Uses of Package
psidev.psi.mi.jami.model
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Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.analysis.graph Class Description Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.analysis.graph.model Class Description Feature Property of a participant that may interfere with the binding of a molecule. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.binary Class Description CvTerm A controlled vocabulary term defined by an ontology.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Participant Participant identified in an interaction -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.binary.expansion Class Description Complex An interactor composed of interacting molecules that can be copurified.ComplexType The type of complex that can describe this interaction.CvTerm A controlled vocabulary term defined by an ontology.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.binary.impl Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.Checksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.NamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesSource Source of the data.VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.chebi Class Description BioactiveEntity Molecules showing activity in a living system and which can interact with other molecules -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.europubmedcentral Class Description Publication A scientific publication which has been curated by an interaction database. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.fetcher Class Description CvTerm A controlled vocabulary term defined by an ontology.Gene Interactor for genetic interactionsInteractor Molecule or complex of molecules that interacts with other molecules/complexesOntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Publication A scientific publication which has been curated by an interaction database. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.fetcher.mock Class Description BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesCvTerm A controlled vocabulary term defined by an ontology.Gene Interactor for genetic interactionsOntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Protein Polymer of amino acids which can interact with other molecules.Publication A scientific publication which has been curated by an interaction database.Source Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.imex Class Description Publication A scientific publication which has been curated by an interaction database. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.imex.extension Class Description CurationDepth Flag to determine the curation depth.Publication A scientific publication which has been curated by an interaction database.Source Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.imex.mock Class Description Publication A scientific publication which has been curated by an interaction database. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.mapper Class Description Protein Polymer of amino acids which can interact with other molecules. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.mapper.listener Class Description Protein Polymer of amino acids which can interact with other molecules. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.mapper.mock Class Description Protein Polymer of amino acids which can interact with other molecules. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.obo Class Description CvTerm A controlled vocabulary term defined by an ontology.OntologyTerm Ontology term with definition, parents and childrenSource Source of the data.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.ols Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CvTerm A controlled vocabulary term defined by an ontology.OntologyTerm Ontology term with definition, parents and childrenPublication A scientific publication which has been curated by an interaction database.Source Source of the data.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.ontologymanager Class Description OntologyTerm Ontology term with definition, parents and children -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.ontologymanager.impl Class Description OntologyTerm Ontology term with definition, parents and children -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.uniprot Class Description CvTerm A controlled vocabulary term defined by an ontology.Gene Interactor for genetic interactionsProtein Polymer of amino acids which can interact with other molecules. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.uniprot.taxonomy Class Description Organism The organism is defined by a taxonomy identifier. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.bridges.uniprot.util Class Description Organism The organism is defined by a taxonomy identifier. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.commons Class Description Annotation An Annotations gives some information about a specific topic.ComplexType The type of complex that can describe this interaction.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.Source Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.crosslink Class Description ComplexType The type of complex that can describe this interaction. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.crosslink.extension Class Description CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalEntity An experimental entity with experimental featuresExperimentalParticipantCandidate Interface for experimental participant candidatesExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesMolecule This interface represents a simple molecule such as a protein, nucleic acid, gene, small molecule but excludes complexes and interactorSetOrganism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequenceProtein Polymer of amino acids which can interact with other molecules.Range A feature range indicates the positions of a feature in the interactor sequenceResultingSequence This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.)Source Source of the data.Stoichiometry The stoichiometry of a participantXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.crosslink.extension.datasource Class Description CvTerm A controlled vocabulary term defined by an ontology.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesParticipant Participant identified in an interaction -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.crosslink.io.iterator Class Description InteractionEvidence Interaction involving one to several molecules supported by experiments. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.crosslink.io.parser Class Description InteractionEvidence Interaction involving one to several molecules supported by experiments.ParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.datasource Class Description CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Organism The organism is defined by a taxonomy identifier.Publication A scientific publication which has been curated by an interaction database. