Schema MIF2.xsd


schema location:  S:\pro6\psi\mi\rel2\src\MIF2.xsd
targetNamespace:  net:sf:psidev:mi
 
Elements  Complex types 
entrySet  attributeListType 
availabilityType 
baseLocationType 
bibrefType 
bioSourceType 
confidenceListType 
confidenceType 
cvType 
dbReferenceType 
dnaInteractorType 
dnaParticipantType 
experimentType 
featureType 
fullNameType 
interactionElementType 
intervalType 
labelType 
namesType 
openCvType 
positionType 
proteinInteractorType 
proteinParticipantType 
refType 
rnaInteractorType 
rnaParticipantType 
smallMoleculeInteractorType 
smallMoleculeParticipantType 
xrefType 


element entrySet
diagram
namespace net:sf:psidev:mi
children entry
attributes
Name  Type  Use  Default  Fixed  Annotation
level  xs:int  required      
version  xs:int  required      
annotation
documentation 
Root element of the Molecular Interaction Format

element entrySet/entry
diagram
namespace net:sf:psidev:mi
children source availabilityList experimentList interactorList interactionList attributeList
identity constraints
  Name  Refer  Selector  Field(s)  
key  experimentKey    experimentList/experimentDescription  @id  
keyref  experimentRef  experimentKey  interactionList/interaction/experimentsList/experimentRef  @ref  
key  interactorKey    interactorList/proteinInteractor  @id  
keyref  interactorRef  interactorKey  interactionList/interaction/participantList/proteinParticipant/proteinInteractorRef  @ref  
key  availabilityKey    availabilityList/availabilityDescription  @id  
keyref  availabilityRef  availabilityKey  availabilityList/availability  @ref  
annotation
documentation 
Describes one or more interactions as a self-contained unit. Multiple entries from different files can be concatenated into a single entrySet.

element entrySet/entry/source
diagram
namespace net:sf:psidev:mi
children names bibref xref attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
release  xs:string  optional      
releaseDate  xs:date  optional      
annotation
documentation 
Desciption of the source of the entry, usually an organisation

element entrySet/entry/source/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias
annotation
documentation 
Name(s) of the data source, for example the organisation name.

element entrySet/entry/source/bibref
diagram
namespace net:sf:psidev:mi
type bibrefType
children xref attributeList
annotation
documentation 
Bibliographic reference for the data source. Example: A paper which describes all interactions of the entry.

element entrySet/entry/source/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
Cross reference for the data source. Example: Entry in a database of databases.

element entrySet/entry/source/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
children attribute
annotation
documentation 
Further description of the source.

element entrySet/entry/availabilityList
diagram
namespace net:sf:psidev:mi
children availability
annotation
documentation 
Data availability statements, for example copyrights

element entrySet/entry/availabilityList/availability
diagram
namespace net:sf:psidev:mi
type availabilityType
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Describes data availability, e.g. through a copyright statement. If no availability is given, the data is assumed to be freely available.

element entrySet/entry/experimentList
diagram
namespace net:sf:psidev:mi
children experimentDescription
annotation
documentation 
All experiments in which the interactions of this entry have been determined

element entrySet/entry/experimentList/experimentDescription
diagram
namespace net:sf:psidev:mi
type experimentType
children names bibref xref hostOrganism interactionDetectionMethod participantIdentificationMethod featureDetectionMethod confidenceList attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Describes one set of experimental parameters, usually associated with a single publication.

element entrySet/entry/interactorList
diagram
namespace net:sf:psidev:mi
children proteinInteractor dnaInteractor rnaInteractor smallMoleculeInteractor
annotation
documentation 
List of all interactors occurring in the entry

element entrySet/entry/interactorList/proteinInteractor
diagram
namespace net:sf:psidev:mi
type proteinInteractorType
children names xref organism sequence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
A protein object in its native state, as described in sequence databases.
documentation 
Usage: A protein interactor must contain an xref to UniProt and NCBI-GI where possible.

element entrySet/entry/interactorList/dnaInteractor
diagram
namespace net:sf:psidev:mi
type dnaInteractorType
children names xref organism sequence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
A dna molecule in its native state, as described in sequence databases.

element entrySet/entry/interactorList/rnaInteractor
diagram
namespace net:sf:psidev:mi
type rnaInteractorType
children names xref organism sequence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
A rna molecule in its native state, as described in sequence databases.

element entrySet/entry/interactorList/smallMoleculeInteractor
diagram
namespace net:sf:psidev:mi
type smallMoleculeInteractorType
children names xref attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
A small molecule.

