seen at once.
reactant¶
A species a reaction consumes.
The link is two links of one kind: from the reaction to every species reference of its list of reactants, and from each of those to the species it names. Every link starts at the element which carries the reference, so a species reference is part of the graph instead of standing alone.
It is shown under "References" of the reaction, where it lists what the reaction consumes, and under "Referenced by" of the species, where it answers which reactions consume it.
product¶
A species a reaction produces.
The link is two links of one kind: from the reaction to every species reference of its list of products, and from each of those to the species it names.
It is shown under "References" of the reaction and under "Referenced by" of the species, where it answers which reactions produce it.
modifier¶
A species which influences a reaction without being consumed.
The link is two links of one kind: from the reaction to every modifier species reference of its list of modifiers, and from each of those to the species it names: a catalyst, an inhibitor or an activator.
It is shown under "References" of the reaction and under "Referenced by" of the species. A species which is a modifier of a reaction usually also appears in the math of its kinetic law, which is a link of the kind "math".
kineticLaw¶
The formula which gives the speed of a reaction.
A reaction holds the formula of its speed in a kinetic law of its own, and the link runs from the reaction to it. The elements the formula reads are linked from the kinetic law with math links, and its local parameters are among them.
It is shown under "References" of the reaction and under "Referenced by" of the kinetic law. A reaction has one kinetic law at most, and its formula is the speed of the reaction, so the other links look across it: the reaction lists what its formula reads under "math", and a species or a parameter the formula reads lists the reaction there, not the kinetic law. The kinetic law keeps its own links.
localParameter¶
A parameter which only the formula of one kinetic law can read.
A kinetic law names every local parameter it lists, whether its formula reads it or not. A local parameter is not part of the identifiers of the model, only the formula of its own kinetic law can name it, so this link is what says which reaction a local parameter belongs to.
It is shown under "References" of the kinetic law and under "Referenced by" of the local parameter.
trigger¶
The condition an event fires on.
An event holds its condition in a trigger of its own, and the link runs from the event to it. The elements the condition reads are linked from the trigger, not from the event, so a reader sees which of the formulas of an event uses a species or a parameter.
It is shown under "References" of the event and under "Referenced by" of the trigger.
priority¶
The formula which orders an event against the events of the same moment.
An event may hold a priority of its own, and the link runs from the event to it.
It is shown under "References" of the event and under "Referenced by" of the priority.
delay¶
The formula which postpones the execution of an event.
An event may hold a delay of its own, and the link runs from the event to it.
It is shown under "References" of the event and under "Referenced by" of the delay.
eventAssignment¶
A new value an event gives to an element of the model.
An event names every event assignment of its list, and each assignment names the element it sets with a variable link and the elements its formula reads with math links. An assignment carries no identifier in most models, so this link is what says which event it belongs to.
It is shown under "References" of the event and under "Referenced by" of the assignment.
variable¶
The element a rule, an event assignment or a constraint component is about.
An assignment rule, a rate rule and an event assignment name the element they set in their variable: a compartment, a species, a parameter or the stoichiometry of a species reference. A component of a user defined constraint of fbc names the reaction or the parameter it weighs with the same attribute, which it does not set but reads; the second factor of a quadratic component is a link of its own, second variable.
The link is shown under "References" of the rule or of the assignment, and under "Referenced by" of the element, where it shows what determines its value.
variable2¶
The second factor of a quadratic term of a user defined constraint.
A quadratic component of a user defined constraint weighs the product of two variables, the reaction or the parameter of its variable and the one of its second variable. The second one has a link of its own, so that the element it names says that it is the second factor of a product and not a term of its own.
It is shown under "References" of the component and under "Referenced by" of the reaction or the parameter.
symbol¶
The element whose initial value an initial assignment computes.
An initial assignment names the element it computes in its symbol. It is the same relation as the variable of a rule, at the start of the simulation instead of during it, and the specification gives it a name of its own.
The link is shown under "References" of the initial assignment and under "Referenced by" of the element.
units¶
The unit definition an element declares its units with.
A model, a compartment, a species, a parameter, a local parameter and an uncert parameter may name a unit definition of the model in one of their units attributes. A units attribute which names a base unit of SBML instead of a unit definition produces no link, because there is no element to link to.
Two more references carry the same relation. A number in a formula of Level 3 may name its units with the attribute sbml:units, and the element which holds the formula links that unit definition. A model of Level 1 or Level 2 changes the units every element without units of its own uses by defining a unit of the id substance, time, volume, area or length, and the model links such a definition, the way a model of Level 3 links the unit definitions of its units attributes.
