Schema MIF25.xsd


schema location:  http://psidev.sf.net/mi/rel25/src/MIF25.xsd
attribute form default:  unqualified
element form default:  qualified
targetNamespace:  net:sf:psidev:mi
 
Elements  Complex types 
entrySet  attributeListType 
availabilityType 
baseLocationType 
bibrefType 
bioSourceType 
confidenceListType 
confidenceType 
cvType 
dbReferenceType 
experimentRefListType 
experimentType 
featureElementType 
fullNameType 
interactionElementType 
interactorElementType 
intervalType 
labelType 
namesType 
openCvType 
parameterType 
participantType 
positionType 
xrefType 


element entrySet
diagram
namespace net:sf:psidev:mi
properties
content complex
children entry
attributes
Name  Type  Use  Default  Fixed  Annotation
level  xs:intrequired    2  
documentation 
PSI MI level
version  xs:intrequired    5  
documentation 
PSI MI version within given level
minorVersion  xs:intoptional    3  
annotation
documentation 
Root element of the Molecular Interaction Format

element entrySet/entry
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children source availabilityList experimentList interactorList interactionList attributeList
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
properties
isRef 0
content complex
children names bibref xref attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
release  optional      
releaseDate  xs:dateoptional      
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
properties
isRef 0
content complex
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
properties
isRef 0
content complex
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
properties
isRef 0
content complex
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
properties
isRef 0
content complex
children attribute
annotation
documentation 
Further description of the source.

element entrySet/entry/availabilityList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children availability
annotation
documentation 
Data availability statements, for example copyrights

element entrySet/entry/availabilityList/availability
diagram
namespace net:sf:psidev:mi
type availabilityType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
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
properties
isRef 0
content complex
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
properties
isRef 0
content complex
children names bibref xref hostOrganismList interactionDetectionMethod participantIdentificationMethod featureDetectionMethod confidenceList attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
documentation 
All major objects have a numerical id which must be unique to that object within an entry. The object may be repeated, though, e.g. in the denormalised representation.
annotation
documentation 
Describes one set of experimental parameters, usually associated with a single publication.

element entrySet/entry/interactorList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children interactor
annotation
documentation 
List of all interactors occurring in the entry

element entrySet/entry/interactorList/interactor
diagram
namespace net:sf:psidev:mi
type interactorElementType
properties
isRef 0
content complex
children names xref interactorType organism sequence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
documentation 
All major objects have a numerical id which is unique to that object within a PSI MI file. The object may be repeated, though, e.g. in the denormalised representation.
annotation
documentation 
A molecule object in its native state, as described in databases.
documentation 
Usage: A protein interactor must contain an xref to UniProt and NCBI-GI where possible.

element entrySet/entry/interactionList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children interaction
annotation
documentation 
List of interactions

element entrySet/entry/interactionList/interaction
diagram
namespace net:sf:psidev:mi
type extension of interactionElementType
properties
isRef 0
content complex
children names xref availabilityRef availability experimentList participantList inferredInteractionList interactionType modelled intraMolecular negative confidenceList parameterList attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
imexId  xs:stringoptional      
documentation 
Interaction identifier assigned by the IMEx consortium. Will be unique for an interaction determined in one publication. Details defined in the IMEx documents.
id  xs:intrequired      
documentation 
All major objects have a numerical id which is unique to that object within a PSI MI file. The object may be repeated, though, e.g. in the denormalised representation.
annotation
documentation 
A set of molecules interacting.

element entrySet/entry/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
properties
isRef 0
content complex
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 dbReferenceType/attributeList bibrefType/attributeList openCvType/attributeList featureElementType/attributeList experimentType/attributeList interactionElementType/attributeList interactorElementType/attributeList participantType/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
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
name  required      
documentation 
The name of the attribute.
nameAc  optional      
documentation 
Enables control of the attribute type through reference to an external controlled vocabulary. Root element in the PSI MI CV is MI:0590.