element entrySet/entry/interactionList
diagram
namespace net:sf:psidev:mi
children interaction
annotation
documentation 
List of interactions

element entrySet/entry/interactionList/interaction
diagram
namespace net:sf:psidev:mi
type extension of interactionElementType
children names xref availabilityRef availability experimentList participantList experimentalFormList inferredInteractionList interactionType negative confidenceList attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
A set of molecules interacting.

element entrySet/entry/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
children attribute
annotation
documentation 
Semi-structured additional description of the data contained in the entry.

complexType attributeListType
diagram
namespace net:sf:psidev:mi
children attribute
used by
elements entrySet/entry/source/attributeList entrySet/entry/attributeList bibrefType/attributeList openCvType/attributeList experimentType/attributeList interactionElementType/attributeList proteinInteractorType/attributeList smallMoleculeInteractorType/attributeList dnaInteractorType/attributeList rnaInteractorType/attributeList
annotation
documentation 
A list of additional attributes. Open tag-value list to allow the inclusion of additional data.

element attributeListType/attribute
diagram
namespace net:sf:psidev:mi
type extension of xs:string
attributes
Name  Type  Use  Default  Fixed  Annotation
name  xs:string  required      

complexType availabilityType
diagram
namespace net:sf:psidev:mi
type extension of xs:string
used by
elements entrySet/entry/availabilityList/availability interactionElementType/availability
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
A text describing the availability of data, e.g. a copyright statement.

complexType baseLocationType
diagram
namespace net:sf:psidev:mi
children begin beginInterval beginUndetermined end endInterval endUndetermined isLink
used by
element featureType/location
annotation
documentation 
A location on a sequence. Both begin and end can be a defined position, a fuzzy position, or undetermined.

element baseLocationType/begin
diagram
namespace net:sf:psidev:mi
type positionType
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLong  required      
status  xs:string  optional  certain    
annotation
documentation 
The integer position gives the begin position of the feature. The first base or amino acid is position 1. In combination with the numeric value, the attribute 'status' allows to express fuzzy positions, e.g. 'less than 4'.

element baseLocationType/beginInterval
diagram
namespace net:sf:psidev:mi
type intervalType
attributes
Name  Type  Use  Default  Fixed  Annotation
begin  xs:unsignedLong  required      
end  xs:unsignedLong  required      
annotation
documentation 
The begin position may be varying or unclear, but localisable to a certain range. Usually written as e.g. 3..5.

element baseLocationType/beginUndetermined
diagram
namespace net:sf:psidev:mi
type xs:boolean
annotation
documentation 
True if the begin postion of the feature is undetermined. If the entire feature position is unknown, both beginUndetermined and endUndetermined are set.

element baseLocationType/end
diagram
namespace net:sf:psidev:mi
type positionType
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLong  required      
status  xs:string  optional  certain    
annotation
documentation 
The integer position gives the end position of the feature. The first base or amino acid is position 1. In combination with the numeric value, the attribute 'status' allows to express fuzzy positions, e.g. 'less than 4'.

element baseLocationType/endInterval
diagram
namespace net:sf:psidev:mi
type intervalType
attributes
Name  Type  Use  Default  Fixed  Annotation
begin  xs:unsignedLong  required      
end  xs:unsignedLong  required      
annotation
documentation 
The end position may be varying or unclear, but localisable to a certain range. Usually written as e.g. 3..5.

element baseLocationType/endUndetermined
diagram
namespace net:sf:psidev:mi
type xs:boolean
annotation
documentation 
True if the end postion of the feature is undetermined. If the entire feature position is unknown, both beginUndetermined and endUndetermined are set.

element baseLocationType/isLink
diagram
namespace net:sf:psidev:mi
type xs:boolean
annotation
documentation 
True if the described feature is a linking feature connecting two amino acids rather than extending along the sequence. 'begin' references the first amino acid, 'end' the second. Standard example is a disulfide bridge. Does not reference another feature, therefore is only suitable for linking features on the same amino acid chain.

complexType bibrefType
diagram
namespace net:sf:psidev:mi
children xref attributeList
used by
elements entrySet/entry/source/bibref experimentType/bibref
annotation
documentation 
Bibliographic reference.

element bibrefType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
Bibliographic reference in external database, usually PubMed.

element bibrefType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
children attribute
annotation
documentation 
Alternative description of bibliographic reference if no external database entry is available.

complexType bioSourceType
diagram
namespace net:sf:psidev:mi
children names cellType compartment tissue
used by
elements experimentType/hostOrganism proteinInteractorType/organism dnaInteractorType/organism rnaInteractorType/organism
annotation
documentation 
Describes the biological source of an object, in simple form only the NCBI taxid.

