Schema for SigPath XML submissions
Last updated: January 2006

The root element for the SigPath XML schema is sigpath-submission

schema location:	http://icb.med.cornell.edu/schemas/sigpath/2006/January/sp_submission2.xsd
attribute form default:	unqualified
element form default:	qualified

Elements

ac

alias

binding-declaration

change_log

comments

complex

components

concentration_measurement

concentration_measurements

database

description

enzymatic-parameters

enzymatic-reaction

enzyme

external-reference

formula

interaction-ref

interaction_site

internal-links

KBackward

KBKP

KForward

kinetic

kinetic-bindings

kinetic-ref

kinetic-type

kinetics

KMichaelis

Kp

left

model

model-compartments

model-concentration

model-reaction

modified-chemical

modifiers

molecule

molecule-excluded

name

named-chemical

named-chemical-interaction

named-chemical-interactions

named-chemicals

other_reference

parameter

parameter-binding

parameters

parameters-bindings-declaration

pathway

pathway-reaction

previousVersion

protein

proteins

publications

reaction

ref

reviews

right

sigpath-submission

small-molecule

small-molecules

smiles

source

species-binding

species-bindings-declaration

target-unit

type

unit

user-comment

user-comments

value

VMax

VMax_EnzymeConcentration

element ac

diagram
type	xs:string
properties	content  simple nillable  false
used by	element  external-reference
annotation	documentation Identifies a molecule by accession code

element alias

diagram
type	xs:string
properties	content  simple nillable  false
used by	elements  protein small-molecule
annotation	documentation Used to describe aliases for a molecule

element binding-declaration

diagram
properties	content  complex
children	name description unit
used by	elements  parameters-bindings-declaration species-bindings-declaration
annotation	documentation indicates that the requirement deals with a constant. These differenciation may be usefull for kinetic instantiation user interfaces

element binding-declaration/name

diagram
type	xs:string
properties	isRef  0 content  simple
used by	elements  complex enzymatic-reaction model modified-chemical molecule named-chemical-interaction pathway sigpath-submission/pending_reviews/pending_list protein reaction small-molecule

element binding-declaration/description

diagram
type	xs:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple
used by	elements  model-compartments/compartment complex enzymatic-reaction model/excluded-reactions/excluded-reaction model model-compartments model-concentration model-reaction modified-chemical molecule named-chemical named-chemical-interaction pathway pathway-reaction sigpath-submission/pending_reviews/pending_list protein reaction reviews/review small-molecule

element change_log

diagram
properties	content  complex
children	user_name dateSubmitted dateLastModified
used by	elements  complex enzymatic-reaction kinetic model modified-chemical named-chemical named-chemical-interaction pathway sigpath-submission/pending_reviews/pending_list protein reaction small-molecule
annotation	documentation Used to annotate change log information, including who submitted this record, when the record was submitted, and when the record was last modified.

element change_log/user_name

diagram
type	xs:string
properties	isRef  0 content  simple
annotation	documentation Name of the user associated with the change log information.

element change_log/dateSubmitted

diagram
type	xs:dateTime
properties	isRef  0 content  simple
annotation	documentation Date of submission for a SigPath entity.

element change_log/dateLastModified

diagram
type	xs:dateTime
properties	isRef  0 content  simple
annotation	documentation Date at which SigPath entity was last modified.

element comments

diagram
type	xs:string
properties	content  simple
used by	elements  complex enzymatic-reaction model modified-chemical molecule named-chemical named-chemical-interaction pathway sigpath-submission/pending_reviews/pending_list protein reaction small-molecule
annotation	documentation Allows you  to annotate SigPath submission components with comments

element complex

diagram
properties	content  complex
children	name description comments molecule internal-links publications change_log fully-defined reviews user-comments
used by	element  components
attributes	Name   Type   Use   Default   Fixed   Annotation id   xs:ID required         spid   xs:string optional
annotation	documentation element used to define a complex in SigPath

element complex/fully-defined

diagram
type	xs:boolean
properties	isRef  0 minOcc  0 maxOcc  1 content  simple
annotation	documentation 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 components

diagram
properties	content  complex
children	complex modified-chemical
used by	element  sigpath-submission
annotation	documentation Groups complex and modified chemical definitions in SigPath

