Root element used to encapsulate data for SigPath Export or Import Optional field containing the date and time, populated on xml export. Optional field containing build version of the running sigpath, populated on xml export. Groups pending reviews Defines a list of pending items specifies date/time stamp when pending list was created specifies user who initially created the pending list Defines a pending item Defines the KBKP value for an enzymatic reaction Defines the KMichaelis value for an enzymatic reaction Defines the any parameter Defines the Kp (KCat) value for an enzymatic reaction Defines the Vmax value for an enzymatic reaction The concentration of the enzyme used to measure the value of VMax. Defines the KBackward value for a basic reaction Defines the KForward value for a basic reaction Selects the concentration units required for creating/submitting a model encapsulates data defining a pathway Used to identify a reaction within a pathway Used to reference an interaction. encapsulates data defining a model Used to identify a reaction within a model Description for this reaction Summary of the reaction. Will look like A + B < ... > C Selects molecule concentrations in a model Defines the initial concentration of a molecule in a model element used to define a small molecule in SigPath element used to define a protein in SigPath Organism of origin for a protein Species of origin for a protein Common name for the species of origin element used to define a complex in SigPath Used to annotate the fully-defined value of the complex. If the fully-defined value is true, the complex is believed to be complete. If the fully-defined value is false, the list of chemicals that form the complex is known to be incomplete. Other molecules that are not explicitly listed here may participate in this complex. element used to encapsulate data defining an enzymatic reaction in SigPath Identifies the enzyme for an enzymatic reaction Identifies a molecule in SigPath (for example as part of a reaction or as part of a complex) by using at least one of three attributes: idref (unique identifier for new molecules; this attribute has the highest precedence), ac. (accession number; this attribute has the second highest precedence) or spid (unique SigPath identifier; this identifier has the lowest precedence) Allows you to locate a molecule in one or more compartment if null compatible old data When true, indicates that this molecule is a substrate of the enclosing enzymatic reaction. When true, indicates that this molecule is a product of the enclosing enzymatic reaction. Reference to an identifier defined in this file (with the id attribute). When provided, the molecule will match the molecule that has the id attribute equals to idref. Accession code of the molecule to be matched. Organism of the molecule to be matched. This is useful to further define the molecule matched by accession code when the match is still ambiguous. Groups the parameters of a reaction in SigPath Groups the parameters of an enzymatic reaction in SigPath Defines a modified chemical (for example the active isoform of a specified molecule) in SigPath. Annotates publications in relation to a reaction or molecule concentration element used to encapsulate data defining a reaction in SigPath Contains molecules on the left side of a reaction Contains molecules on the right side of a reaction Contains molecules that influence the velocities of the reaction annotates a reference which has a PubMed ID Annotates references without PubMed IDs binds a name (a common parametername as Kf) with a parameter. Ex : kf with aParameter binds a name(usually the function of the chemical) with a chemical. Ex : enzyme and anEnzyme indicates that the requirement deals with a constant. These differenciation may be usefull for kinetic instantiation user interfaces Type of this kinetic. One of: org.sigpath.datamodel.KineticMassAction, org.sigpath.datamodel.KineticMichaelisMenten, or org.sigpath.datamodel.KineticCustom.". name to constant/chemical elements there are two way to define a kinetic, either indicating a class which realizes a specified kinetic, either indication a kinetic declaration, also part of the submission This element declares a new type of kinetic. Two ways to define kinetic types are currently supported: (1) Reference kinetics can be implemented in a Java class and referenced by class name. (2) Custom kinetics that can be expressed with rate laws and described directly in the XML file. If defined in the XML file, the kinetic declaration must contain formulae, species and constant bindings declarations. can be an expression like k*p1*p2, but also a numerical value (0 for instance) can be an expression like k*p1*p2, but also a numerical value (0 for instance) can be an expression like k*p1*p2, but also a numerical value (0 for instance) Groups small molecule definitions in SigPath Groups protein definitions in SigPath Groups concentration measurements in SigPath Groups complex and modified chemical definitions in SigPath Selects units for the reaction parameter Annotates the site at which two molecules interact Defines the value of a reaction parameter Allows you to name a molecule or a model - Allows you to attach a description to a reaction, molecule, compartment, model or review Used to describe aliases for a molecule Used to describe the chemical formula (SMILE) of a molecule Identifies a molecule by accession code Specifies the database from which an accession number for a molecule has been acquired Allows you to annotate SigPath submission components with comments Specifies whether a modified chemical is a protein or a small molecule Annotates external references. For example, a chemical may have an accession code within another database, such as SWISS-PROT. Used to describe concentration measurements for molecules in SigPath Tissue in which the concentration was measured Allows you to include comments Used to annotate the concentration measurement method Used to annotate sample preparation methods Used to describe internal links within SigPath Used to list reactions that a molecule is involved in by spid (unique SigPath identifier) Used to annotate change log information, including who submitted this record, when the record was submitted, and when the record was last modified. Name of the user associated with the change log information. Date of submission for a SigPath entity. Date at which SigPath entity was last modified. Used to annotate SigPath reviews Used to annotate a SigPath review, including review description, who conducted the review, and date/time review was conducted. User who conducted the review Date/time at which the review was conducted group of kinetics declaration in SigPath Groups compartments of a model Annotates a SigPath chemical with a name but no accession code Annotates the name of the chemical. Groups named-chemical definitions in SigPath Annotates an interaction between two named-chemicals in SigPath. In situations when it is a target-source interaction, the source named-chemical should be listed first, followed by the target named-chemical. The reference value of a named chemical. Annotates the role of the named-chemical in an interaction, e.g. binding partner, substrate. Groups named-chemical-interaction definitions in SigPath previous version of a sigpathEntity Annotates a SigPath user-comment User who submitted the comment Date/time at which the comment was submitted Content of the comment Groups user-comment