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

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

element baseLocationType/startStatus
diagram
namespace net:sf:psidev:mi
type cvType
properties
isRef 0
content complex
children names xref
annotation
documentation 
Attribute of the start positions, e.g. "certain" or "n-terminal"

element baseLocationType/begin
diagram
namespace net:sf:psidev:mi
type positionType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLongrequired      
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
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
begin  xs:unsignedLongrequired      
end  xs:unsignedLongrequired      
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/endStatus
diagram
namespace net:sf:psidev:mi
type cvType
properties
isRef 0
content complex
children names xref
annotation
documentation 
Attribute of the end positions, e.g. "certain" or "c-terminal"

element baseLocationType/end
diagram
namespace net:sf:psidev:mi
type positionType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLongrequired      
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. 'more than 400'.

element baseLocationType/endInterval
diagram
namespace net:sf:psidev:mi
type intervalType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
begin  xs:unsignedLongrequired      
end  xs:unsignedLongrequired      
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/isLink
diagram
namespace net:sf:psidev:mi
type xs:boolean
properties
isRef 0
content simple
default false
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
properties
isRef 0
content complex
children primaryRef secondaryRef
annotation
documentation 
Bibliographic reference in external database, usually PubMed.

element bibrefType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
properties
isRef 0
content complex
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/hostOrganismList/hostOrganism participantType/hostOrganismList/hostOrganism interactorElementType/organism
attributes
Name  Type  Use  Default  Fixed  Annotation
ncbiTaxId  xs:intrequired      
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
properties
isRef 0
content complex
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
properties
isRef 0
content complex
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
properties
isRef 0
content complex
children names xref attributeList
annotation
documentation 
The subcellular compartment 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
properties
isRef 0
content complex
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 participantType/confidenceList
annotation
documentation 
A list of confidence values.

element confidenceListType/confidence
diagram
namespace net:sf:psidev:mi
type extension of confidenceType
properties
isRef 0
content complex
children unit value experimentRefList

element confidenceListType/confidence/experimentRefList
diagram
namespace net:sf:psidev:mi
type experimentRefListType
properties
isRef 0
content complex
children experimentRef
annotation
documentation 
Each experiment might assign a different confidence to this object. If no experimentRef is given, it is assumed this confidence refers to all experiments linked to the object.

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
properties
isRef 0
content complex
children names xref attributeList

element confidenceType/value
diagram
namespace net:sf:psidev:mi
type restriction of xs:string
properties
isRef 0
content simple
facets
minLength 1

complexType cvType
diagram
namespace net:sf:psidev:mi
children names xref
used by
elements participantType/biologicalRole baseLocationType/endStatus participantType/experimentalPreparationList/experimentalPreparation participantType/experimentalRoleList/experimentalRole featureElementType/featureDetectionMethod experimentType/featureDetectionMethod featureElementType/featureType experimentType/interactionDetectionMethod interactionElementType/interactionType interactorElementType/interactorType experimentType/participantIdentificationMethod participantType/participantIdentificationMethodList/participantIdentificationMethod baseLocationType/startStatus
annotation
documentation 
Reference to an external controlled vocabulary.

element cvType/names
diagram
namespace net:sf:psidev:mi
type namesType
properties
isRef 0
content complex
children shortLabel fullName alias
annotation
documentation 
Name of the controlled vocabulary term.

element cvType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
properties
isRef 0
content complex
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
children attributeList
used by
elements xrefType/primaryRef xrefType/secondaryRef
attributes
Name  Type  Use  Default  Fixed  Annotation
db  required      
documentation 
Name of the external database. Taken from the controlled vocabulary of databases.
dbAc  optional      
documentation 
Accession number of the database in the database CV. This element is controlled by the PSI-MI controlled vocabulary "database citation", root term id MI:0444.
id  required      
documentation 
Primary identifier of the object in the external database, e.g. UniProt accession number.
secondary  optional      
documentation 
Secondary identifier of the object in the external database, e.g. UniProt ID.
version  optional      
documentation 
The version number of the object in the external database.
refType  optional      
documentation 
Reference type, e.g. "identity" if this reference referes to an identical object in the external database, or "see-also" for additional information. Controlled by CV.
refTypeAc  optional      
documentation 
Reference type accession number from the CV of reference types. This element is controlled by the PSI-MI controlled vocabulary "xref type", root term id MI:0353.
annotation
documentation 
Refers to a unique object in an external database.