element concentration_measurement

diagram
properties	content  complex nillable  false
children	value unit molecule tissue comments measurement_method sample_prep ref
used by	element  concentration_measurements
attributes	Name   Type   Use   Default   Fixed   Annotation id   xs:ID optional         spid   xs:string optional
annotation	documentation Used to describe concentration measurements for molecules in SigPath

element concentration_measurement/tissue

diagram
type	xs:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple nillable  false
annotation	documentation Tissue in which the concentration was measured

element concentration_measurement/comments

diagram
type	xs:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple nillable  false
used by	elements  complex enzymatic-reaction model modified-chemical molecule named-chemical named-chemical-interaction pathway sigpath-submission/pending_reviews/pending_list protein reaction small-molecule
annotation	documentation Allows you to include comments

element concentration_measurement/measurement_method

diagram
type	xs:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple nillable  false
annotation	documentation Used to annotate the concentration measurement method

element concentration_measurement/sample_prep

diagram
type	xs:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple nillable  false
annotation	documentation Used to annotate sample preparation methods

element concentration_measurements

diagram
properties	content  complex nillable  false
children	concentration_measurement
used by	element  sigpath-submission
annotation	documentation Groups concentration measurements in SigPath

element database

diagram
type	xs:string
properties	content  simple nillable  false
used by	element  external-reference
annotation	documentation Specifies the database from which an accession number for a molecule has been acquired

element description

diagram
type	xs:string
properties	content  simple nillable  false
used by	elements  model-compartments/compartment complex enzymatic-reaction model/excluded-reactions/excluded-reaction model model-compartments model-concentration model-reaction modified-chemical molecule named-chemical named-chemical-interaction pathway pathway-reaction sigpath-submission/pending_reviews/pending_list protein reaction reviews/review small-molecule
annotation	documentation Allows you to attach a description to a reaction, molecule, compartment, model or review

element enzymatic-parameters

diagram
properties	content  complex
children	KMichaelis VMax VMax_EnzymeConcentration Kp KBKP
used by	element  enzymatic-reaction
annotation	documentation Groups the parameters of an enzymatic reaction in SigPath

element enzymatic-reaction

diagram
properties	content  complex
children	name description comments reaction enzyme enzymatic-parameters kinetic-ref kinetic-bindings change_log reviews publications user-comments
used by	element  sigpath-submission
attributes	Name   Type   Use   Default   Fixed   Annotation id   xs:ID optional         spid   xs:string optional
annotation	documentation element used to encapsulate data defining an enzymatic reaction in SigPath

element enzyme

diagram
properties	content  complex
children	molecule
used by	element  enzymatic-reaction
annotation	documentation Identifies the enzyme for an enzymatic reaction

element external-reference

diagram
properties	content  complex
children	ac database
used by	elements  named-chemical named-chemical-interaction protein small-molecule
annotation	documentation Annotates external references.  For example, a chemical may have an accession code within another database, such as SWISS-PROT.

element formula

diagram
properties	content  complex
children	forward backward
used by	element  kinetic/custom-kinetic
annotation	documentation can be an expression like k*p1*p2, but also a numerical value (0 for instance)

element formula/forward

diagram
type	xs:string
properties	isRef  0 content  simple

element formula/backward

diagram
type	xs:string
properties	isRef  0 content  simple

element interaction-ref

diagram
properties	content  complex
used by	element  pathway
attributes	Name   Type   Use   Default   Fixed   Annotation idref   xs:IDREF optional         spid   xs:string optional
annotation	documentation Used to reference an interaction.

