Root element of the Molecular Interaction Format Describes one or more interactions as a self-contained unit. Multiple entries from different files can be concatenated into a single entrySet. PSI MI level PSI MI version within given level Desciption of the source of the entry, usually an organisation Name(s) of the data source, for example the organisation name. Bibliographic reference for the data source. Example: A paper which describes all interactions of the entry. Cross reference for the data source. Example: Entry in a database of databases. Further description of the source. All experiments in which the interactions of this entry have been determined Describes one set of experimental parameters, usually associated with a single publication. List of experiments in which this interaction has been determined. Either refer to an already defined experiment in this entry or insert description. References an experiment already present in this entry. An experiment in which this interaction has been determined. List of all interactors occurring in the entry A molecule object in its native state, as described in databases. Usage: A protein interactor must contain an xref to UniProt and NCBI-GI where possible. List of interactions Data availability statements, for example copyrights Describes data availability, e.g. through a copyright statement. If no availability is given, the data is assumed to be freely available. 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. Primary reference to an external database. Further external objects describing the object. 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-MI controlled vocabulary "database citation", root term id MI:0444. 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-MI controlled vocabulary "xref type", root term id MI:0353. Bibliographic reference. Bibliographic reference in 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. 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. 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. The full name should be the full name of the species (i.e. genus species). 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. 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 to the data provider. A list of confidence values. 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 short string, suitable to remember the object. Can be e.g. a gene name, the first author of a paper, etc. 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. 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. Names 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-MI controlled vocabulary "feature", root term id MI:0116. Experimental method used to identify the feature. A setting here overrides the global setting given in the experimentDescription. External controlled vocabulary. If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction. 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. Semi-structured additional description of the data contained in the entry. 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. The host organism(s) in which the experiment has been performed. Describes one set of experimental parameters. Publication describing the experiment. Refers to external database description of the experiment. Experimental method to determine the interaction. This element is controlled by the PSI-MI controlled vocabulary "interaction detection method", root term id MI:0001. 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. 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. Confidence in this experiment. Usually a statistical measure. Semi-structured additional description of the experiment. 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. Interaction database ID Either refer to an already defined availability statement in this entry or insert description. 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. External controlled vocabulary characterising the interaction type, for example "physical interaction". 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. If true, this interaction is an intramolecular interaction, e.g. an autophosphorylation. If missing, this element is assumed to be false. 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. 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 list of molecules participating in this interaction. An interaction has one (intramolecular), two (binary), or more (n-ary, complexes) participants. 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. Participant of the inferred interaction. Describes a molecular interactor. Name(s). The short label is typically a short name that could appear as a label on a diagram. 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. The molecule type of the participant, e.g. protein. This element is controlled by the PSI-MI controlled vocabulary "interactor", root term id MI:0313. The normal source organism of the interactor. Sequence in uppercase Usage: Allows semi-structured additional annotation of the interactor. 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 given by the authors of a publication. Contains the xref(s) for the participant given by the authors of a publication. Description of the Interactor. Refers to an already defined interactor in this entry, fully describes an interactor, or references another interaction defined in this entry, to allow the hierarchical building up of complexes from subunits. References an interactor described in the interactorList of the entry Fully describes an interactor References an interaction described in this entry. Used for the hierarchical buildup of complexes. 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. Confidence in participant detection. Semi-structured additional description of the data contained in the entry. The method(s) by which this participant has been determined. If this element is present, its value supersedes experimentDescription/ participantIdentificationMethod. 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. If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction. The role(s) of the participant in the interaction, e.g. bait. This element is controlled by the PSI-MI controlled vocabulary "experimentalRole", root term id MI:0495. If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction. Terms describing the experimental sample preparation. This element is controlled by the PSI-MI controlled vocabulary "experimentalPreparation", root term id MI:0346. If no experimentRef is given, it is assumed this refers to all experiments linked to the interaction. 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. 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. Sequence features relevant for the interaction, for example binding domains, and experimental modifications, e.g. protein tags. Lists parameters which are relevant for the Interaction, e.g. kinetics. 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.