element dbReferenceType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
properties
isRef 0
content complex
children attribute

complexType experimentRefListType
diagram
namespace net:sf:psidev:mi
children experimentRef
used by
elements confidenceListType/confidence/experimentRefList featureElementType/experimentRefList interactionElementType/inferredInteractionList/inferredInteraction/experimentRefList participantType/participantIdentificationMethodList/participantIdentificationMethod/experimentRefList participantType/experimentalRoleList/experimentalRole/experimentRefList participantType/experimentalPreparationList/experimentalPreparation/experimentRefList participantType/experimentalInteractorList/experimentalInteractor/experimentRefList participantType/hostOrganismList/hostOrganism/experimentRefList
annotation
documentation 
Refers to a list of experiments within the same entry.

element experimentRefListType/experimentRef
diagram
namespace net:sf:psidev:mi
type xs:int
properties
isRef 0
content simple
annotation
documentation 
References an experiment already present in this entry.

complexType experimentType
diagram
namespace net:sf:psidev:mi
children names bibref xref hostOrganismList interactionDetectionMethod participantIdentificationMethod featureDetectionMethod confidenceList attributeList
used by
elements entrySet/entry/experimentList/experimentDescription interactionElementType/experimentList/experimentDescription
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
documentation 
All major objects have a numerical id which must be unique to that object within an entry. The object may be repeated, though, e.g. in the denormalised representation.
annotation
documentation 
Describes one set of experimental parameters.

element experimentType/names
diagram
namespace net:sf:psidev:mi
type namesType
properties
isRef 0
content complex
children shortLabel fullName alias

element experimentType/bibref
diagram
namespace net:sf:psidev:mi
type bibrefType
properties
isRef 0
content complex
children xref attributeList
annotation
documentation 
Publication describing the experiment.

element experimentType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
properties
isRef 0
content complex
children primaryRef secondaryRef
annotation
documentation 
Refers to external database description of the experiment.

element experimentType/hostOrganismList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children hostOrganism
annotation
documentation 
The host organism(s) in which the experiment has been performed.

element experimentType/hostOrganismList/hostOrganism
diagram
namespace net:sf:psidev:mi
type extension of bioSourceType
properties
isRef 0
content complex
children names cellType compartment tissue
attributes
Name  Type  Use  Default  Fixed  Annotation
ncbiTaxId  xs:intrequired      

element experimentType/interactionDetectionMethod
diagram
namespace net:sf:psidev:mi
type cvType
properties
isRef 0
content complex
children names xref
annotation
documentation 
Experimental method to determine the interaction. This element is controlled by the PSI-MI controlled vocabulary "interaction detection method", root term id MI:0001.

element experimentType/participantIdentificationMethod
diagram
namespace net:sf:psidev:mi
type cvType
properties
isRef 0
content complex
children names xref
annotation
documentation 
Experimental method to determine the interactors involved in the interaction. This element is controlled by the PSI-MI controlled vocabulary "participant identification method", root term id MI:0002.

element experimentType/featureDetectionMethod
diagram
namespace net:sf:psidev:mi
type cvType
properties
isRef 0
content complex
children names xref
annotation
documentation 
Experimental method to determine the features of interactors. If this element is filled it is assumed to apply to all features described in the experiment. But can be overridden by the featureDetectionMethod given in the individual feature. This element is controlled by the PSI-MI controlled vocabulary "feature detection method", root term id MI:0003.

element experimentType/confidenceList
diagram
namespace net:sf:psidev:mi
type confidenceListType
properties
isRef 0
content complex
children confidence
annotation
documentation 
Confidence in this experiment.  Usually a statistical measure.

element experimentType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
properties
isRef 0
content complex
children attribute
annotation
documentation 
Semi-structured additional description of the experiment.

complexType featureElementType
diagram
namespace net:sf:psidev:mi
children names xref featureType featureDetectionMethod experimentRefList featureRangeList attributeList
used by
element participantType/featureList/feature
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
annotation
documentation 
A feature, e.g. domain, on a sequence.

element featureElementType/names
diagram
namespace net:sf:psidev:mi
type namesType
properties
isRef 0
content complex
children shortLabel fullName alias
annotation
documentation 
Names for the feature, e.g. SH3 domain.

element featureElementType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
properties
isRef 0
content complex
children primaryRef secondaryRef
annotation
documentation 
Reference to an external feature description, for example InterPro entry.

