Root element of the Format Describes one or more interactions (PAR or target protein production or characterization event) as a self-contained unit. Multiple entries from different files can be concatenated into a single entrySet. Desciption of the source of the entry, for example a PAR or target protein production or characterization centre. Name(s) of the data source, for example the name of a group, institute or company. Bibliographic reference for the data source. Example: An article which describes the data in the entry. Cross reference for the data source. Example: Entry in a database of databases. Further description of the source. Available attributes are found in the PSI-PAR CV "attribute name". Data availability statements, for example copyrights. The element can also be used to define intellectual properties. Describes data availability, e.g. through a copyright statement. If no availability is given, the data is assumed to be freely available. List of all PAR or target protein production or characterization experiments of this entry Describes one experiment. List of all interactors (e.g. PARs and target proteins) contained in this entry A molecule in its generic/canonical form, as described in a database. (The specific version is described in interaction-participant.) Usage: A protein interactor must contain an xref to UniProt and NCBI-GI where possible. List of interactions (PAR and protein target production and characterization events). An interaction is a PAR production or characterization events. List of additional attributes of the entry. Available attributes are found in the PSI-PAR CV "attribute name". PSI MI level PSI MI version within given level A short alphanumeric label identifying an object. Not necessarily unique. Full, descriptive object name. Refers to a list of experiments within the same entry. References an experiment already present in this entry. 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. This element is controlled by the PSI-MI controlled vocabularies "cross-reference type" and "database citation". Primary reference to an external database. Further references to external databases. Refers to a unique object in an external database. Name of the external database. Taken from the controlled vocabulary of databases. Accession number of the database in the database CV. This element is controlled by the PSI-PAR CV "database citation". Primary identifier of the object in the external database, e.g. UniProt accession number. Secondary identifier of the object in the external database, e.g. UniProt ID. The version number of the object in the external database. 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. Reference type accession number from the CV of reference types. This element is controlled by the PSI-PAR CV "xref type". Bibliographic reference. Bibliographic reference in an external database, usually PubMed. Alternative description of bibliographic reference if no external database entry is available. A list of additional attributes. Open tag-value list to allow the inclusion of additional data. The name of the attribute. Enables control of the attribute type through reference to an external controlled vocabulary. Root element in the PSI MI CV is MI:0590. A confidence value. Describes the biological source of an object, in simple form only the NCBI taxid. The names of the organism. The short label should be a common name if it exists e.g. "mouse". The full name should be genus species, e.g. "Mus musculus". 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. The subcellular compartment of the object. It is strongly recommended to refer to the Gene Ontology cellular component in this element. Description of the source tissue. Currently no species-independent controlled vocabulary for tissues is available, therefore the choice of reference database(s) is open. A list of confidence values. Each experiment might assign a different confidence to this object. If no experimentRef is given, this confidence will refer to all experiments associated with the object. Reference to an external controlled vocabulary. Name of the controlled vocabulary term. Source of the controlled vocabulary term. E.g. the name of the CV and the term ID. Allows to reference an external controlled vocabulary, or to directly include a value if no suitable external definition is available. This contains the controlled vocabulary terms, as a short and optionally as a long form. Refers to the term of the controlled vocabulary in an external database. 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. Names for an object. A catchy short designation, suitable to remember the object. Can be e.g. a gene name, the first author of a paper, etc. A full, detailed name of the object. Can be e.g. the full title of a publication. Alias of the object. This element is controlled by the PSI-PAR CV "alias type". A numeric parameter, e.g. for a kinetic value The kind of parameter, e.g. "dissociation constant". Accession number of the term in the associated controlled vocabulary. The unit of the term, e.g. "kiloDalton". Accession number of the unit in the associated controlled vocabulary. Base of the parameter expression. Defaults to 10. Exponent of the value. The "main" value of the parameter. A feature, e.g. domain, on a sequence. Name(s) for the feature, e.g. SH3 domain. Reference to an external feature description, for example InterPro entry. Description and classification of the feature. This element is controlled by the PSI-PAR CV "feature type". Experimental method used to identify the feature. A setting here overrides the global setting given in the experimentDescription. This element is controlled by the PSI-PAR CV "feature detection method". If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction. Location(s) of the feature on the sequence of the participant (e.g. a PAR or target protein). 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. This element is controlled by the PSI-PAR CV "feature range status". List of additional attributes of the feature. Available attributes are found in the PSI-PAR CV "attribute name". A interval on a sequence. A location on a sequence. Both begin and end can be a defined position, a fuzzy position, or undetermined. Attribute of the start positions, e.g. "certain" or "n-terminal" 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'. The begin position may be varying or unclear, but localisable to a certain range. Usually written as e.g. 3..5. Attribute of the end positions, e.g. "certain" or "c-terminal" 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'. The end position may be varying or unclear, but localisable to a certain range. Usually written as e.g. 3..5. 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. A text describing the availability of data, e.g. a copyright statement. Describes one set of experimental parameters. Publication describing the experiment. Reference to a description of the experiment in an external database. The organism(s) in which the experiment has been performed for example yeast for a yeast-two-hybrid experiment. Experimental method to produce or characterize a PAR or target protein. This element is controlled by the PSI-PAR CVs "molecule production method" and "interaction detection method", respectively. Experimental method to determine the identity of the interactors (e.g. PAR or target protein). This element is controlled by the PSI-PAR CV "participant identification method". Experimental method used to indentify the experimental and biological features (see interaction-participant-feature). If this element is filled it is assumed to apply to all features associated with the experiment. This can be overridden by specifying a featureDetectionMethod in the individual feature. This element is controlled by the PSI-PAR CV "feature detection method". Confidence in this experiment. Usually a statistical measure. List of additional attributes of the experiment. Available attributes are found in the PSI-PAR CV "attribute name". 