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.enricher Class Description CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeable -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.enricher.impl Class Description BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesCvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)ExperimentalEntity An experimental entity with experimental featuresFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Gene Interactor for genetic interactionsInteractor Molecule or complex of molecules that interacts with other molecules/complexesModelledEntity An modelled entity with modelled featuresModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledParticipant Participant of a modelled interaction.ModelledParticipantPool A pool of modelled participant candidatesParticipant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequence -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.enricher.impl.full Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.Checksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...OntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequenceProtein Polymer of amino acids which can interact with other molecules.Publication A scientific publication which has been curated by an interaction database.Source Source of the data.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.enricher.impl.minimal Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Gene Interactor for genetic interactionsInteraction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...OntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeableProtein Polymer of amino acids which can interact with other molecules.Publication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceSource Source of the data.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.enricher.listener Class Description CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequence -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.enricher.listener.impl Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CurationDepth Flag to determine the curation depth.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...OntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequencePublication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceSource Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.enricher.listener.impl.log Class Description Complex An interactor composed of interacting molecules that can be copurified.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...OntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePublication A scientific publication which has been curated by an interaction database.Source Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.enricher.listener.impl.writer Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CurationDepth Flag to determine the curation depth.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...OntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequencePublication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceSource Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.enricher.util Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Confidence A Confidence gives information about how reliable an object is.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeableRange A feature range indicates the positions of a feature in the interactor sequenceXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.examples.core Class Description Interaction Interaction involving one to several molecules. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.factory Class Description BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesComplex An interactor composed of interacting molecules that can be copurified.CvTerm A controlled vocabulary term defined by an ontology.Gene Interactor for genetic interactionsInteraction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.NucleicAcid Polymers of nucleotides which can interact with other moleculesParticipant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesPolymer A polymer is an interactor with a sequenceProtein Polymer of amino acids which can interact with other molecules.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.html Class Description CvTerm A controlled vocabulary term defined by an ontology.Feature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.Organism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesPublication A scientific publication which has been curated by an interaction database. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.imex Class Description Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.Publication A scientific publication which has been curated by an interaction database. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.imex.actions Class Description Experiment Experiment in which some interactions has been determined.InteractionEvidence Interaction involving one to several molecules supported by experiments.Publication A scientific publication which has been curated by an interaction database. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.imex.actions.impl Class Description Experiment Experiment in which some interactions has been determined.InteractionEvidence Interaction involving one to several molecules supported by experiments.Publication A scientific publication which has been curated by an interaction database.Source Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.imex.listener Class Description CurationDepth Flag to determine the curation depth.Experiment Experiment in which some interactions has been determined.InteractionEvidence Interaction involving one to several molecules supported by experiments.Publication A scientific publication which has been curated by an interaction database.Source Source of the data.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.imex.listener.impl Class Description CurationDepth Flag to determine the curation depth.Experiment Experiment in which some interactions has been determined.InteractionEvidence Interaction involving one to several molecules supported by experiments.Publication A scientific publication which has been curated by an interaction database.Source Source of the data.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.json Class Description ComplexType The type of complex that can describe this interaction.Interaction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.Interactor Molecule or complex of molecules that interacts with other molecules/complexesXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.json.binary Class Description Complex An interactor composed of interacting molecules that can be copurified.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc... -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.json.binary.elements Class Description Feature Property of a participant that may interfere with the binding of a molecule.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.json.elements Class Description Annotation An Annotations gives some information about a specific topic.Confidence A Confidence gives information about how reliable an object is.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Feature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Organism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesPublication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceStoichiometry The stoichiometry of a participantXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.json.nary Class Description Complex An interactor composed of interacting molecules that can be copurified.