element featureElementType/featureType
diagram
namespace net:sf:psidev:mi
type cvType
properties
isRef 0
content complex
children names xref
annotation
documentation 
Description and classification of the feature. This element is controlled by the PSI-MI controlled vocabulary "featureType", root term id MI:0116.

element featureElementType/featureDetectionMethod
diagram
namespace net:sf:psidev:mi
type cvType
properties
isRef 0
content complex
children names xref
annotation
documentation 
Experimental method used to identify the feature. A setting here overrides the global setting given in the experimentDescription. External controlled vocabulary.

element featureElementType/experimentRefList
diagram
namespace net:sf:psidev:mi
type experimentRefListType
properties
isRef 0
content complex
children experimentRef
annotation
documentation 
If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.

element featureElementType/featureRangeList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children featureRange

element featureElementType/featureRangeList/featureRange
diagram
namespace net:sf:psidev:mi
type baseLocationType
properties
isRef 0
content complex
children startStatus begin beginInterval endStatus end endInterval isLink
annotation
documentation 
Location of the feature on the sequence of the interactor. One feature may have more than one featureRange, 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.

element featureElementType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
properties
isRef 0
content complex
children attribute
annotation
documentation 
Semi-structured additional description of the data contained in the entry.

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

complexType interactionElementType
diagram
namespace net:sf:psidev:mi
children names xref availabilityRef availability experimentList participantList inferredInteractionList interactionType modelled intraMolecular negative confidenceList parameterList attributeList
used by
element entrySet/entry/interactionList/interaction
attributes
Name  Type  Use  Default  Fixed  Annotation
imexId  xs:stringoptional      
documentation 
Interaction identifier assigned by the IMEx consortium. Will be unique for an interaction determined in one publication. Details defined in the IMEx documents.
id  xs:intrequired      
documentation 
All major objects have a numerical id which is unique to that object within a PSI MI file. The object may be repeated, though, e.g. in the denormalised representation.
annotation
documentation 
A molecular interaction.

element interactionElementType/names
diagram
namespace net:sf:psidev:mi
type namesType
properties
isRef 0
content complex
children shortLabel fullName alias
annotation
documentation 
Name(s) of the interaction.

element interactionElementType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
properties
isRef 0
content complex
children primaryRef secondaryRef
annotation
documentation 
Interaction database ID

element interactionElementType/availabilityRef
diagram
namespace net:sf:psidev:mi
type xs:int
properties
isRef 0
content simple
annotation
documentation 
References an availability statement already present in this entry.

element interactionElementType/availability
diagram
namespace net:sf:psidev:mi
type availabilityType
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
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
properties
isRef 0
content complex
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 xs:int
properties
isRef 0
content simple
annotation
documentation 
References an experiment already present in this entry.

element interactionElementType/experimentList/experimentDescription
diagram
namespace net:sf:psidev:mi
type experimentType
properties
isRef 0
content complex
children names bibref xref hostOrganismList interactionDetectionMethod participantIdentificationMethod featureDetectionMethod confidenceList attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
documentation 
All major objects have a numerical id which must be unique to that object within an entry. The object may be repeated, though, e.g. in the denormalised representation.
annotation
documentation 
An experiment in which this interaction has been determined.

element interactionElementType/participantList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children participant
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/participant
diagram
namespace net:sf:psidev:mi
type participantType
properties
isRef 0
content complex
children names xref interactorRef interactor interactionRef participantIdentificationMethodList biologicalRole experimentalRoleList experimentalPreparationList experimentalInteractorList featureList hostOrganismList confidenceList parameterList attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      

element interactionElementType/inferredInteractionList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
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
properties
isRef 0
content complex
children participant experimentRefList

element interactionElementType/inferredInteractionList/inferredInteraction/participant
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children participantRef participantFeatureRef
annotation
documentation 
Participant of the inferred interaction.

element interactionElementType/inferredInteractionList/inferredInteraction/participant/participantRef
diagram
namespace net:sf:psidev:mi
type xs:int
properties
isRef 0
content simple

element interactionElementType/inferredInteractionList/inferredInteraction/participant/participantFeatureRef
diagram
namespace net:sf:psidev:mi
type xs:int
properties
isRef 0
content simple

element interactionElementType/inferredInteractionList/inferredInteraction/experimentRefList
diagram
namespace net:sf:psidev:mi
type experimentRefListType
properties
isRef 0
content complex
children experimentRef
annotation
documentation 
If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.