element bioSourceType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias
annotation
documentation 
The names of the organism.  The short label should be a common name if it exists.  The full name should be the full name of the species (i.e. genus species).

element bioSourceType/cellType
diagram
namespace net:sf:psidev:mi
type openCvType
children names xref attributeList
annotation
documentation 
Description of the cell type. Currently no species-independent controlled vocabulary for cell types is available, therefore the choice of reference database(s) is open to the data provider.

element bioSourceType/compartment
diagram
namespace net:sf:psidev:mi
type openCvType
children names xref attributeList
annotation
documentation 
The subcellular compartement of the object. It is strongly recommended to refer to the Gene Ontology cellular component in this element.

element bioSourceType/tissue
diagram
namespace net:sf:psidev:mi
type openCvType
children names xref attributeList
annotation
documentation 
Description of the source tissue. Currently no species-independent controlled vocabulary for tissues is available, therefore the choice of reference database(s) is open to the data provider.

complexType confidenceListType
diagram
namespace net:sf:psidev:mi
children confidence
used by
elements experimentType/confidenceList interactionElementType/confidenceList proteinParticipantType/confidenceList smallMoleculeParticipantType/confidenceList dnaParticipantType/confidenceList rnaParticipantType/confidenceList
annotation
documentation 
A list of confidence values.

element confidenceListType/confidence
diagram
namespace net:sf:psidev:mi
type confidenceType
children unit value

complexType confidenceType
diagram
namespace net:sf:psidev:mi
children unit value
used by
element confidenceListType/confidence
annotation
documentation 
A confidence value.

element confidenceType/unit
diagram
namespace net:sf:psidev:mi
type openCvType
children names xref attributeList

element confidenceType/value
diagram
namespace net:sf:psidev:mi
type xs:string

complexType cvType
diagram
namespace net:sf:psidev:mi
children names xref
used by
elements interactionElementType/experimentalFormList/proteinExperimentalForm/experimentalForm interactionElementType/experimentalFormList/dnaExperimentalForm/experimentalForm interactionElementType/experimentalFormList/rnaExperimentalForm/experimentalForm interactionElementType/experimentalFormList/proteinExperimentalForm/experimentalRole interactionElementType/experimentalFormList/dnaExperimentalForm/experimentalRole interactionElementType/experimentalFormList/rnaExperimentalForm/experimentalRole featureType/featureDetectionMethod experimentType/featureDetectionMethod featureType/featureType experimentType/interactionDetectionMethod interactionElementType/interactionType experimentType/participantIdentificationMethod proteinParticipantType/participantRole smallMoleculeParticipantType/participantRole dnaParticipantType/participantRole rnaParticipantType/participantRole
annotation
documentation 
Reference to an external controlled vocabulary.

element cvType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias
annotation
documentation 
Name of the controlled vocabulary term.

element cvType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
Source of the controlled vocabulary term.  E.g. the name of the CV and the term ID.

complexType dbReferenceType
diagram
namespace net:sf:psidev:mi
used by
elements xrefType/primaryRef xrefType/secondaryRef
attributes
Name  Type  Use  Default  Fixed  Annotation
db  xs:string  required      
id  xs:string  required      
secondary  xs:string  optional      
version  xs:string  optional      
annotation
documentation 
Refers to a unique object in an external database.

complexType dnaInteractorType
diagram
namespace net:sf:psidev:mi
children names xref organism sequence attributeList
used by
elements entrySet/entry/interactorList/dnaInteractor dnaParticipantType/dnaInteractor
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Describes a DNA interactor.

element dnaInteractorType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias
annotation
documentation 
Name(s).  The short label is typically a short name that could appear as a label on a diagram.

element dnaInteractorType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
An interactor should have an xref whenever possible. If the interactor is not available in external databases, it must be characterised within this object e.g. by its sequence.

element dnaInteractorType/organism
diagram
namespace net:sf:psidev:mi
type extension of bioSourceType
children names cellType compartment tissue
attributes
Name  Type  Use  Default  Fixed  Annotation
ncbiTaxId  xs:int  required      
annotation
documentation 
The normal source organism of the interactor.

element dnaInteractorType/sequence
diagram
namespace net:sf:psidev:mi
type xs:token
annotation
documentation 
Sequence in uppercase

element dnaInteractorType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
children attribute
annotation
documentation 
Allows semi-structured additional annotation of the interactor.

complexType dnaParticipantType
diagram
namespace net:sf:psidev:mi
children dnaInteractorRef dnaInteractor featureList confidenceList participantRole
used by
element interactionElementType/participantList/dnaParticipant
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
A dna molecule participating in an interaction.