element interaction_site

diagram
type	restriction of xs:string
properties	content  simple
used by	element  molecule
annotation	documentation Annotates the site at which two molecules interact

element internal-links

diagram
properties	content  complex
children	involved-in-reaction
used by	elements  complex modified-chemical protein small-molecule
annotation	documentation Used to describe internal links within SigPath

element internal-links/involved-in-reaction

diagram
properties	isRef  0 minOcc  0 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation spid   xs:string required
annotation	documentation Used to list reactions that a molecule is involved in by spid (unique SigPath identifier)

element KBackward

diagram
properties	content  complex
children	unit value
used by	element  parameters
annotation	documentation Defines the KBackward value for a basic reaction

element KBKP

diagram
properties	content  complex
children	value
used by	element  enzymatic-parameters
annotation	documentation Defines the KBKP value for an enzymatic reaction

element KForward

diagram
properties	content  complex
children	unit value
used by	element  parameters
annotation	documentation Defines the KForward value for a basic reaction

element kinetic

diagram
properties	content  complex
children	name description custom-kinetic kinetic-type publications change_log reviews user-comments
used by	element  kinetics
attributes	Name   Type   Use   Default   Fixed   Annotation id   xs:ID          spid   xs:string
annotation	documentation 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.

element kinetic/name

diagram
type	xs:string
properties	isRef  0 content  simple
used by	elements  complex enzymatic-reaction model modified-chemical molecule named-chemical-interaction pathway sigpath-submission/pending_reviews/pending_list protein reaction small-molecule

element kinetic/description

diagram
type	xs:string
properties	isRef  0 content  simple
used by	elements  model-compartments/compartment complex enzymatic-reaction model/excluded-reactions/excluded-reaction model model-compartments model-concentration model-reaction modified-chemical molecule named-chemical named-chemical-interaction pathway pathway-reaction sigpath-submission/pending_reviews/pending_list protein reaction reviews/review small-molecule

element kinetic/custom-kinetic

diagram
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
children	formula species-bindings-declaration parameters-bindings-declaration unit

element kinetic-bindings

diagram
properties	content  complex
children	species-binding parameter-binding
used by	elements  enzymatic-reaction reaction
annotation	documentation name to constant/chemical elements

element kinetic-ref

diagram
properties	content  complex
used by	elements  enzymatic-reaction reaction
attributes	Name   Type   Use   Default   Fixed   Annotation idref   xs:IDREF optional         spid   xs:string optional
annotation	documentation 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

element kinetic-type

diagram
type	restriction of xs:string
properties	content  simple
used by	element  kinetic
facets	enumeration  org.sigpath.datamodel.KineticMassAction enumeration  org.sigpath.datamodel.KineticMichaelisMenten enumeration  org.sigpath.datamodel.KineticCustom
annotation	documentation Type of this kinetic. One of: org.sigpath.datamodel.KineticMassAction, org.sigpath.datamodel.KineticMichaelisMenten, or org.sigpath.datamodel.KineticCustom.".

element kinetics

diagram
properties	content  complex nillable  false
children	kinetic
used by	element  sigpath-submission
annotation	documentation group of kinetics declaration in SigPath

element KMichaelis

diagram
properties	content  complex
children	unit value
used by	element  enzymatic-parameters
annotation	documentation Defines the KMichaelis value for an enzymatic reaction

element Kp

diagram
properties	content  complex
children	unit value
used by	element  enzymatic-parameters
annotation	documentation Defines the Kp (KCat) value for an enzymatic reaction

element left

diagram
properties	content  complex
children	molecule
used by	element  reaction
annotation	documentation Contains molecules on the left side of a reaction

element model

diagram
properties	content  complex
children	name description comments target-unit model-reaction model-compartments model-concentration excluded-reactions publications change_log previousVersion
used by	element  sigpath-submission
attributes	Name   Type   Use   Default   Fixed   Annotation id   derived by: xs:ID optional         spid   xs:string optional
annotation	documentation encapsulates data defining a model

element model/excluded-reactions

diagram
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
children	excluded-reaction

element model/excluded-reactions/excluded-reaction

diagram
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	on-left on-right description
attributes	Name   Type   Use   Default   Fixed   Annotation ReactionSpid   xs:string optional         ReactionIdRef   xs:IDREF optional

element model/excluded-reactions/excluded-reaction/on-left

diagram
properties	isRef  0 content  complex
children	molecule-excluded

element model/excluded-reactions/excluded-reaction/on-right

diagram
properties	isRef  0 content  complex
children	molecule-excluded

element model-compartments

diagram
properties	content  complex
children	compartment description
used by	element  model
annotation	documentation Groups compartments of a model