element interactionElementType/interactionType
diagram
namespace net:sf:psidev:mi
type cvType
properties
isRef 0
content complex
children names xref
annotation
documentation 
External controlled vocabulary characterising the interaction type, for example "physical interaction".

element interactionElementType/modelled
diagram
namespace net:sf:psidev:mi
type xs:boolean
properties
isRef 0
content simple
annotation
documentation 
If true, this element describes an interaction in a species of interest, e.g. human, but has actually been investigated in another organism, e.g. mouse. The transfer will usually be based on a homology statement made by the data producer. If this optional element is missing, it is assumed to be set to false.

element interactionElementType/intraMolecular
diagram
namespace net:sf:psidev:mi
type xs:boolean
properties
isRef 0
content simple
default false
annotation
documentation 
If true, this interaction is an intramolecular interaction, e.g. an autophosphorylation. If missing, this element is assumed to be false.

element interactionElementType/negative
diagram
namespace net:sf:psidev:mi
type xs:boolean
properties
isRef 0
content simple
default false
annotation
documentation 
If true, this interaction has been shown NOT to occur under the described experimental conditions. Default false. If this optional element is missing, it is assumed to be set to false.

element interactionElementType/confidenceList
diagram
namespace net:sf:psidev:mi
type confidenceListType
properties
isRef 0
content complex
children confidence
annotation
documentation 
Confidence in this interaction.  Usually a statistical measure.

element interactionElementType/parameterList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children parameter
annotation
documentation 
Lists parameters which are relevant for the Interaction, e.g. kinetics.

element interactionElementType/parameterList/parameter
diagram
namespace net:sf:psidev:mi
type extension of parameterType
properties
isRef 0
content complex
children experimentRef
attributes
Name  Type  Use  Default  Fixed  Annotation
term  required      
documentation 
The kind of parameter, e.g. "dissociation constant".
termAc  optional      
documentation 
Accession number of the term in the associated controlled vocabulary.
unit  optional      
documentation 
The unit of the term, e.g. "kiloDalton".
unitAc  optional      
documentation 
Accession number of the unit in the associated controlled vocabulary.
base  xs:shortoptional  10    
documentation 
Base of the parameter expression. Defaults to 10.
exponent  xs:shortoptional  0    
documentation 
Exponent of the value.
factor  xs:decimalrequired      
documentation 
The "main" value of the parameter.
uncertainty  xs:decimaloptional      

element interactionElementType/parameterList/parameter/experimentRef
diagram
namespace net:sf:psidev:mi
type xs:int
properties
isRef 0
content simple
annotation
documentation 
Reference to the experiment in which this parameter has been determined. If not given, it is assumed that this is valid for all experiments attached to the interaction.

element interactionElementType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
properties
isRef 0
content complex
children attribute
annotation
documentation 
Semi-structured additional description of the data contained in the entry.

complexType interactorElementType
diagram
namespace net:sf:psidev:mi
children names xref interactorType organism sequence attributeList
used by
elements entrySet/entry/interactorList/interactor participantType/interactor participantType/experimentalInteractorList/experimentalInteractor/interactor
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
documentation 
All major objects have a numerical id which is unique to that object within a PSI MI file. The object may be repeated, though, e.g. in the denormalised representation.
annotation
documentation 
Describes a molecular interactor.

element interactorElementType/names
diagram
namespace net:sf:psidev:mi
type namesType
properties
isRef 0
content complex
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 interactorElementType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
properties
isRef 0
content complex
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 interactorElementType/interactorType
diagram
namespace net:sf:psidev:mi
type cvType
properties
isRef 0
content complex
children names xref
annotation
documentation 
The molecule type of the participant, e.g. protein. This element is controlled by the PSI-MI controlled vocabulary "interactorType", root term id MI:0313.

element interactorElementType/organism
diagram
namespace net:sf:psidev:mi
type extension of bioSourceType
properties
isRef 0
content complex
children names cellType compartment tissue
attributes
Name  Type  Use  Default  Fixed  Annotation
ncbiTaxId  xs:intrequired      
annotation
documentation 
The normal source organism of the interactor.

element interactorElementType/sequence
diagram
namespace net:sf:psidev:mi
type restriction of xs:string
properties
isRef 0
content simple
facets
minLength 1
annotation
documentation 
Sequence in uppercase
documentation 
Usage:

element interactorElementType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
properties
isRef 0
content complex
children attribute
annotation
documentation 
Allows semi-structured additional annotation of the interactor.