element dnaParticipantType/dnaInteractorRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
References an interactor described in the interactorList of the entry

element dnaParticipantType/dnaInteractor
diagram
namespace net:sf:psidev:mi
type dnaInteractorType
children names xref organism sequence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Fully describes an interactor

element dnaParticipantType/featureList
diagram
namespace net:sf:psidev:mi
children feature
annotation
documentation 
Sequence features relevant for the interaction, for example binding domains

element dnaParticipantType/featureList/feature
diagram
namespace net:sf:psidev:mi
type extension of featureType
children names xref featureType featureDetectionMethod location
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      

element dnaParticipantType/confidenceList
diagram
namespace net:sf:psidev:mi
type confidenceListType
children confidence
annotation
documentation 
Confidence in participant detection.

element dnaParticipantType/participantRole
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
The role of the participant in the interaction.

complexType experimentType
diagram
namespace net:sf:psidev:mi
children names bibref xref hostOrganism interactionDetectionMethod participantIdentificationMethod featureDetectionMethod confidenceList attributeList
used by
elements entrySet/entry/experimentList/experimentDescription interactionElementType/experimentList/experimentDescription
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Describes one set of experimental parameters.

element experimentType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias

element experimentType/bibref
diagram
namespace net:sf:psidev:mi
type bibrefType
children xref attributeList
annotation
documentation 
Publication describing the experiment.

element experimentType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
Refers to external database description of the experiment.

element experimentType/hostOrganism
diagram
namespace net:sf:psidev:mi
type extension of bioSourceType
children names cellType compartment tissue
attributes
Name  Type  Use  Default  Fixed  Annotation
ncbiTaxId  xs:int  required      
annotation
documentation 
The host organism in which the experiment has been performed.

element experimentType/interactionDetectionMethod
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
Experimental method to determine the interaction. External controlled vocabulary.

element experimentType/participantIdentificationMethod
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
Experimental method to determine the interactors involved in the interaction. External controlled vocabulary.

element experimentType/featureDetectionMethod
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
Experimental method to determine the features of interactors. External controlled vocabulary.

element experimentType/confidenceList
diagram
namespace net:sf:psidev:mi
type confidenceListType
children confidence
annotation
documentation 
Confidence in this experiment.  Usually a statistical measure.

element experimentType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
children attribute
annotation
documentation 
Semi-structured additional description of the experiment.

complexType featureType
diagram
namespace net:sf:psidev:mi
children names xref featureType featureDetectionMethod location
used by
elements proteinParticipantType/featureList/feature dnaParticipantType/featureList/feature rnaParticipantType/featureList/feature
annotation
documentation 
A feature, e.g. domain, on a sequence.

element featureType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias
annotation
documentation 
Names for the feature, e.g. SH3 domain.

element featureType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
Reference to an external feature description, for example InterPro entry.

element featureType/featureType
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
Description and classification of the feature

element featureType/featureDetectionMethod
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
Experimental method used to identify the feature.

element featureType/location
diagram
namespace net:sf:psidev:mi
type baseLocationType
children begin beginInterval beginUndetermined end endInterval endUndetermined isLink
annotation
documentation 
Location of the feature on the sequence of the interactor. On feature may have more than one location, used e.g. for features which involve sequence positions close in the folded, three-dimensional state of a protein, but non-continuous along the sequence.

complexType fullNameType
diagram
namespace net:sf:psidev:mi
type extension of xs:string
annotation
documentation 
Full, descriptive object name.

complexType interactionElementType
diagram
namespace net:sf:psidev:mi
children names xref availabilityRef availability experimentList participantList experimentalFormList inferredInteractionList interactionType negative confidenceList attributeList
used by
element entrySet/entry/interactionList/interaction
annotation
documentation 
A molecular interaction.

element interactionElementType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias
annotation
documentation 
Name(s) of the interaction.

element interactionElementType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
Interaction database ID

element interactionElementType/availabilityRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
References an availability statement already present in this entry.

element interactionElementType/availability
diagram
namespace net:sf:psidev:mi
type availabilityType
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Describes the availability of the interaction data. If no availability is given, the data is assumed to be freely available.

element interactionElementType/experimentList
diagram
namespace net:sf:psidev:mi
children experimentRef experimentDescription
annotation
documentation 
List of experiments in which this interaction has been determined.

element interactionElementType/experimentList/experimentRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
References an experiment already present in this entry.