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.Interactor Molecule or complex of molecules that interacts with other molecules/complexesParticipant Participant identified in an interaction -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.listener Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CurationDepth Flag to determine the curation depth.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...OntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequencePublication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceSource Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.listener.comparator.event Class Description Complex An interactor composed of interacting molecules that can be copurified. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.listener.comparator.observer Class Description Complex An interactor composed of interacting molecules that can be copurified. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.listener.impl Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CurationDepth Flag to determine the curation depth.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...OntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequencePublication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceSource Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.model Class Description Alias Alias is a synonym.AllostericEffector The effector that elicits an allosteric response.AllostericEffectorType The types of allosteryEffectorsAnnotation An Annotations gives some information about a specific topic.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.ComplexType The type of complex that can describe this interaction.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CooperativityEvidence The experimental method and corresponding publication from which a cooperative effect has been inferred.CurationDepth Flag to determine the curation depth.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalEntity An experimental entity with experimental featuresFeature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledComparableParticipant ModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledEntity An modelled entity with modelled featuresModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.Molecule This interface represents a simple molecule such as a protein, nucleic acid, gene, small molecule but excludes complexes and interactorSetNamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.OntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.ParameterValue A parameter numeric value.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequencePublication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceResultingSequence This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.)Source Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug.VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.model.impl Class Description Alias Alias is a synonym.AllostericEffector The effector that elicits an allosteric response.AllostericEffectorType The types of allosteryEffectorsAllostery The allostery cooperative Effect.Annotation An Annotations gives some information about a specific topic.BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesCausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CooperativityEvidence The experimental method and corresponding publication from which a cooperative effect has been inferred.CurationDepth Flag to determine the curation depth.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalEntity An experimental entity with experimental featuresExperimentalParticipantCandidate Interface for experimental participant candidatesExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.FeatureModificationEffector The modification (feature) that elicits an allosteric response in an allosteric molecule.Gene Interactor for genetic interactionsInteraction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledEntity An modelled entity with modelled featuresModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.ModelledParticipantCandidate Interface for modelled participant candidatesModelledParticipantPool A pool of modelled participant candidatesMolecule This interface represents a simple molecule such as a protein, nucleic acid, gene, small molecule but excludes complexes and interactorSetMoleculeEffector The participant that elicits an allosteric response in an allosteric molecule upon binding to that molecule.NamedExperiment A named experiment is an experiment with a shortname, fullname and aliasesNamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.NamedParticipant A named entity is an entity having a short name and a fullname in addition to aliases.NucleicAcid Polymers of nucleotides which can interact with other moleculesOntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.ParameterValue A parameter numeric value.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequencePreassembly The pre-assembly cooperative effect.Protein Polymer of amino acids which can interact with other molecules.Publication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceResultingSequence This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.)Source Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug.VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.tab.extension Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesCausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CurationDepth Flag to determine the curation depth.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalEntity An experimental entity with experimental featuresFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Gene Interactor for genetic interactionsInteraction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledEntity An modelled entity with modelled featuresModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.Molecule This interface represents a simple molecule such as a protein, nucleic acid, gene, small molecule but excludes complexes and interactorSetNamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.NucleicAcid Polymers of nucleotides which can interact with other moleculesOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.ParameterValue A parameter numeric value.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesPolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequenceProtein Polymer of amino acids which can interact with other molecules.Publication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceResultingSequence This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.)Source Source of the data.Stoichiometry The stoichiometry of a participantXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.tab.extension.datasource Class Description ComplexType The type of complex that can describe this interaction.CvTerm A controlled vocabulary term defined by an ontology.Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Participant Participant identified in an interaction -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.tab.extension.factory Class Description ComplexType The type of complex that can describe this interaction.CvTerm A controlled vocabulary term defined by an ontology.