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

complexType labelType
diagram
namespace net:sf:psidev:mi
type extension of xs:string
properties
base 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 featureElementType/names experimentType/names interactionElementType/names interactorElementType/names participantType/names
annotation
documentation 
Names for an object.

element namesType/shortLabel
diagram
namespace net:sf:psidev:mi
type restriction of xs:string
properties
isRef 0
content simple
facets
minLength 1
annotation
documentation 
A short string, suitable to remember the object. Can be e.g. a gene name, the first author of a paper, etc.

element namesType/fullName
diagram
namespace net:sf:psidev:mi
type restriction of xs:string
properties
isRef 0
content simple
facets
minLength 1
annotation
documentation 
A full, detailed name or description of the object. Can be e.g. the full title of a publication, or the scientific name of a species.

element namesType/alias
diagram
namespace net:sf:psidev:mi
type extension of xs:string
properties
isRef 0
content complex
attributes
Name  Type  Use  Default  Fixed  Annotation
typeAc  optional      
type  optional      

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
properties
isRef 0
content complex
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
properties
isRef 0
content complex
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
properties
isRef 0
content complex
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 parameterType
diagram
namespace net:sf:psidev:mi
used by
elements interactionElementType/parameterList/parameter participantType/parameterList/parameter
attributes
Name  Type  Use  Default  Fixed  Annotation
term  required      
documentation 
The kind of parameter, e.g. "dissociation constant".
termAc  optional      
documentation 
Accession number of the term in the associated controlled vocabulary.
unit  optional      
documentation 
The unit of the term, e.g. "kiloDalton".
unitAc  optional      
documentation 
Accession number of the unit in the associated controlled vocabulary.
base  xs:shortoptional  10    
documentation 
Base of the parameter expression. Defaults to 10.
exponent  xs:shortoptional  0    
documentation 
Exponent of the value.
factor  xs:decimalrequired      
documentation 
The "main" value of the parameter.
annotation
documentation 
A numeric parameter, e.g. for a kinetic value

complexType participantType
diagram
namespace net:sf:psidev:mi
children names xref interactorRef interactor interactionRef participantIdentificationMethodList biologicalRole experimentalRoleList experimentalPreparationList experimentalInteractorList featureList hostOrganismList confidenceList parameterList attributeList
used by
element interactionElementType/participantList/participant
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
annotation
documentation 
A molecule participating in an interaction.

element participantType/names
diagram
namespace net:sf:psidev:mi
type namesType
properties
isRef 0
content complex
children shortLabel fullName alias
annotation
documentation 
This contains the name(s) for the participant given by the authors of a publication.

element participantType/xref
diagram
namespace net:sf:psidev:mi
type xrefType
properties
isRef 0
content complex
children primaryRef secondaryRef
annotation
documentation 
Contains the xref(s) for the participant given by the authors of a publication.

element participantType/interactorRef
diagram
namespace net:sf:psidev:mi
type xs:int
properties
isRef 0
content simple
annotation
documentation 
References an interactor described in the interactorList of the entry

element participantType/interactor
diagram
namespace net:sf:psidev:mi
type interactorElementType
properties
isRef 0
content complex
children names xref interactorType organism sequence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
documentation 
All major objects have a numerical id which is unique to that object within a PSI MI file. The object may be repeated, though, e.g. in the denormalised representation.
annotation
documentation 
Fully describes an interactor

element participantType/interactionRef
diagram
namespace net:sf:psidev:mi
type xs:int
properties
isRef 0
content simple
annotation
documentation 
References an interaction described in this entry. Used for the hierarchical buildup of complexes.

element participantType/participantIdentificationMethodList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children participantIdentificationMethod
annotation
documentation 
The method(s) by which this participant has been determined. If this element is present, its value supersedes experimentDescription/ participantIdentificationMethod.

element participantType/participantIdentificationMethodList/participantIdentificationMethod
diagram
namespace net:sf:psidev:mi
type extension of cvType
properties
isRef 0
content complex
children names xref experimentRefList
annotation
documentation 
Experimental method to determine the interactors involved in the interaction. This element is controlled by the PSI-MI controlled vocabulary "participant identification method", root term id MI:0002.