element model-compartments/compartment

diagram
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	description value unit InContactWith
attributes	Name   Type   Use   Default   Fixed   Annotation name   xs:string optional         id   xs:ID optional         outside   xs:IDREF optional

element model-compartments/compartment/InContactWith

diagram
properties	isRef  0 minOcc  0 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation contactcompartment   xs:IDREF optional

element model-concentration

diagram
properties	content  complex
children	description molecule molecule-concentration
used by	element  model
attributes	Name   Type   Use   Default   Fixed   Annotation isBuffered   xs:boolean optional   false      isModelWillProvide   xs:boolean optional   false
annotation	documentation Selects molecule concentrations in a model

element model-concentration/molecule-concentration

diagram
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
children	value unit
annotation	documentation Defines the initial concentration of a molecule in a model

element model-reaction

diagram
properties	content  complex
children	description summary
used by	element  model
attributes	Name   Type   Use   Default   Fixed   Annotation idref   xs:IDREF optional         spid   xs:string optional
annotation	documentation Used to identify a reaction within a model

element model-reaction/summary

diagram
type	xs:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple
annotation	documentation Summary of the reaction. Will look like A + B < ... > C

element modified-chemical

diagram
properties	content  complex
children	name description comments type molecule internal-links publications change_log reviews user-comments
used by	element  components
attributes	Name   Type   Use   Default   Fixed   Annotation id   xs:ID required         spid   xs:string optional
annotation	documentation Defines a modified chemical (for example the active isoform of a specified molecule) in SigPath.

element modifiers

diagram
properties	content  complex
children	molecule
used by	element  reaction
annotation	documentation Contains molecules that influence the velocities of the reaction

element molecule

diagram
properties	content  complex nillable  false
children	interaction_site name description comments location
used by	elements  complex concentration_measurement enzyme left model-concentration modified-chemical modifiers right species-binding
attributes	Name   Type   Use   Default   Fixed   Annotation spid   xs:string optional         isSubstrate   xs:boolean optional         documentation When true, indicates that this molecule is a substrate of the enclosing enzymatic reaction. isProduct   xs:boolean optional         documentation When true, indicates that this molecule is a product of the enclosing enzymatic reaction. idref   xs:IDREF optional         documentation 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. ac   xs:string optional         documentation Accession code of the molecule to be matched. organism   xs:string optional         documentation 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. isBuffered   xs:boolean optional   false      isModelWillProvide   xs:boolean optional   false
annotation	documentation 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)

element molecule/location

diagram
properties	isRef  0 minOcc  0 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation idref   xs:IDREF required         fraction   derived by: xs:int required
annotation	documentation Allows you to locate a molecule in one or more compartment if null compatible old data

element molecule-excluded

diagram
properties	content  complex
used by	elements  model/excluded-reactions/excluded-reaction/on-left model/excluded-reactions/excluded-reaction/on-right
attributes	Name   Type   Use   Default   Fixed   Annotation moleculeIdRef   xs:IDREF optional         moleculelocalisation   xs:IDREF required         moleculeSpid   xs:string optional

element name

diagram
type	xs:string
properties	content  simple nillable  false
used by	elements  complex enzymatic-reaction model modified-chemical molecule named-chemical-interaction pathway sigpath-submission/pending_reviews/pending_list protein reaction small-molecule
annotation	documentation Allows you to name a molecule or a model -

element named-chemical

diagram
properties	content  complex nillable  false
children	name description comments user-comments change_log external-reference
used by	element  named-chemicals
attributes	Name   Type   Use   Default   Fixed   Annotation id   xs:ID optional         spid   xs:string optional
annotation	documentation Annotates a SigPath chemical with a name but no accession code

element named-chemical/name

diagram
type	xs:string
properties	isRef  0 content  simple
used by	elements  complex enzymatic-reaction model modified-chemical molecule named-chemical-interaction pathway sigpath-submission/pending_reviews/pending_list protein reaction small-molecule
annotation	documentation Annotates the name of the chemical.

element named-chemical-interaction

diagram
properties	content  complex
children	name description comments named-chemical-ref publications change_log external-reference user-comments
used by	element  named-chemical-interactions
attributes	Name   Type   Use   Default   Fixed   Annotation type   xs:string optional         id   xs:ID optional         spid   xs:string optional
annotation	documentation 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.