element interactionElementType/experimentList/experimentDescription
diagram
namespace net:sf:psidev:mi
type experimentType
children names bibref xref hostOrganism interactionDetectionMethod participantIdentificationMethod featureDetectionMethod confidenceList attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
An experiment in which this interaction has been determined.

element interactionElementType/participantList
diagram
namespace net:sf:psidev:mi
children proteinParticipant dnaParticipant rnaParticipant smallMoleculeParticipant
annotation
documentation 
A list of molecules participating in this interaction. An interaction has one (intramolecular), two (binary), or more (n-ary, complexes)  participants.

element interactionElementType/participantList/proteinParticipant
diagram
namespace net:sf:psidev:mi
type extension of proteinParticipantType
children proteinInteractorRef proteinInteractor featureList confidenceList participantRole
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      

element interactionElementType/participantList/dnaParticipant
diagram
namespace net:sf:psidev:mi
type dnaParticipantType
children dnaInteractorRef dnaInteractor featureList confidenceList participantRole
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      

element interactionElementType/participantList/rnaParticipant
diagram
namespace net:sf:psidev:mi
type rnaParticipantType
children rnaInteractorRef rnaInteractor featureList confidenceList participantRole
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      

element interactionElementType/participantList/smallMoleculeParticipant
diagram
namespace net:sf:psidev:mi
type smallMoleculeParticipantType
children smallMoleculeInteractorRef smallMoleculeInteractor confidenceList participantRole
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      

element interactionElementType/experimentalFormList
diagram
namespace net:sf:psidev:mi
children proteinExperimentalForm dnaExperimentalForm rnaExperimentalForm
annotation
documentation 
The specific experimental form of molecules in an experiment, e.g. chemical modifications and added 'tags'.

element interactionElementType/experimentalFormList/proteinExperimentalForm
diagram
namespace net:sf:psidev:mi
children experimentRef proteinParticipantRef isTagged isOverexpressed experimentalForm experimentalRole
annotation
documentation 
Describes the experimental form of a protein in a specific experiment.

element interactionElementType/experimentalFormList/proteinExperimentalForm/experimentRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
This experimental form has been used in the experiment referred to.

element interactionElementType/experimentalFormList/proteinExperimentalForm/proteinParticipantRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
A reference to the experimental form of the participant.

element interactionElementType/experimentalFormList/proteinExperimentalForm/isTagged
diagram
namespace net:sf:psidev:mi
type xs:boolean
annotation
documentation 
True if the protein has been tagged in the experiment.

element interactionElementType/experimentalFormList/proteinExperimentalForm/isOverexpressed
diagram
namespace net:sf:psidev:mi
type xs:boolean
annotation
documentation 
True if the protein has been overexpressed in the experiment.

element interactionElementType/experimentalFormList/proteinExperimentalForm/experimentalForm
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
The form of the participant in the interaction, e.g. protein tags.

element interactionElementType/experimentalFormList/proteinExperimentalForm/experimentalRole
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
The role of the participant in the interaction, e.g. bait.

element interactionElementType/experimentalFormList/dnaExperimentalForm
diagram
namespace net:sf:psidev:mi
children experimentRef dnaParticipantRef experimentalForm experimentalRole
annotation
documentation 
Describes the experimental form of DNA in a specific experiment.

element interactionElementType/experimentalFormList/dnaExperimentalForm/experimentRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
This experimental form has been used in the experiment referred to.

element interactionElementType/experimentalFormList/dnaExperimentalForm/dnaParticipantRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
A reference to the experimental form of the participant.

element interactionElementType/experimentalFormList/dnaExperimentalForm/experimentalForm
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
The form of the participant in the interaction.

element interactionElementType/experimentalFormList/dnaExperimentalForm/experimentalRole
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
The role of the participant in the interaction.

element interactionElementType/experimentalFormList/rnaExperimentalForm
diagram
namespace net:sf:psidev:mi
children experimentRef rnaParticipantRef isOverexpressed experimentalForm experimentalRole
annotation
documentation 
Describes the experimental form of RNA in a specific experiment.

element interactionElementType/experimentalFormList/rnaExperimentalForm/experimentRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
This experimental form has been used in the experiment referred to.

element interactionElementType/experimentalFormList/rnaExperimentalForm/rnaParticipantRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
A reference to the experimental form of the participant.

element interactionElementType/experimentalFormList/rnaExperimentalForm/isOverexpressed
diagram
namespace net:sf:psidev:mi
type xs:boolean
annotation
documentation 
True if the RNA has been overexpressed in the experiment.

element interactionElementType/experimentalFormList/rnaExperimentalForm/experimentalForm
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
The form of the participant in the interaction.