The link is shown under "References" of the element and under "Referenced by" of the unit definition, where it shows which elements are measured in it.
conversionFactor¶
The parameter which converts the values of an element.
A model and a species name a conversion factor parameter for the amounts of species, and a replaced element names one for the element it replaces. In every case the link goes to a constant parameter of the model. The two conversion factors of a submodel are links of their own, time conversion factor and extent conversion factor.
It is shown under "References" of the element and under "Referenced by" of the parameter.
timeConversionFactor¶
The parameter which converts the time of a submodel.
A submodel names the parameter which converts the units of time of the model it instantiates into the units of time of the model which contains it, in its time conversion factor.
It is shown under "References" of the submodel and under "Referenced by" of the parameter.
extentConversionFactor¶
The parameter which converts the reaction extent of a submodel.
A submodel names the parameter which converts the units of reaction extent of the model it instantiates into those of the model which contains it, in its extent conversion factor.
It is shown under "References" of the submodel and under "Referenced by" of the parameter.
fluxBound¶
The reaction a flux bound of fbc Version 1 constrains.
In a document of fbc Version 1 a flux bound is an object of its own, which names the reaction whose flux it constrains together with an operation and a value. From Version 2 on the bounds are attributes of the reaction, which names their parameters with a lower flux bound and an upper flux bound link.
The link is shown under "References" of the flux bound and under "Referenced by" of the reaction, where it shows what bounds its flux.
lowerFluxBound¶
The parameter which holds the lowest flux of a reaction.
A reaction of a model which uses fbc Version 2 or later names the parameter of its lower flux bound. A genome scale model gives hundreds of reactions the same parameter, and the link says of every one of them that it is their lower bound.
It is shown under "References" of the reaction and under "Referenced by" of the parameter.
upperFluxBound¶
The parameter which holds the highest flux of a reaction.
A reaction of a model which uses fbc Version 2 or later names the parameter of its upper flux bound. A genome scale model gives hundreds of reactions the same parameter, and the link says of every one of them that it is their upper bound.
It is shown under "References" of the reaction and under "Referenced by" of the parameter.
geneProduct¶
A gene product a reaction needs, named by a reference of its association.
The link goes from a gene product reference, the leaf of the gene product association of a reaction, to the gene product it names. It starts at the reference and not at the reaction because that is where the file writes the identifier, and because a reaction may name one gene in several branches of its association.
It is shown under "References" of the reference and under "Referenced by" of the gene product. The inspector looks across the tree of the association, which is the question a reader asks: a reaction lists the gene products it needs under this kind, and a gene product lists the reactions which need it, each of them once.
geneProductAssociation¶
A node of the gene association of a reaction, from the reaction down to its genes.
A reaction names the gene product association it carries, the association names the node at the root of its tree, and every and and or names the nodes below it, all of them with this kind. The tree ends at the gene product references, which name the genes.
The chain is what makes the structure of the association walkable: it says which genes belong to the same complex and which of them are alternatives, which the flat list of the genes of a reaction cannot.
It is shown under "References" of the reaction and of every node, and under "Referenced by" of the node below.
associatedSpecies¶
The species a gene product stands for.
A gene product may name the species which represents it in the reaction network, which is how some reconstructions encode gene products.
The link is shown under "References" of the gene product and under "Referenced by" of the species.
fluxObjective¶
A term of an objective function and the reaction whose flux it weighs.
An objective names every flux objective it is the sum of, and each of those names the reaction whose flux it weighs. Both hops carry this kind, the way a reaction and its species reference both carry the kind of the participation. From Version 3 of fbc on a quadratic term may multiply the flux with the flux of a second reaction, which is a link of its own, second reaction.
The coefficient is an attribute of the flux objective, not of the link. The chain is shown under "References" of the objective and of the flux objective, and under "Referenced by" of the reaction, where it says that this reaction is what the model optimises.
reaction2¶
The second flux of a quadratic term of an objective.
A quadratic flux objective of fbc Version 3 weighs the product of the flux of its reaction and the flux of its second reaction. The second one has a link of its own, so that the reaction it names says that it is the second factor of a product and not a term of the objective of its own.
It is shown under "References" of the flux objective and under "Referenced by" of the reaction.
activeObjective¶
The objective a model declares as the one which is optimised.
A model which defines several objectives names the one an analysis optimises unless it is told otherwise. It is the only link which starts at the model itself, because the attribute belongs to the list of the objectives, which the report shows as the section of that type.