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. A molecular interaction. Name(s) of the interaction (generation or characterization event). Reference to an entry/ID of this interaction in a database e.g. the local database of a PAR or target protein production or characterization center. Either refer to an already defined availability statement in this entry (entry-availability) or insert new description here. References an availability statement already present in this entry. Describes the availability of the interaction data. If no availability is given, the data is assumed to be freely available. List of experiments. Either refer to an already defined experiment in this entry (entry-experimentDescription) or insert new description here. References an experiment already present in this entry. Describes the set of experimental parameters for one experiment. Specific information for one or more molecules being generated or experimentally analysed. The participant holds additional information than is described for the same molecule in the interactor element (entry-interactor). This element is not used for the representation of PAR data. This element is not used for the representation of PAR data. Participant of the inferred interaction. If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction. Describes the interaction type, for example "physical interaction". This element is controlled by the PSI-MI controlled vocabularies "interaction type" and "experimental scope". This element is not used for the representation of PAR data. If true, this interaction is an intramolecular interaction, e.g. an autophosphorylation. If missing, this element is assumed to be false. This element can be used to show that an interaction has been shown NOT to occur under the described experimental conditions (defaults false). Typically used for PAR interactions with negative controls in experiments assessing cross-reactivity. Confidence in this interaction. Usually a statistical measure. Lists parameters which are relevant for the Interaction. This includes both experimental parameters, such as reaction time and concentration, and results such as affinity and kinetic measurements. Experimental parameter or result, that have a numeric value and an unit, e.g. affinity. This element is controlled by the PSI-PAR CV "parameter type". Reference to the experiment that this parameter describes or resutls from. If not given, it is assumed that this is valid for all experiments attached to the interaction. List of additional attributes of the interaction. Available attributes are found in the PSI-PAR CV "attribute name". Interaction identifier assigned by the IMEx consortium. Will be unique for an interaction determined in one publication. Details defined in the IMEx documents. 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. Describes a molecular interactor. Name(s). The short label is typically a short name e.g. a gene name. A cross-reference to a database. If the interactor is not available in any external database, it must be defined by its sequence or structure formula. The molecular type of the interactor, e.g. protein, gene or small molecule. This element is controlled by the PSI-PAR CV "interactorType". The native organism of the interactor. Sequence in uppercase Usage: List of additional attributes of the interactor. Available attributes are found in the PSI-PAR CV "attribute name". 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. A molecule participating in an interaction. This contains the name(s) for the participant. Contains the cross-references for the participant. Description of the Interactor (generic version of e.g. a PAR or target protein). Can either 1) refer to an already defined interactor (entry-interactor), 2) describe an interactor here, or 3) reference another interaction (entry-interaction) defined in this entry. References an interactor described in the interactorList of the entry. Full description of an interactor. References an interaction described in this entry. Used for the hierarchical buildup of complexes. The method(s) by which the identity of the participant (e.g. PAR or target proteint) has been determined. If this element is present, its value overrides any description given in experimentDescription/ participantIdentificationMethod. Experimental method to determine the identity of a participant e.g. a PAR or target protein. This element is controlled by the PSI-PAR CV "participant identification method". If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction. The biological role of the participant (e.g. PAR or target proteint), e.g. "protein affinity reagent" or "PAR target". This element is controlled by the PSI-PAR CV "biological role". The role(s) of the participant (e.g. PAR or target protein) in the experiment e.g "bait", "prey" or "negative control". This element is controlled by the PSI-PAR CV "experimental role". The role of the participant (e.g. PAR or target protein) in the experiment e.g "bait", "prey" or "negative control". This element is controlled by the PSI-PAR CV "experimental role". If no experimentRef is given, it is assumed this refers to all experiments associated with the interaction. Terms describing the preparation of the participant. Terms describing the preparation of the participant. This element is controlled by the PSI-PAR CV "experimental preparation". If no experimentRef is given, it is assumed this refers to all experiments associated with the interaction. This element is not used for the representation of PAR data. Either refer to an already defined protein interactor in this entry or insert description. References an interactor described in the interactorList of the entry Fully describes an interactor If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction. Relevant sequence features, for example binding domains, and experimental modifications, e.g. protein tags. The host organism(s) in which the participant (e.g. a PAR or target protein) has been produced, e.g. expressed. If not given, it is assumed to be the native species. If no experimentRef is given, it is assumed this refers to all experiments associated with the interaction. Confidence in the identity of the participant i.e. the correctness of the participantIdentificationMethod. Usually a statistical measure. Lists properties of the participant (e.g. a PAR or target protein) that can be described as parameters having a numeric value and an unit, e.g. molecular weight. A property that can be described as parameters having a numeric value and an unit, e.g. molecular weight. This element is controlled by the PSI-PAR CV "parameter type". This element is not used here. List of additional attributes of the participant (e.g. a PAR or target protein). Available attributes are found in the PSI-PAR CV "attribute name".