element named-chemical-interaction/named-chemical-ref

diagram
properties	isRef  0 minOcc  2 maxOcc  2 content  complex
children	role
attributes	Name   Type   Use   Default   Fixed   Annotation idref   xs:IDREF optional         spid   xs:string optional         ac   xs:string optional         organism   xs:string optional
annotation	documentation The reference value of a named chemical.

element named-chemical-interaction/named-chemical-ref/role

diagram
type	xs:string
properties	isRef  0 content  simple
annotation	documentation Annotates the role of the named-chemical in an interaction, e.g. binding partner, substrate.

element named-chemical-interactions

diagram
properties	content  complex
children	named-chemical-interaction
used by	element  sigpath-submission
annotation	documentation Groups named-chemical-interaction definitions in SigPath

element named-chemicals

diagram
properties	content  complex
children	named-chemical
used by	element  sigpath-submission
annotation	documentation Groups named-chemical definitions in SigPath

element other_reference

diagram
type	xs:string
properties	content  simple nillable  false
used by	element  publications
annotation	documentation Annotates references without PubMed IDs

element parameter

diagram
properties	content  complex
children	unit value
used by	element  parameter-binding
annotation	documentation Defines the any parameter

element parameter-binding

diagram
properties	content  complex
children	name parameter
used by	element  kinetic-bindings
annotation	documentation binds a name (a common parametername as Kf) with a parameter. Ex : kf with aParameter

element parameter-binding/name

diagram
type	xs:string
properties	isRef  0 content  simple
used by	elements  complex enzymatic-reaction model modified-chemical molecule named-chemical-interaction pathway sigpath-submission/pending_reviews/pending_list protein reaction small-molecule

element parameters

diagram
properties	content  complex
children	KForward KBackward
used by	element  reaction
annotation	documentation Groups the parameters of a reaction in SigPath

element parameters-bindings-declaration

diagram
properties	content  complex
children	binding-declaration
used by	element  kinetic/custom-kinetic
annotation	documentation can be an expression like k*p1*p2, but also a numerical value (0 for instance)

element pathway

diagram
properties	content  complex
children	name description comments pathway-reaction interaction-ref publications user-comments change_log
used by	element  sigpath-submission
attributes	Name   Type   Use   Default   Fixed   Annotation id   xs:ID optional         spid   xs:string optional
annotation	documentation encapsulates data defining a pathway

element pathway-reaction

diagram
properties	content  complex
children	description
used by	element  pathway
attributes	Name   Type   Use   Default   Fixed   Annotation idref   xs:IDREF optional         spid   xs:string optional
annotation	documentation Used to identify a reaction within a pathway

element previousVersion

diagram
properties	content  complex
used by	element  model
attributes	Name   Type   Use   Default   Fixed   Annotation spid   xs:string optional         idref   xs:IDREF optional
annotation	documentation previous version of a sigpathEntity

element protein

diagram
properties	content  complex nillable  false
children	external-reference name description comments alias organism internal-links change_log
used by	element  proteins
attributes	Name   Type   Use   Default   Fixed   Annotation id   xs:ID optional         spid   xs:string optional
annotation	documentation element used to define a protein in SigPath

element protein/organism

diagram
properties	isRef  0 content  complex nillable  false
children	species common_name
annotation	documentation Organism of origin for a protein

element protein/organism/species

diagram
type	xs:string
properties	isRef  0 content  simple nillable  false
annotation	documentation Species of origin for a protein

element protein/organism/common_name

diagram
type	xs:string
properties	isRef  0 content  simple nillable  false
annotation	documentation Common name for the species of origin

element proteins

diagram
properties	content  complex nillable  false
children	protein
used by	element  sigpath-submission
annotation	documentation Groups protein definitions in SigPath

element publications

diagram
properties	content  complex nillable  false
children	ref other_reference
used by	elements  complex enzymatic-reaction kinetic model modified-chemical named-chemical-interaction pathway reaction
annotation	documentation Annotates publications in relation to a reaction or molecule concentration