It is shown under "References" of the model and under "Referenced by" of the objective, where it says that this objective is the one the model was published with.
lowerBound¶
The parameter which holds the lowest value of a user defined constraint.
A user defined constraint keeps the weighted sum of its components between two numbers, and it names the parameter of the lower one in its lower bound. The bound limits the sum and not the flux of one reaction, which is why it is not a flux bound.
It is shown under "References" of the constraint and under "Referenced by" of the parameter.
upperBound¶
The parameter which holds the highest value of a user defined constraint.
A user defined constraint keeps the weighted sum of its components between two numbers, and it names the parameter of the upper one in its upper bound. The bound limits the sum and not the flux of one reaction, which is why it is not a flux bound.
It is shown under "References" of the constraint and under "Referenced by" of the parameter.
constraintComponent¶
A term of a user defined constraint.
A user defined constraint names every component it is the sum of, the way a reaction names its species references, and each component names the variable it weighs and the parameter of its coefficient with links of their own.
It is shown under "References" of the constraint and under "Referenced by" of the component.
coefficient¶
The parameter which holds the weight of a term.
A component of a user defined constraint does not write its weight into the file: it names the parameter which holds it, so that the weights of a model are changed in one place.
It is shown under "References" of the component and under "Referenced by" of the parameter, where it says which constraints a number belongs to.
input¶
A qualitative species a transition reads.
A transition names every input it lists and each input names the qualitative species whose level it reads, the way a reaction names its species references. The sign of the input says whether that species activates or inhibits, so the inputs and the outputs of a model together are its influence graph.
It is shown under "References" of the transition and of the input and under "Referenced by" of the qualitative species, where it says which transitions read it.
output¶
A qualitative species a transition changes.
A transition names every output it lists and each output names the qualitative species whose level it changes.
It is shown under "References" of the transition and of the output and under "Referenced by" of the qualitative species, where it says which transitions decide its level.
functionTerm¶
A row of the transition table of a transition.
A transition names every function term of its list, in the order in which they are read, and the math of a term reaches the qualitative species, the inputs and the outputs it names with math links of its own.
It is shown under "References" of the transition and under "Referenced by" of the term. The terms are the rows of the table of their transition, so the other links look across them, the way they look across the kinetic law of a reaction: the transition lists what its conditions read under "math", and a qualitative species a condition reads lists the transition there. A term keeps its own links.
defaultTerm¶
The term of a transition which holds where no other one does.
A transition has exactly one default term, which gives the level of every state its function terms do not cover. It is a link of its own and not a function term link, because the term carries no condition and is the last row of the transition table whatever the order of the others.
It is shown under "References" of the transition and under "Referenced by" of the term.
listOf¶
A list of the element which states something of its own.
An element names every list it owns which carries a meta id, an SBO term, notes, an annotation, an id or a name: a model its listOfSpecies, a reaction its listOfReactants, a unit definition its listOfUnits. A list which states nothing is no element of the report and has no link. A port, a deletion or a replacement of the comp package which names a list by its meta id or its id ends at the list with a link of its own kind.
It is shown under "References" of the element which owns the list and under "Referenced by" of the list, which is how a reader gets from a list back to its owner.
uncertainty¶
A set of measures of how well the value of an element is known.
An element whose value is uncertain names every uncertainty it carries, and each uncertainty names the uncert parameters which are its measures with uncert parameter links. An element may carry several uncertainties, one per experiment or publication, so the link is what says which element a set of measures describes.
It is shown under "References" of the element and under "Referenced by" of the uncertainty, which is how a reader gets from an uncertainty back to the value it is about.
uncertParameter¶
A measure of an uncertainty.
An uncertainty names every uncert parameter it lists, and a parameter of the type distribution or externalParameter names the parameters which define it in turn, so the link carries the whole tree of a distribution.
It is shown under "References" of the uncertainty and of a parameter with parameters of its own, and under "Referenced by" of the measure, which is how a reader gets from a measure back to the set it belongs to.
var¶
The element which holds the number of a measure.
A measure of an uncertainty which is not a fixed number names the element of the model which holds it in the var of an uncert parameter. The two ends of the interval of an uncert span are links of their own, var lower and var upper.
It is shown under "References" of the measure and under "Referenced by" of the element it names, where it says which measurement that element stands for.
varLower¶
The element which holds the lower end of the interval of a measure.
An uncert span whose lower end is not a fixed number names the element of the model which holds it in its var lower. The link says of that element that it is the lower end of the interval, which the element does not say itself.