element participantType/participantIdentificationMethodList/participantIdentificationMethod/experimentRefList
diagram
namespace net:sf:psidev:mi
type experimentRefListType
properties
isRef 0
content complex
children experimentRef
annotation
documentation 
If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.

element participantType/biologicalRole
diagram
namespace net:sf:psidev:mi
type cvType
properties
isRef 0
content complex
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 experimentalForm. This element is controlled by the PSI-MI controlled vocabulary "biologicalRole", root term id MI:0500.

element participantType/experimentalRoleList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children experimentalRole
annotation
documentation 
The role(s) of the participant in the interaction, e.g. bait.

element participantType/experimentalRoleList/experimentalRole
diagram
namespace net:sf:psidev:mi
type extension of cvType
properties
isRef 0
content complex
children names xref experimentRefList
annotation
documentation 
This element is controlled by the PSI-MI controlled vocabulary "experimentalRole", root term id MI:0495.

element participantType/experimentalRoleList/experimentalRole/experimentRefList
diagram
namespace net:sf:psidev:mi
type experimentRefListType
properties
isRef 0
content complex
children experimentRef
annotation
documentation 
If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.

element participantType/experimentalPreparationList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children experimentalPreparation
annotation
documentation 
Terms describing the experimental sample preparation.

element participantType/experimentalPreparationList/experimentalPreparation
diagram
namespace net:sf:psidev:mi
type extension of cvType
properties
isRef 0
content complex
children names xref experimentRefList
annotation
documentation 
This element is controlled by the PSI-MI controlled vocabulary "experimentalPreparation", root term id MI:0346.

element participantType/experimentalPreparationList/experimentalPreparation/experimentRefList
diagram
namespace net:sf:psidev:mi
type experimentRefListType
properties
isRef 0
content complex
children experimentRef
annotation
documentation 
If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.

element participantType/experimentalInteractorList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children experimentalInteractor
annotation
documentation 
Describes molecules which have been used in specific experiments if these molecules are different from the one listed as interactors. Example: The author of a paper makes a statement about human proteins, but has really worked with mouse proteins. In this case the human protein would be the main interactor, while the experimentalForm would be the mouse protein listed in this element. Optionally this can refer to the experiment(s) in which this form has been used.

element participantType/experimentalInteractorList/experimentalInteractor
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children interactorRef interactor experimentRefList

element participantType/experimentalInteractorList/experimentalInteractor/interactorRef
diagram
namespace net:sf:psidev:mi
type xs:int
properties
isRef 0
content simple
annotation
documentation 
References an interactor described in the interactorList of the entry

element participantType/experimentalInteractorList/experimentalInteractor/interactor
diagram
namespace net:sf:psidev:mi
type interactorElementType
properties
isRef 0
content complex
children names xref interactorType organism sequence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      
documentation 
All major objects have a numerical id which is unique to that object within a PSI MI file. The object may be repeated, though, e.g. in the denormalised representation.
annotation
documentation 
Fully describes an interactor

element participantType/experimentalInteractorList/experimentalInteractor/experimentRefList
diagram
namespace net:sf:psidev:mi
type experimentRefListType
properties
isRef 0
content complex
children experimentRef
annotation
documentation 
If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.

element participantType/featureList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children feature
annotation
documentation 
Sequence features relevant for the interaction, for example binding domains, and experimental modifications, e.g. protein tags.

element participantType/featureList/feature
diagram
namespace net:sf:psidev:mi
type featureElementType
properties
isRef 0
content complex
children names xref featureType featureDetectionMethod experimentRefList featureRangeList attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:intrequired      

element participantType/hostOrganismList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children hostOrganism
annotation
documentation 
The host organism(s) in which the protein has been expressed. If not given, it is assumed to be the native species of the protein.

element participantType/hostOrganismList/hostOrganism
diagram
namespace net:sf:psidev:mi
type extension of bioSourceType
properties
isRef 0
content complex
children names cellType compartment tissue experimentRefList
attributes
Name  Type  Use  Default  Fixed  Annotation
ncbiTaxId  xs:intrequired      

element participantType/hostOrganismList/hostOrganism/experimentRefList
diagram
namespace net:sf:psidev:mi
type experimentRefListType
properties
isRef 0
content complex
children experimentRef
annotation
documentation 
If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction.