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.Interactor Molecule or complex of molecules that interacts with other molecules/complexes -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.tab.io.iterator Class Description Feature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.tab.io.parser Class Description CvTerm A controlled vocabulary term defined by an ontology.Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Participant Participant identified in an interaction -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.tab.io.writer Class Description Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.tab.io.writer.extended Class Description Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc... -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.tab.io.writer.feeder Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.Checksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Confidence A Confidence gives information about how reliable an object is.CvTerm A controlled vocabulary term defined by an ontology.Feature Property of a participant that may interfere with the binding of a molecule.ModelledParticipant Participant of a modelled interaction.Organism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesPublication A scientific publication which has been curated by an interaction database.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.tab.io.writer.feeder.extended Class Description Alias Alias is a synonym.Confidence A Confidence gives information about how reliable an object is.Feature Property of a participant that may interfere with the binding of a molecule.ModelledParticipant Participant of a modelled interaction.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.tab.utils Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.ModelledParticipant Participant of a modelled interaction.ParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.ComplexType The type of complex that can describe this interaction.Confidence A Confidence gives information about how reliable an object is.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Gene Interactor for genetic interactionsInteraction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledComparableParticipant ModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.NamedExperiment A named experiment is an experiment with a shortname, fullname and aliasesNucleicAcid Polymers of nucleotides which can interact with other moleculesOntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesPolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequenceProtein Polymer of amino acids which can interact with other molecules.Publication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.clone Class Description AllostericEffector The effector that elicits an allosteric response.Allostery The allostery cooperative Effect.Complex An interactor composed of interacting molecules that can be copurified.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CooperativityEvidence The experimental method and corresponding publication from which a cooperative effect has been inferred.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalParticipantCandidate Interface for experimental participant candidatesFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.ModelledParticipantCandidate Interface for modelled participant candidatesOntologyTerm Ontology term with definition, parents and childrenOrganism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesPolymer A polymer is an interactor with a sequencePublication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceSource Source of the data.VariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions). -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator Class Description Alias Alias is a synonym.CvTerm A controlled vocabulary term defined by an ontology.Parameter A numeric parameter e.g.Range A feature range indicates the positions of a feature in the interactor sequenceXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.alias Class Description Alias Alias is a synonym.CvTerm A controlled vocabulary term defined by an ontology. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.annotation Class Description Annotation An Annotations gives some information about a specific topic.CvTerm A controlled vocabulary term defined by an ontology. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.checksum Class Description Checksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.CvTerm A controlled vocabulary term defined by an ontology. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.confidence Class Description Confidence A Confidence gives information about how reliable an object is.CvTerm A controlled vocabulary term defined by an ontology. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.cooperativity Class Description Allostery The allostery cooperative Effect.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CooperativityEvidence The experimental method and corresponding publication from which a cooperative effect has been inferred.CvTerm A controlled vocabulary term defined by an ontology.FeatureModificationEffector The modification (feature) that elicits an allosteric response in an allosteric molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...MoleculeEffector The participant that elicits an allosteric response in an allosteric molecule upon binding to that molecule.Publication A scientific publication which has been curated by an interaction database. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.cv Class Description CvTerm A controlled vocabulary term defined by an ontology.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.experiment Class Description CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Publication A scientific publication which has been curated by an interaction database.VariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug.VariableParameterValueSet Set of variable parameter values applied together in a same experiment -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.feature Class Description CvTerm A controlled vocabulary term defined by an ontology.Feature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.ModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.Range A feature range indicates the positions of a feature in the interactor sequenceXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.interaction Class Description CvTerm A controlled vocabulary term defined by an ontology.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesVariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.interactor Class Description Alias Alias is a synonym.BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesComplex An interactor composed of interacting molecules that can be copurified.CvTerm A controlled vocabulary term defined by an ontology.Gene Interactor for genetic interactionsInteractor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.NucleicAcid Polymers of nucleotides which can interact with other moleculesPolymer A polymer is an interactor with a sequenceProtein Polymer of amino acids which can interact with other molecules.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.organism Class Description CvTerm A controlled vocabulary term defined by an ontology.Organism The organism is defined by a taxonomy identifier. