Schema MIF.xsd


schema location:  X:\pro6\psi\mi\xml\src\MIF.xsd
targetNamespace:  net:sf:psidev:mi
 
Elements  Complex types 
entrySet  attributeListType 
availabilityType 
baseLocationType 
bibrefType 
bioSourceType 
cvType 
dbReferenceType 
experimentType 
featureType 
fullNameType 
interactionElementType 
intervalType 
labelType 
namesType 
openCvType 
positionType 
proteinInteractorType 
proteinParticipantType 
refType 
xrefType 


element entrySet
diagram
namespace net:sf:psidev:mi
children entry
attributes
Name  Type  Use  Default  Fixed  Annotation
level  xs:integer  required      
version  xs:integer  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
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:ID  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 interactionDetection participantDetection featureDetection confidence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:ID  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
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
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:ID  required      
annotation
documentation 
A protein object participating in an interaction.

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 interactionElementType
children names availabilityRef availabilityDescription experimentList participantList interactionType confidence xref attributeList
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 experimentType/attributeList bibrefType/attributeList openCvType/attributeList interactionElementType/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/availabilityDescription
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:ID  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 end endInterval position positionInterval site
used by
element featureType/location
annotation
documentation 
A location can be either a position, site or have a start and end, only start, only end or is an empty element if the position is unknown.

element baseLocationType/begin
diagram
namespace net:sf:psidev:mi
type positionType
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLong  required      

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      

element baseLocationType/end
diagram
namespace net:sf:psidev:mi
type positionType
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLong  required      

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      

element baseLocationType/position
diagram
namespace net:sf:psidev:mi
type positionType
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLong  required      

element baseLocationType/positionInterval
diagram
namespace net:sf:psidev:mi
type intervalType
attributes
Name  Type  Use  Default  Fixed  Annotation
begin  xs:unsignedLong  required      
end  xs:unsignedLong  required      

element baseLocationType/site
diagram
namespace net:sf:psidev:mi
type positionType
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLong  required      

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
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
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 cvType
diagram
namespace net:sf:psidev:mi
children names xref
used by
elements featureType/featureDescription featureType/featureDetection experimentType/featureDetection experimentType/interactionDetection interactionElementType/interactionType experimentType/participantDetection
annotation
documentation 
Reference to an external controlled vocabulary.

element cvType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName
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 experimentType
diagram
namespace net:sf:psidev:mi
children names bibref xref hostOrganism interactionDetection participantDetection featureDetection confidence attributeList
used by
elements entrySet/entry/experimentList/experimentDescription interactionElementType/experimentList/experimentDescription
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:ID  required      
annotation
documentation 
Describes one set of experimental parameters.

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

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:integer  required      
annotation
documentation 
The host organism in which the experiment has been performed.

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

element experimentType/participantDetection
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/featureDetection
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/confidence
diagram
namespace net:sf:psidev:mi
attributes
Name  Type  Use  Default  Fixed  Annotation
unit  xs:string  required      
value  xs:string  required      
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 xref featureDescription location featureDetection
used by
element proteinParticipantType/featureList/feature
annotation
documentation 
A feature, e.g. domain, on a sequence.

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

element featureType/location
diagram
namespace net:sf:psidev:mi
type baseLocationType
children begin beginInterval end endInterval position positionInterval site
annotation
documentation 
Location of the feature on the sequence of the interactor

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

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 availabilityRef availabilityDescription experimentList participantList interactionType confidence xref 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
annotation
documentation 
Name(s) of the interaction.

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

element interactionElementType/availabilityDescription
diagram
namespace net:sf:psidev:mi
type availabilityType
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:ID  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:string  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 interactionDetection participantDetection featureDetection confidence attributeList
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:ID  required      
annotation
documentation 
An experiment in which this interaction has been determined.

element interactionElementType/participantList
diagram
namespace net:sf:psidev:mi
children proteinParticipant
annotation
documentation 
A list of molecules participating in this interaction.

element interactionElementType/participantList/proteinParticipant
diagram
namespace net:sf:psidev:mi
type proteinParticipantType
children proteinInteractorRef proteinInteractor featureList confidence role isTaggedProtein isOverexpressedProtein
annotation
documentation 
An interaction has two or more participants, thereby covering binary and n-ary interactions.

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/confidence
diagram
namespace net:sf:psidev:mi
attributes
Name  Type  Use  Default  Fixed  Annotation
unit  xs:string  required      
value  xs:string  required      
annotation
documentation 
Confidence in this interaction.  Usually a statistical measure.

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

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 baseLocationType/positionInterval
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
used by
elements entrySet/entry/source/names bioSourceType/names experimentType/names cvType/names openCvType/names proteinInteractorType/names interactionElementType/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

complexType openCvType
diagram
namespace net:sf:psidev:mi
children names xref attributeList
used by
elements bioSourceType/cellType bioSourceType/compartment bioSourceType/tissue
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
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 baseLocationType/position baseLocationType/site
attributes
Name  Type  Use  Default  Fixed  Annotation
position  xs:unsignedLong  required      
annotation
documentation 
A specified position a a sequence.

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

element proteinInteractorType/names
diagram
namespace net:sf:psidev:mi
type namesType
children shortLabel fullName
annotation
documentation 
Protein 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 proteinInteractor 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:integer  required      
annotation
documentation 
The normal source organism of the interactor. If a human protein has been expressed in yeast, this attribute would describe human.

element proteinInteractorType/sequence
diagram
namespace net:sf:psidev:mi
type xs:string
annotation
documentation 
Amino acid sequence in uppercase

complexType proteinParticipantType
diagram
namespace net:sf:psidev:mi
children proteinInteractorRef proteinInteractor featureList confidence role isTaggedProtein isOverexpressedProtein
used by
element interactionElementType/participantList/proteinParticipant
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:string  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
attributes
Name  Type  Use  Default  Fixed  Annotation
id  xs:ID  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 featureType
children xref featureDescription location featureDetection

element proteinParticipantType/confidence
diagram
namespace net:sf:psidev:mi
attributes
Name  Type  Use  Default  Fixed  Annotation
unit  xs:string  required      
value  xs:string  required      
annotation
documentation 
Confidence in participant detection.

element proteinParticipantType/role
diagram
namespace net:sf:psidev:mi
type restriction of xs:string
facets
enumeration bait
enumeration prey
enumeration neutral
enumeration unspecified
annotation
documentation 
The role of the participant in the interaction, e.g. "bait".  Choose an enumerated value.

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

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

complexType refType
diagram
namespace net:sf:psidev:mi
used by
elements interactionElementType/availabilityRef interactionElementType/experimentList/experimentRef proteinParticipantType/proteinInteractorRef
attributes
Name  Type  Use  Default  Fixed  Annotation
ref  xs:string  required      
annotation
documentation 
Refers to an object within the same file by its id.

complexType xrefType
diagram
namespace net:sf:psidev:mi
children primaryRef secondaryRef
used by
elements entrySet/entry/source/xref featureType/xref experimentType/xref bibrefType/xref cvType/xref openCvType/xref proteinInteractorType/xref interactionElementType/xref
annotation
documentation 
Crossreference to an external database.

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.


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