element interactionElementType/experimentalFormList/rnaExperimentalForm/experimentalRole
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
The role of the participant in the interaction.

element interactionElementType/inferredInteractionList
diagram
namespace net:sf:psidev:mi
children inferredInteraction
annotation
documentation 
Describes inferred interactions, usually combining data from more than one experiment. Examples: 1: Show the topology of binary interactions within a complex. 2: Interaction inferred from multiple experiments which on their own would not support the interaction. Example: A-B in experiment 1, B-C- in experiment 2, A-C is the inferred interaction.

element interactionElementType/inferredInteractionList/inferredInteraction
diagram
namespace net:sf:psidev:mi
children experimentRef participant

element interactionElementType/inferredInteractionList/inferredInteraction/experimentRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
Reference to experiment which provides evidence for the inferred interaction.

element interactionElementType/inferredInteractionList/inferredInteraction/participant
diagram
namespace net:sf:psidev:mi
children proteinParticipantRef proteinFeatureRef dnaParticipantRef dnaFeatureRef rnaParticipantRef rnaFeatureRef smallMoleculeParticipantRef
annotation
documentation 
Participant of the inferred interaction.

element interactionElementType/inferredInteractionList/inferredInteraction/participant/proteinParticipantRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      

element interactionElementType/inferredInteractionList/inferredInteraction/participant/proteinFeatureRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      

element interactionElementType/inferredInteractionList/inferredInteraction/participant/dnaParticipantRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      

element interactionElementType/inferredInteractionList/inferredInteraction/participant/dnaFeatureRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      

element interactionElementType/inferredInteractionList/inferredInteraction/participant/rnaParticipantRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      

element interactionElementType/inferredInteractionList/inferredInteraction/participant/rnaFeatureRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      

element interactionElementType/inferredInteractionList/inferredInteraction/participant/smallMoleculeParticipantRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      

element interactionElementType/interactionType
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
External controlled vocabulary characterising the interaction type, for example "aggregation".

element interactionElementType/negative
diagram
namespace net:sf:psidev:mi
type xs:boolean
annotation
documentation 
If true, this interaction has been shown NOT to occur under the described experimental conditions. Default false. If this optional attribute is missing, it is assumed to be set to false.

element interactionElementType/confidenceList
diagram
namespace net:sf:psidev:mi
type confidenceListType
children confidence
annotation
documentation 
Confidence in this interaction.  Usually a statistical measure.

element interactionElementType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
children attribute
annotation
documentation 
Semi-structured additional description of the data contained in the entry.

complexType intervalType
diagram
namespace net:sf:psidev:mi
used by
elements baseLocationType/beginInterval baseLocationType/endInterval
attributes
Name  Type  Use  Default  Fixed  Annotation
begin  xs:unsignedLong  required      
end  xs:unsignedLong  required      
annotation
documentation 
A interval on a sequence.

complexType labelType
diagram
namespace net:sf:psidev:mi
type extension of xs:string
annotation
documentation 
A short alphanumeric label identifying an object. Not necessarily unique.

complexType namesType
diagram
namespace net:sf:psidev:mi
children shortLabel fullName alias
used by
elements entrySet/entry/source/names bioSourceType/names cvType/names openCvType/names featureType/names experimentType/names interactionElementType/names proteinInteractorType/names smallMoleculeInteractorType/names dnaInteractorType/names rnaInteractorType/names
annotation
documentation 
Names for an object.

element namesType/shortLabel
diagram
namespace net:sf:psidev:mi
type xs:string

element namesType/fullName
diagram
namespace net:sf:psidev:mi
type xs:string

element namesType/alias
diagram
namespace net:sf:psidev:mi
type xs:string

complexType openCvType
diagram
namespace net:sf:psidev:mi
children names xref attributeList
used by
elements bioSourceType/cellType bioSourceType/compartment bioSourceType/tissue confidenceType/unit
annotation
documentation 
Allows to reference an external controlled vocabulary, or to directly include a value if no suitable external definition is available.

element openCvType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias
annotation
documentation 
This contains the controlled vocabulary terms, as a short and optionally as a long form.

element openCvType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
Refers to the term of the controlled vocabulary in an external database.

element openCvType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
children attribute
annotation
documentation 
If no suitable external controlled vocabulary is available, this attributeList can be used to describe the term. Example: Attribute name: Mouse atlas tissue name; attribute value: spinal cord, day 30.