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.parameter Class Description CvTerm A controlled vocabulary term defined by an ontology.Parameter A numeric parameter e.g.ParameterValue A parameter numeric value. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.participant Class Description CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termCvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)ExperimentalEntity An experimental entity with experimental featuresExperimentalParticipantPool A pool of experimental participantsFeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.ModelledComparableParticipant ModelledEntity An modelled entity with modelled featuresModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledParticipant Participant of a modelled interaction.ModelledParticipantPool A pool of modelled participant candidatesParameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeableStoichiometry The stoichiometry of a participant -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.publication Class Description CvTerm A controlled vocabulary term defined by an ontology.Publication A scientific publication which has been curated by an interaction database.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.range Class Description CvTerm A controlled vocabulary term defined by an ontology.Position The position of a feature in the interactor sequenceRange A feature range indicates the positions of a feature in the interactor sequenceResultingSequence This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.) -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.utils.comparator.xref Class Description Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml Class Description Complex An interactor composed of interacting molecules that can be copurified.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledEntity An modelled entity with modelled featuresModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.cache Class Description Complex An interactor composed of interacting molecules that can be copurified.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledEntity An modelled entity with modelled featuresModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.iterator Class Description Complex An interactor composed of interacting molecules that can be copurified.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc... -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.parser Class Description Interaction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Participant Participant identified in an interaction -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer Class Description Annotation An Annotations gives some information about a specific topic.ComplexType The type of complex that can describe this interaction.Interaction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Source Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.compact Class Description Complex An interactor composed of interacting molecules that can be copurified.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeableSource Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.compact.extended Class Description Complex An interactor composed of interacting molecules that can be copurified.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Source Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements Class Description Alias Alias is a synonym.Allostery The allostery cooperative Effect.Annotation An Annotations gives some information about a specific topic.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.ComplexType The type of complex that can describe this interaction.Confidence A Confidence gives information about how reliable an object is.CooperativityEvidence The experimental method and corresponding publication from which a cooperative effect has been inferred.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.Interactor Molecule or complex of molecules that interacts with other molecules/complexesOrganism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsPosition The position of a feature in the interactor sequencePreassembly The pre-assembly cooperative effect.Publication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceResultingSequence This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.)VariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug.VariableParameterValueSet Set of variable parameter values applied together in a same experiment -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.Checksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Confidence A Confidence gives information about how reliable an object is.CvTerm A controlled vocabulary term defined by an ontology.Feature Property of a participant that may interfere with the binding of a molecule.Interactor Molecule or complex of molecules that interacts with other molecules/complexesOrganism The organism is defined by a taxonomy identifier.Polymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequencePublication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceSource Source of the data.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.Checksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Confidence A Confidence gives information about how reliable an object is.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.Organism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePosition The position of a feature in the interactor sequencePublication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml25 Class Description CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeableStoichiometry The stoichiometry of a participant -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.abstracts.xml30 Class Description Allostery The allostery cooperative Effect.Annotation An Annotations gives some information about a specific topic.Complex An interactor composed of interacting molecules that can be copurified.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CooperativityEvidence The experimental method and corresponding publication from which a cooperative effect has been inferred.CvTerm A controlled vocabulary term defined by an ontology.ExperimentalParticipantCandidate Interface for experimental participant candidatesFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.ModelledParticipantCandidate Interface for modelled participant candidatesOrganism The organism is defined by a taxonomy identifier.ParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePreassembly The pre-assembly cooperative effect.Stoichiometry The stoichiometry of a participantVariableParameterValueSet Set of variable parameter values applied together in a same experiment -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml25 Class Description Alias Alias is a synonym.Complex An interactor composed of interacting molecules that can be copurified.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.ParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.compact.xml30 Class Description Alias Alias is a synonym.CvTerm A controlled vocabulary term defined by an ontology.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.ParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml25 Class Description Alias Alias is a synonym.Complex An interactor composed of interacting molecules that can be copurified.