element participantType/confidenceList
diagram
namespace net:sf:psidev:mi
type confidenceListType
properties
isRef 0
content complex
children confidence
annotation
documentation 
Confidence in participant detection.

element participantType/parameterList
diagram
namespace net:sf:psidev:mi
properties
isRef 0
content complex
children parameter
annotation
documentation 
Lists parameters which are relevant for the Interaction, e.g. kinetics.

element participantType/parameterList/parameter
diagram
namespace net:sf:psidev:mi
type extension of parameterType
properties
isRef 0
content complex
children experimentRef
attributes
Name  Type  Use  Default  Fixed  Annotation
term  required      
documentation 
The kind of parameter, e.g. "dissociation constant".
termAc  optional      
documentation 
Accession number of the term in the associated controlled vocabulary.
unit  optional      
documentation 
The unit of the term, e.g. "kiloDalton".
unitAc  optional      
documentation 
Accession number of the unit in the associated controlled vocabulary.
base  xs:shortoptional  10    
documentation 
Base of the parameter expression. Defaults to 10.
exponent  xs:shortoptional  0    
documentation 
Exponent of the value.
factor  xs:decimalrequired      
documentation 
The "main" value of the parameter.
uncertainty  xs:decimaloptional      

element participantType/parameterList/parameter/experimentRef
diagram
namespace net:sf:psidev:mi
type xs:int
properties
isRef 0
content simple
annotation
documentation 
Reference to the experiment in which this parameter has been determined. If not given, it is assumed that this is valid for all experiments attached to the interaction.

element participantType/attributeList
diagram
namespace net:sf:psidev:mi
type attributeListType
properties
isRef 0
content complex
children attribute
annotation
documentation 
Semi-structured additional description of the data contained in the entry.

complexType positionType
diagram
namespace net:sf:psidev:mi
used by
elements baseLocationType/begin baseLocationType/end
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLongrequired      

complexType xrefType
diagram
namespace net:sf:psidev:mi
children primaryRef secondaryRef
used by
elements entrySet/entry/source/xref bibrefType/xref cvType/xref openCvType/xref featureElementType/xref experimentType/xref interactionElementType/xref interactorElementType/xref participantType/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
properties
isRef 0
content complex
children attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
db  required      
documentation 
Name of the external database. Taken from the controlled vocabulary of databases.
dbAc  optional      
documentation 
Accession number of the database in the database CV. This element is controlled by the PSI-MI controlled vocabulary "database citation", root term id MI:0444.
id  required      
documentation 
Primary identifier of the object in the external database, e.g. UniProt accession number.
secondary  optional      
documentation 
Secondary identifier of the object in the external database, e.g. UniProt ID.
version  optional      
documentation 
The version number of the object in the external database.
refType  optional      
documentation 
Reference type, e.g. "identity" if this reference referes to an identical object in the external database, or "see-also" for additional information. Controlled by CV.
refTypeAc  optional      
documentation 
Reference type accession number from the CV of reference types. This element is controlled by the PSI-MI controlled vocabulary "xref type", root term id MI:0353.
annotation
documentation 
Primary reference to an external database.

element xrefType/secondaryRef
diagram
namespace net:sf:psidev:mi
type dbReferenceType
properties
isRef 0
content complex
children attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
db  required      
documentation 
Name of the external database. Taken from the controlled vocabulary of databases.
dbAc  optional      
documentation 
Accession number of the database in the database CV. This element is controlled by the PSI-MI controlled vocabulary "database citation", root term id MI:0444.
id  required      
documentation 
Primary identifier of the object in the external database, e.g. UniProt accession number.
secondary  optional      
documentation 
Secondary identifier of the object in the external database, e.g. UniProt ID.
version  optional      
documentation 
The version number of the object in the external database.
refType  optional      
documentation 
Reference type, e.g. "identity" if this reference referes to an identical object in the external database, or "see-also" for additional information. Controlled by CV.
refTypeAc  optional      
documentation 
Reference type accession number from the CV of reference types. This element is controlled by the PSI-MI controlled vocabulary "xref type", root term id MI:0353.
annotation
documentation 
Further external objects describing the object.


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