complexType positionType
diagram
namespace net:sf:psidev:mi
used by
elements baseLocationType/begin baseLocationType/end
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLong  required      
status  xs:string  optional  certain    

complexType proteinInteractorType
diagram
namespace net:sf:psidev:mi
children names xref organism sequence attributeList
used by
elements entrySet/entry/interactorList/proteinInteractor proteinParticipantType/proteinInteractor
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Describes a protein interactor.

element proteinInteractorType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias
annotation
documentation 
Name(s).  The short label is typically a short name that could appear as a label on a diagram.

element proteinInteractorType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
An interactor should have an xref whenever possible. If the interactor is not available in external databases, it must be characterised within this object e.g. by its sequence.

element proteinInteractorType/organism
diagram
namespace net:sf:psidev:mi
type extension of bioSourceType
children names cellType compartment tissue
attributes
Name  Type  Use  Default  Fixed  Annotation
ncbiTaxId  xs:int  required      
annotation
documentation 
The normal source organism of the interactor.

element proteinInteractorType/sequence
diagram
namespace net:sf:psidev:mi
type xs:token
annotation
documentation 
Sequence in uppercase
documentation 
Usage:

element proteinInteractorType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
children attribute
annotation
documentation 
Allows semi-structured additional annotation of the interactor.

complexType proteinParticipantType
diagram
namespace net:sf:psidev:mi
children proteinInteractorRef proteinInteractor featureList confidenceList participantRole
used by
element interactionElementType/participantList/proteinParticipant
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
A protein participating in an interaction.

element proteinParticipantType/proteinInteractorRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
References an interactor described in the interactorList of the entry

element proteinParticipantType/proteinInteractor
diagram
namespace net:sf:psidev:mi
type proteinInteractorType
children names xref organism sequence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Fully describes an interactor

element proteinParticipantType/featureList
diagram
namespace net:sf:psidev:mi
children feature
annotation
documentation 
Sequence features relevant for the interaction, for example binding domains

element proteinParticipantType/featureList/feature
diagram
namespace net:sf:psidev:mi
type extension of featureType
children names xref featureType featureDetectionMethod location
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      

element proteinParticipantType/confidenceList
diagram
namespace net:sf:psidev:mi
type confidenceListType
children confidence
annotation
documentation 
Confidence in participant detection.

element proteinParticipantType/participantRole
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
The role of the participant in the interaction. This describes the biological role, e.g. enzyme or enzyme target. The experimental role of the participant, e.g. 'bait', is shown in proteinExperimentalForm.

complexType refType
diagram
namespace net:sf:psidev:mi
used by
elements interactionElementType/availabilityRef interactionElementType/inferredInteractionList/inferredInteraction/participant/dnaFeatureRef dnaParticipantType/dnaInteractorRef interactionElementType/experimentalFormList/dnaExperimentalForm/dnaParticipantRef interactionElementType/inferredInteractionList/inferredInteraction/participant/dnaParticipantRef interactionElementType/experimentList/experimentRef interactionElementType/experimentalFormList/proteinExperimentalForm/experimentRef interactionElementType/experimentalFormList/dnaExperimentalForm/experimentRef interactionElementType/experimentalFormList/rnaExperimentalForm/experimentRef interactionElementType/inferredInteractionList/inferredInteraction/experimentRef interactionElementType/inferredInteractionList/inferredInteraction/participant/proteinFeatureRef proteinParticipantType/proteinInteractorRef interactionElementType/inferredInteractionList/inferredInteraction/participant/proteinParticipantRef interactionElementType/experimentalFormList/proteinExperimentalForm/proteinParticipantRef interactionElementType/inferredInteractionList/inferredInteraction/participant/rnaFeatureRef rnaParticipantType/rnaInteractorRef interactionElementType/experimentalFormList/rnaExperimentalForm/rnaParticipantRef interactionElementType/inferredInteractionList/inferredInteraction/participant/rnaParticipantRef smallMoleculeParticipantType/smallMoleculeInteractorRef interactionElementType/inferredInteractionList/inferredInteraction/participant/smallMoleculeParticipantRef
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
Refers to an object within the same entry by its id.

complexType rnaInteractorType
diagram
namespace net:sf:psidev:mi
children names xref organism sequence attributeList
used by
elements entrySet/entry/interactorList/rnaInteractor rnaParticipantType/rnaInteractor
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Describes a RNA interactor.

element rnaInteractorType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias
annotation
documentation 
Name(s).  The short label is typically a short name that could appear as a label on a diagram.

element rnaInteractorType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
An interactor should have an xref whenever possible. If the interactor is not available in external databases, it must be characterised within this object e.g. by its sequence.