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.ParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.expanded.xml30 Class Description Alias Alias is a synonym.CvTerm A controlled vocabulary term defined by an ontology.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.ParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Position The position of a feature in the interactor sequenceXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact Class Description Interactor Molecule or complex of molecules that interacts with other molecules/complexes -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml25 Class Description Complex An interactor composed of interacting molecules that can be copurified.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.compact.xml30 Class Description CvTerm A controlled vocabulary term defined by an ontology.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded Class Description Interactor Molecule or complex of molecules that interacts with other molecules/complexes -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml25 Class Description Complex An interactor composed of interacting molecules that can be copurified.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.expanded.xml30 Class Description CvTerm A controlled vocabulary term defined by an ontology.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25 Class Description Alias Alias is a synonym.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Source Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml253 Class Description Confidence A Confidence gives information about how reliable an object is.CvTerm A controlled vocabulary term defined by an ontology.Organism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml25.xml254 Class Description Confidence A Confidence gives information about how reliable an object is.CvTerm A controlled vocabulary term defined by an ontology.Organism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.extended.xml30 Class Description Allostery The allostery cooperative Effect.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Organism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.Preassembly The pre-assembly cooperative effect.VariableParameterValueSet Set of variable parameter values applied together in a same experiment -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.xml25 Class Description Alias Alias is a synonym.Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.ModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.Parameter A numeric parameter e.g.Publication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequence -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.elements.impl.xml30 Class Description Alias Alias is a synonym.Allostery The allostery cooperative Effect.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termConfidence A Confidence gives information about how reliable an object is.CooperativityEvidence The experimental method and corresponding publication from which a cooperative effect has been inferred.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.ModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.Parameter A numeric parameter e.g.Participant Participant identified in an interactionPreassembly The pre-assembly cooperative effect.Publication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceResultingSequence This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.)Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug.VariableParameterValueSet Set of variable parameter values applied together in a same experiment -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.expanded Class Description Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Source Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.io.writer.expanded.extended Class Description ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Source Source of the data. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.listener Class Description CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Organism The organism is defined by a taxonomy identifier. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model Class Description Annotation An Annotations gives some information about a specific topic.Interaction Interaction involving one to several molecules.Interactor Molecule or complex of molecules that interacts with other molecules/complexes -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.Checksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalEntity An experimental entity with experimental featuresFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...NamedExperiment A named experiment is an experiment with a shortname, fullname and aliasesNamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.NamedParticipant A named entity is an entity having a short name and a fullname in addition to aliases.Organism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesSource Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.binary Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.Checksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.NamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.Parameter A numeric parameter e.g.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidencesSource Source of the data.VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.binary.xml253 Class Description CvTerm A controlled vocabulary term defined by an ontology.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.NamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.ParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.binary.xml254 Class Description CvTerm A controlled vocabulary term defined by an ontology.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.NamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.ParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.binary.xml30 Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.Checksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CvTerm A controlled vocabulary term defined by an ontology.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.NamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.Organism The organism is defined by a taxonomy identifier.ParticipantEvidence Participant of an interaction which is supported by experimental evidencesSource Source of the data.Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.datasource Class Description Complex An interactor composed of interacting molecules that can be copurified.ComplexType The type of complex that can describe this interaction.CvTerm A controlled vocabulary term defined by an ontology.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...Organism The organism is defined by a taxonomy identifier.Participant Participant identified in an interaction -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.factory Class Description BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesComplex An interactor composed of interacting molecules that can be copurified.ComplexType The type of complex that can describe this interaction.CvTerm A controlled vocabulary term defined by an ontology.Gene Interactor for genetic interactionsInteractionCategory Enum to recognize the object category of an interaction : - evidence : for InteractionEvidence implementations.