element reaction

diagram
properties	content  complex
children	name description comments left right modifiers parameters kinetic-ref kinetic-bindings publications change_log reviews user-comments
used by	elements  enzymatic-reaction sigpath-submission
attributes	Name   Type   Use   Default   Fixed   Annotation id   xs:ID optional         spid   xs:string optional
annotation	documentation element used to encapsulate data defining a reaction in SigPath

element ref

diagram
properties	content  complex
used by	elements  concentration_measurement publications
attributes	Name   Type   Use   Default   Fixed   Annotation pmid   xs:long required
annotation	documentation annotates a reference which has a PubMed ID

element reviews

diagram
properties	content  complex
children	review
used by	elements  complex enzymatic-reaction kinetic modified-chemical reaction
annotation	documentation Used to annotate SigPath reviews

element reviews/review

diagram
properties	isRef  0 minOcc  1 maxOcc  unbounded content  complex
children	description reviewedBy dateReviewed
annotation	documentation Used to annotate a SigPath review, including review description, who conducted the review, and date/time review was conducted.

element reviews/review/reviewedBy

diagram
type	xs:string
properties	isRef  0 content  simple
annotation	documentation User who conducted the review

element reviews/review/dateReviewed

diagram
type	xs:dateTime
properties	isRef  0 content  simple
annotation	documentation Date/time at which the review was conducted

element right

diagram
properties	content  complex
children	molecule
used by	element  reaction
annotation	documentation Contains molecules on the  right side of a reaction

element sigpath-submission

diagram
properties	content  complex
children	export-date-time export-build-version small-molecules proteins components named-chemicals concentration_measurements named-chemical-interactions kinetics reaction enzymatic-reaction model pathway pending_reviews
annotation	documentation Root element used to encapsulate data for SigPath Export or Import

element sigpath-submission/export-date-time

diagram
type	xs:dateTime
properties	isRef  0 minOcc  0 maxOcc  1 content  simple
annotation	documentation Optional field containing the date and time, populated on xml export.

element sigpath-submission/export-build-version

diagram
type	xs:string
properties	isRef  0 minOcc  0 maxOcc  1 content  simple
annotation	documentation Optional field containing build version of the running sigpath, populated on xml export.

element sigpath-submission/pending_reviews

diagram
properties	isRef  0 minOcc  0 maxOcc  1 content  complex
children	pending_list
annotation	documentation Groups pending reviews

element sigpath-submission/pending_reviews/pending_list

diagram
properties	isRef  0 minOcc  0 maxOcc  unbounded content  complex
children	name description comments dateCreated createdBy change_log pending_item
attributes	Name   Type   Use   Default   Fixed   Annotation spid   xs:string optional         id   xs:ID optional
annotation	documentation Defines a list of pending items

element sigpath-submission/pending_reviews/pending_list/dateCreated

diagram
type	xs:dateTime
properties	isRef  0 content  simple
annotation	documentation specifies date/time stamp when pending list was created

element sigpath-submission/pending_reviews/pending_list/createdBy

diagram
type	xs:string
properties	isRef  0 content  simple
annotation	documentation specifies user who initially created the pending list

element sigpath-submission/pending_reviews/pending_list/pending_item

diagram
properties	isRef  0 minOcc  0 maxOcc  unbounded content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation spid   xs:string optional         isReviewed   xs:boolean required         ac   xs:string optional         organism   xs:string optional         idref   xs:IDREF optional
annotation	documentation Defines a pending item

element small-molecule

diagram
properties	content  complex
children	external-reference name description comments smiles alias internal-links change_log
used by	element  small-molecules
attributes	Name   Type   Use   Default   Fixed   Annotation id   xs:ID optional         spid   xs:string optional
annotation	documentation element used to define a small molecule in SigPath

element small-molecules

diagram
properties	content  complex
children	small-molecule
used by	element  sigpath-submission
annotation	documentation Groups small molecule definitions in SigPath

element smiles

diagram
type	xs:string
properties	content  simple
used by	element  small-molecule
annotation	documentation Used to describe the chemical formula (SMILE) of a molecule

element source

diagram
properties	content  complex
attributes	Name   Type   Use   Default   Fixed   Annotation spid   xs:string required