element rnaInteractorType/organism
diagram
namespace net:sf:psidev:mi
type extension of bioSourceType
children names cellType compartment tissue
attributes
Name  Type  Use  Default  Fixed  Annotation
ncbiTaxId  xs:int  required      
annotation
documentation 
The normal source organism of the interactor.

element rnaInteractorType/sequence
diagram
namespace net:sf:psidev:mi
type xs:token
annotation
documentation 
Sequence in uppercase

element rnaInteractorType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
children attribute
annotation
documentation 
Allows semi-structured additional annotation of the interactor.

complexType rnaParticipantType
diagram
namespace net:sf:psidev:mi
children rnaInteractorRef rnaInteractor featureList confidenceList participantRole
used by
element interactionElementType/participantList/rnaParticipant
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
A rna molecule participating in an interaction.

element rnaParticipantType/rnaInteractorRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
References an interactor described in the interactorList of the entry

element rnaParticipantType/rnaInteractor
diagram
namespace net:sf:psidev:mi
type rnaInteractorType
children names xref organism sequence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Fully describes an interactor

element rnaParticipantType/featureList
diagram
namespace net:sf:psidev:mi
children feature
annotation
documentation 
Sequence features relevant for the interaction, for example binding domains

element rnaParticipantType/featureList/feature
diagram
namespace net:sf:psidev:mi
type extension of featureType
children names xref featureType featureDetectionMethod location
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      

element rnaParticipantType/confidenceList
diagram
namespace net:sf:psidev:mi
type confidenceListType
children confidence
annotation
documentation 
Confidence in participant detection.

element rnaParticipantType/participantRole
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
The role of the participant in the interaction.

complexType smallMoleculeInteractorType
diagram
namespace net:sf:psidev:mi
children names xref attributeList
used by
elements entrySet/entry/interactorList/smallMoleculeInteractor smallMoleculeParticipantType/smallMoleculeInteractor
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Describes a small molecule interactor.

element smallMoleculeInteractorType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName alias
annotation
documentation 
Protein name(s).  The short label is typically a short name that could appear as a label on a diagram.

element smallMoleculeInteractorType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
children primaryRef secondaryRef
annotation
documentation 
An interactor should have an xref whenever possible. If the interactor is not available in external databases, it must be characterised within this object, using the attrubuteList.

element smallMoleculeInteractorType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
children attribute

complexType smallMoleculeParticipantType
diagram
namespace net:sf:psidev:mi
children smallMoleculeInteractorRef smallMoleculeInteractor confidenceList participantRole
used by
element interactionElementType/participantList/smallMoleculeParticipant
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
A small molecule participating in an interaction.

element smallMoleculeParticipantType/smallMoleculeInteractorRef
diagram
namespace net:sf:psidev:mi
type refType
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:int  required      
annotation
documentation 
References an interactor described in the interactorList of the entry

element smallMoleculeParticipantType/smallMoleculeInteractor
diagram
namespace net:sf:psidev:mi
type smallMoleculeInteractorType
children names xref attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:int  required      
annotation
documentation 
Fully describes an interactor

element smallMoleculeParticipantType/confidenceList
diagram
namespace net:sf:psidev:mi
type confidenceListType
children confidence
annotation
documentation 
Confidence in participant detection.

element smallMoleculeParticipantType/participantRole
diagram
namespace net:sf:psidev:mi
type cvType
children names xref
annotation
documentation 
The role of the participant in the interaction.

complexType xrefType
diagram
namespace net:sf:psidev:mi
children primaryRef secondaryRef
used by
elements entrySet/entry/source/xref bibrefType/xref cvType/xref openCvType/xref featureType/xref experimentType/xref interactionElementType/xref proteinInteractorType/xref smallMoleculeInteractorType/xref dnaInteractorType/xref rnaInteractorType/xref
annotation
documentation 
Crossreference to an external database. Crossreferences to literature databases, e.g. PubMed, should not be put into this structure, but into the bibRef element where possible.

element xrefType/primaryRef
diagram
namespace net:sf:psidev:mi
type dbReferenceType
attributes
Name  Type  Use  Default  Fixed  Annotation
db  xs:string  required      
id  xs:string  required      
secondary  xs:string  optional      
version  xs:string  optional      
annotation
documentation 
Primary reference to an external database.

element xrefType/secondaryRef
diagram
namespace net:sf:psidev:mi
type dbReferenceType
attributes
Name  Type  Use  Default  Fixed  Annotation
db  xs:string  required      
id  xs:string  required      
secondary  xs:string  optional      
version  xs:string  optional      
annotation
documentation 
Further external objects describing the object.


XML Schema documentation generated with XMLSPY Schema Editor http://www.altova.com/xmlspy