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.NucleicAcid Polymers of nucleotides which can interact with other moleculesPolymer A polymer is an interactor with a sequenceProtein Polymer of amino acids which can interact with other molecules. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.factory.xml25 Class Description CvTerm A controlled vocabulary term defined by an ontology.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.factory.xml30 Class Description CvTerm A controlled vocabulary term defined by an ontology.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParticipant Participant of a modelled interaction.Participant Participant identified in an interactionParticipantEvidence Participant of an interaction which is supported by experimental evidences -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.xml253 Class Description Alias Alias is a synonym.AllostericEffector The effector that elicits an allosteric response.AllostericEffectorType The types of allosteryEffectorsAllostery The allostery cooperative Effect.Annotation An Annotations gives some information about a specific topic.BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesCausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CooperativityEvidence The experimental method and corresponding publication from which a cooperative effect has been inferred.CurationDepth Flag to determine the curation depth.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalEntity An experimental entity with experimental featuresExperimentalParticipantCandidate Interface for experimental participant candidatesExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.FeatureModificationEffector The modification (feature) that elicits an allosteric response in an allosteric molecule.Gene Interactor for genetic interactionsInteraction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledEntity An modelled entity with modelled featuresModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.ModelledParticipantCandidate Interface for modelled participant candidatesModelledParticipantPool A pool of modelled participant candidatesMolecule This interface represents a simple molecule such as a protein, nucleic acid, gene, small molecule but excludes complexes and interactorSetMoleculeEffector The participant that elicits an allosteric response in an allosteric molecule upon binding to that molecule.NamedExperiment A named experiment is an experiment with a shortname, fullname and aliasesNamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.NamedParticipant A named entity is an entity having a short name and a fullname in addition to aliases.NucleicAcid Polymers of nucleotides which can interact with other moleculesOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.ParameterValue A parameter numeric value.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequencePreassembly The pre-assembly cooperative effect.Protein Polymer of amino acids which can interact with other molecules.Publication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceResultingSequence This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.)Source Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug.VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.xml254 Class Description Alias Alias is a synonym.AllostericEffector The effector that elicits an allosteric response.AllostericEffectorType The types of allosteryEffectorsAllostery The allostery cooperative Effect.Annotation An Annotations gives some information about a specific topic.BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesCausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CooperativityEvidence The experimental method and corresponding publication from which a cooperative effect has been inferred.CurationDepth Flag to determine the curation depth.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalEntity An experimental entity with experimental featuresExperimentalParticipantCandidate Interface for experimental participant candidatesExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.FeatureModificationEffector The modification (feature) that elicits an allosteric response in an allosteric molecule.Gene Interactor for genetic interactionsInteraction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledEntity An modelled entity with modelled featuresModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.ModelledParticipantCandidate Interface for modelled participant candidatesModelledParticipantPool A pool of modelled participant candidatesMolecule This interface represents a simple molecule such as a protein, nucleic acid, gene, small molecule but excludes complexes and interactorSetMoleculeEffector The participant that elicits an allosteric response in an allosteric molecule upon binding to that molecule.NamedExperiment A named experiment is an experiment with a shortname, fullname and aliasesNamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.NamedParticipant A named entity is an entity having a short name and a fullname in addition to aliases.NucleicAcid Polymers of nucleotides which can interact with other moleculesOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.ParameterValue A parameter numeric value.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequencePreassembly The pre-assembly cooperative effect.Protein Polymer of amino acids which can interact with other molecules.Publication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceResultingSequence This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.)Source Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug.VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.extension.xml300 Class Description Alias Alias is a synonym.AllostericEffector The effector that elicits an allosteric response.AllostericEffectorType The types of allosteryEffectorsAllostery The allostery cooperative Effect.Annotation An Annotations gives some information about a specific topic.BioactiveEntity Molecules showing activity in a living system and which can interact with other moleculesCausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CooperativityEvidence The experimental method and corresponding publication from which a cooperative effect has been inferred.CurationDepth Flag to determine the curation depth.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.ExperimentalEntity An experimental entity with experimental featuresExperimentalParticipantCandidate Interface for experimental participant candidatesExperimentalParticipantPool A pool of experimental participantsFeature Property of a participant that may interfere with the binding of a molecule.FeatureEvidence The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.FeatureModificationEffector The modification (feature) that elicits an allosteric response in an allosteric molecule.Gene Interactor for genetic interactionsInteraction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesInteractorPool InteractorPool represents a collection of potential interactors but we cannot determine which one interacts.ModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledEntity An modelled entity with modelled featuresModelledFeature Biological property of a participant that may be involved with or interfere with the binding of a molecule.