element species-binding

diagram
properties	content  complex
children	name molecule
used by	element  kinetic-bindings
annotation	documentation binds a name(usually the function of the chemical) with a chemical. Ex : enzyme and anEnzyme

element species-binding/name

diagram
type	xs:string
properties	isRef  0 content  simple
used by	elements  complex enzymatic-reaction model modified-chemical molecule named-chemical-interaction pathway sigpath-submission/pending_reviews/pending_list protein reaction small-molecule

element species-bindings-declaration

diagram
properties	content  complex
children	binding-declaration
used by	element  kinetic/custom-kinetic
annotation	documentation can be an expression like k*p1*p2, but also a numerical value (0 for instance)

element target-unit

diagram
properties	content  complex
children	unit
used by	element  model
annotation	documentation Selects the concentration units required for creating/submitting a model

element type

diagram
type	restriction of xs:string
properties	content  simple
used by	element  modified-chemical
facets	enumeration  protein enumeration  small_molecule
annotation	documentation Specifies whether a modified chemical is a protein or a small molecule

element unit

diagram
type	restriction of xs:string
properties	content  simple nillable  false
used by	elements  binding-declaration model-compartments/compartment concentration_measurement kinetic/custom-kinetic KBackward KForward KMichaelis Kp model-concentration/molecule-concentration parameter target-unit VMax VMax_EnzymeConcentration
facets	enumeration  mol/sec enumeration  micromoles/sec enumeration  mol/l enumeration  mol enumeration  sec enumeration  micromoles/l enumeration  sec-1 enumeration  min-1 enumeration  M-1.sec-1 enumeration  milliM-1.sec-1 enumeration  milliM-1.min-1 enumeration  microM-1.sec-1 enumeration  microM-1.min-1 enumeration  M-1.min-1 enumeration  M-2.sec-1 enumeration  milliM-2.sec-1 enumeration  milliM-2.min-1 enumeration  microM-2.sec-1 enumeration  microM-2.min-1 enumeration  M-2.min-1 enumeration  millimoles/l enumeration  atoms/l enumeration  l enumeration  ul enumeration  uM enumeration  M enumeration  mol/s enumeration  mM enumeration  micromol/s enumeration  micromol/sec enumeration  micromoles/s enumeration  molar enumeration  M.sec-1 enumeration  uM.sec-1 enumeration  mM.sec-1 enumeration  M.min-1 enumeration  uM.min-1 enumeration  mM.min-1 enumeration  l.sec-1 enumeration  ul.sec-1 enumeration  atoms enumeration  uM-1.sec-1
annotation	documentation Selects units for the reaction parameter

element user-comment

diagram
properties	content  complex
children	submittedBy dateSubmitted content
used by	element  user-comments
attributes	Name   Type   Use   Default   Fixed   Annotation objectId   xs:string optional
annotation	documentation Annotates a SigPath user-comment

element user-comment/submittedBy

diagram
type	xs:string
properties	isRef  0 content  simple
annotation	documentation User who submitted the comment

element user-comment/dateSubmitted

diagram
type	xs:dateTime
properties	isRef  0 content  simple
annotation	documentation Date/time at which the comment was submitted

element user-comment/content

diagram
type	xs:string
properties	isRef  0 content  simple
annotation	documentation Content of the comment

element user-comments

diagram
properties	content  complex
children	user-comment
used by	elements  complex enzymatic-reaction kinetic modified-chemical named-chemical named-chemical-interaction pathway reaction
annotation	documentation Groups user-comment

element value

diagram
type	xs:double
properties	content  simple nillable  false
used by	elements  model-compartments/compartment concentration_measurement KBackward KBKP KForward KMichaelis Kp model-concentration/molecule-concentration parameter VMax VMax_EnzymeConcentration
annotation	documentation Defines the value of a reaction parameter

element VMax

diagram
properties	content  complex
children	unit value
used by	element  enzymatic-parameters
annotation	documentation Defines the Vmax value for an enzymatic reaction

element VMax_EnzymeConcentration

diagram
properties	content  complex
children	unit value
used by	element  enzymatic-parameters
annotation	documentation The concentration of the enzyme used to measure the value of VMax.

XML Schema documentation generated by XMLSpy Schema Editor http://www.altova.com/xmlspy