It is shown under "References" of the span and under "Referenced by" of the element it names.
varUpper¶
The element which holds the upper end of the interval of a measure.
An uncert span whose upper end is not a fixed number names the element of the model which holds it in its var upper. The link says of that element that it is the upper end of the interval, which the element does not say itself.
It is shown under "References" of the span and under "Referenced by" of the element it names.
model¶
A model the document holds.
The document names the model it holds and, in a document of the comp package, every model definition of its list, which are models a submodel can instantiate. A model definition which no submodel instantiates is still reached from the document.
It is shown under "References" of the document and under "Referenced by" of the model.
externalModelDefinition¶
A model of another document which this document refers to.
The document names every external model definition of its list. The model behind it lives in another file, which the report follows where it has that file, and a submodel instantiates it with a model reference link.
It is shown under "References" of the document and under "Referenced by" of the external model definition.
modelRef¶
The model a submodel instantiates.
A submodel names the model it instantiates, which is either a model definition of the document or an external model definition. The reference is resolved against the models of the document, not within one model, because model identifiers live in a namespace of the document. An external model definition names a model in turn, the one of another document, and carries the same link to it where the report has that document.
The link is shown under "References" of the submodel and under "Referenced by" of the model, where it shows who uses it.
port¶
The element a port names.
A port names exactly one element of its model, by its identifier, by the identifier of a unit definition or by its meta id. All three produce a link of this kind; a port which names a port of a submodel instead is not resolved, because the element lies inside another model.
The link is shown under "References" of the port and under "Referenced by" of the element, where it says that the element is part of the interface of the model.
deletion¶
An element which a submodel removes, and the deletion which removes it.
A submodel names every deletion it carries, and each deletion names the element of the instantiated model which it removes, so the link leads from the submodel over the deletion to the element which the composed model does not contain. The same kind leads from a replaced element to the deletion it stands for, which is how a model records that an element of its own takes the place of something a submodel lost.
Where the model of the submodel is one of another document, the link ends at the element of that document when it is part of the report, as another entry of the same archive. When it is not, the deletion has no element to name and the link ends at the deletion.
The link is shown under "References" of the submodel and of the deletion, and under "Referenced by" of the element which is removed.
replacedBy¶
The element of a submodel which replaces this one.
An element which is replaced names the replacement it carries, and the replacement names the element of the submodel which takes the place of the element, so the link leads from the replaced element over the replacement to the element which stays in the composed model.
Where the model of the submodel is one of another document, the link ends at the element of that document when it is part of the report. Where the reference cannot be resolved, because the report does not have the document of an external model or because the named element is not part of it, the link ends at the submodel, which is as far as the report can follow it.
The link is shown under "References" of the replaced element and of the replacement, and under "Referenced by" of the element which replaces it.
replacedElement¶
The element of a submodel which this one replaces.
An element may replace elements of submodels. It names every replacement it carries, and each replacement names the submodel it reaches into and the element inside it which disappears from the composed model. It is the opposite direction of "replaced by" and the usual way a composed model connects its parts.
Where the model of the submodel is one of another document, the link ends at the element of that document when it is part of the report. Where the reference cannot be resolved, because the report does not have the document of an external model or because the named element is not part of it, the link ends at the submodel.
The link is shown under "References" of the replacing element and of the replacement, and under "Referenced by" of the element which is replaced.
sBaseRef¶
The next link of a chain of references into a submodel of a submodel.
A port, a deletion, a replaced element or a replaced by which has to reach an element deeper than the submodel it names carries a reference of its own, and that reference may carry the next one. Each of them names the reference it carries. The element at the end of the chain is linked from the object which carries the whole chain, so the links in between only say where they belong.
It is shown under "References" of the object which carries the reference and under "Referenced by" of the reference.
math¶
An element a formula refers to.
Every formula of a model refers to elements by their identifier: the species and the parameters of a kinetic law, the elements a rule or a trigger reads, the function definition a formula calls. The report collects these symbols of every formula and links each of them to the element it names, resolving the local parameters of a kinetic law before the elements of the model. The arguments of a function definition are local to it and are no references, and a symbol which names nothing, such as the symbol of time, produces no link.
The link is shown under "References" of the element which carries the formula and under "Referenced by" of the element the formula uses, where it answers in which equations a species or a parameter occurs. The formula of a kinetic law is the speed of its reaction and the condition of a function term a row of the table of its transition, so their links are shown as those of the reaction and of the transition, and the kinetic law and the term keep their own.