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.ModelledParticipantCandidate Interface for modelled participant candidatesModelledParticipantPool A pool of modelled participant candidatesMolecule This interface represents a simple molecule such as a protein, nucleic acid, gene, small molecule but excludes complexes and interactorSetMoleculeEffector The participant that elicits an allosteric response in an allosteric molecule upon binding to that molecule.NamedExperiment A named experiment is an experiment with a shortname, fullname and aliasesNamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.NamedParticipant A named entity is an entity having a short name and a fullname in addition to aliases.NucleicAcid Polymers of nucleotides which can interact with other moleculesOrganism The organism is defined by a taxonomy identifier.Parameter A numeric parameter e.g.ParameterValue A parameter numeric value.Participant Participant identified in an interactionParticipantCandidate A participant candidate is part of a participant pool and contains the molecule which can interact plus some participant details such as features and causal relationshipsParticipantEvidence Participant of an interaction which is supported by experimental evidencesParticipantPool A pool of participants that can be grouped together as a single participant as they are interchangeablePolymer A polymer is an interactor with a sequencePosition The position of a feature in the interactor sequencePreassembly The pre-assembly cooperative effect.Protein Polymer of amino acids which can interact with other molecules.Publication A scientific publication which has been curated by an interaction database.Range A feature range indicates the positions of a feature in the interactor sequenceResultingSequence This interface is for representing a sequence portion that has been changed (by mutation, a variant, etc.)Source Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).VariableParameterValue A value for a specific variableParameter in a specific experiment - eg - the concentration of a specific drug.VariableParameterValueSet Set of variable parameter values applied together in a same experimentXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.reference Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Feature Property of a participant that may interfere with the binding of a molecule.Range A feature range indicates the positions of a feature in the interactor sequenceXref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.reference.xml253 Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.NamedExperiment A named experiment is an experiment with a shortname, fullname and aliasesNamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.NamedParticipant A named entity is an entity having a short name and a fullname in addition to aliases.Organism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionPublication A scientific publication which has been curated by an interaction database.Source Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.reference.xml254 Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.NamedExperiment A named experiment is an experiment with a shortname, fullname and aliasesNamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.NamedParticipant A named entity is an entity having a short name and a fullname in addition to aliases.Organism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionPublication A scientific publication which has been curated by an interaction database.Source Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.reference.xml300 Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CausalRelationship These relationship types denote a causal relationship, or the absence of a causal relationship between a subject and an object termChecksum Checksum is a value for checking consistency of the data and can also be used for identifying objects.Complex An interactor composed of interacting molecules that can be copurified.Confidence A Confidence gives information about how reliable an object is.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.CvTerm A controlled vocabulary term defined by an ontology.Entity An entity which gives more information to a specific molecule (such as features, causal relationships)Experiment Experiment in which some interactions has been determined.Feature Property of a participant that may interfere with the binding of a molecule.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledConfidence A modelled confidence is a confidence for a modelled interaction.ModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc...ModelledParameter A modelled parameter is a parameter for a modelled interaction.ModelledParticipant Participant of a modelled interaction.NamedExperiment A named experiment is an experiment with a shortname, fullname and aliasesNamedInteraction A named interaction is an interaction having a fullname and aliases in addition to a shortname.NamedParticipant A named entity is an entity having a short name and a fullname in addition to aliases.Organism The organism is defined by a taxonomy identifier.Participant Participant identified in an interactionPublication A scientific publication which has been curated by an interaction database.Source Source of the data.Stoichiometry The stoichiometry of a participantVariableParameter A VariableParameter is a variable experimental parameter such as a drug treatment where several drug concentration were used and that affects some interactions (dynamic interactions).Xref Cross reference to an external database/resource which can give more information about an object. -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.xml253 Class Description Annotation An Annotations gives some information about a specific topic.Complex An interactor composed of interacting molecules that can be copurified.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc... -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.xml254 Class Description Annotation An Annotations gives some information about a specific topic.Complex An interactor composed of interacting molecules that can be copurified.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc... -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.model.xml30 Class Description Annotation An Annotations gives some information about a specific topic.Complex An interactor composed of interacting molecules that can be copurified.Experiment Experiment in which some interactions has been determined.Interaction Interaction involving one to several molecules.InteractionEvidence Interaction involving one to several molecules supported by experiments.Interactor Molecule or complex of molecules that interacts with other molecules/complexesModelledInteraction An interaction that is not directly supported by experimental evidence but is based on homology statements, modelling, etc... -
Classes in psidev.psi.mi.jami.model used by psidev.psi.mi.jami.xml.utils Class Description Alias Alias is a synonym.Annotation An Annotations gives some information about a specific topic.CooperativeEffect A cooperative effect an interaction has on a subsequent interaction.NamedExperiment A named experiment is an experiment with a shortname, fullname and aliases