WormBase Model:Interaction

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WormBase Models

Curator Comments/Description

Old Model

////////////////////////////////////////////////////////////////////////////////
//
// ?Interaction class for Andrei WBInteraction00000001             
// Replaces the old interaction model. The main enhancements are information about the interactors and the phenotypes
// relevant to the interaction. For the directional interactions (tags:Regulatory, Suppression, Enhancement, Epistasis) 
// the directionality of the interaction is described by the tags Effector and Effected as follows: Effector "Regulates"
// ("Suppresses", "Enhances", or "IsEpistatic To") Effected.
//
// For the rest of the interactions (the non-directional kind) Effector and Effected are considered equivalent.
//
////////////////////////////////////////////////////////////////////////////////

?Interaction   Evidence #Evidence
               Interactor    ?Gene    XREF Interaction    #Interactor_info
               Interaction_type    Genetic    #Interaction_info
                                   Regulatory    #Interaction_info
                                   No_interaction    #Interaction_info
                                   Predicted_interaction    #Interaction_info
                                   Physical_interaction    #Interaction_info
                                   Suppression    #Interaction_info
                                   Enhancement    #Interaction_info
                                   Synthetic    #Interaction_info
                                   Epistasis    #Interaction_info
                                   Mutual_enhancement    #Interaction_info
                                   Mutual_suppression    #Interaction_info
               Confidence          Confidence_level        UNIQUE Float
                                   P_value                 UNIQUE Float
                                   Log_likelihood_score    UNIQUE Float
               Paper ?Paper XREF Interaction
               DB_info Database ?Database ?Database_field ?Accession_number
               Remark  ?Text   #Evidence

New model

?Interaction	Interaction_type Physical
				 Predicted
				 Regulatory	Change_of_localization	    // Indicates regulation of localization
						Change_of_expression_level  // Indicates regulation of expression level (RNA, protein)
				 Genetic	Genetic_interaction	    // Indicates a generic genetic interaction that may not be accurately captured by any other term
						Negative_genetic	    // General case in which one genetic perturbation exacerbates the effects of second perturbation
						Synthetic		    // Two genetic perturbations are individually wild type but produce a phenotype when combined
						Enhancement		    // One genetic perturbation exacerbates the effects of second perturbation
						Unilateral_enhancement	    // One genetic perturbation exacerbates the effects of a second perturbation, which is otherwise wild type
						Mutual_enhancement	    // Two genetic perturbations individually result in a phenotype and combine to result in a more severe phenotype than either individual perturbation
						Suppression		    // One genetic perturbation suppresses the effects of second perturbation
						Unilateral_suppression	    // One genetic perturbation suppresses the effects of second perturbation, which is otherwise wild type
						Mutual_suppression	    // Two genetic perturbations individually result in a phenotype and combine to result in a less severe phenotype than either individual perturbation
						Asynthetic		    // Two genetic perturbations individually result in an identical phenotype which is also identical to the phenotype of their combination
						Suppression_enhancement	    // A double genetic perturbation yields a phenotype intermediate to that of either individual perturbation
						Epistasis		    // The phenotype of one genetic perturbation masks the phenotype of a second perturbation
						Maximal_epistasis	    // The more severe phenotype exhibited by two genetic perturbations is observed when both perturbations are combined
						Minimal_epistasis	    // The less severe phenotype exhibited by two genetic perturbations is observed when both perturbations are combined
						Suppression_epistasis	    // One genetic perturbation results in a phenotype which is suppressed back to wild type when combined with a second (wild type) perturbation
						Agonistic_epistasis	    // Combined phenotype is identical to the the single perturbation which is closer to the expected phenotype as determined by the neutrality function
						Antagonistic_epistasis	    // Two genetic perturbations each result in opposite phenotypes and the combined phenotype is identical to the the single perturbation which is furthest from the expected phenotype as determined by the neutrality function
						Oversuppression		// One genetic perturbation suppresses the phenotype of a second perturbation beyond wild type (producing an opposite phenotype)
						Unilateral_oversuppression	// One genetic perturbation suppresses the phenotype of a second (wild type) perturbation beyond wild type (producing an opposite phenotype)
						Mutual_oversuppression		// Two genetic perturbations individually result in a similar phenotype but result in an opposite phenotype when combined
						Complex_oversuppression		// Two genetic perturbations each result in opposite phenotypes and the combined phenotype is (relative to expectation) suppressed beyond wild type, resulting in a phenotype opposite to that expected
						Oversuppression_enhancement	// Two genetic perturbations each result in opposite phenotypes and the combined phenotype is oversuppressed relative to one perturbation and enhanced relative to the other perturbation
						Phenotype_bias			// " is less severe than either original phenotype, but deviates from expectation
						Biased_suppression		// Two genetic perturbations each result in opposite phenotypes and the combined phenotype is less severe than either original phenotype, and less severe than expected
						Biased_enhancement		// Two genetic perturbations each result in opposite phenotypes and the combined phenotype is less severe than either original phenotype, but more severe than expected
						Complex_phenotype_bias		// Two genetic perturbations each result in opposite phenotypes, and although the combined phenotype is expected to be wild type, the actual combined perturbations result in a phenotype less severe than either original phenotype
						No_interaction			// Negative data; no interaction was observed after testing

		Interactor	PCR_interactor UNIQUE ?PCR_product	#Interactor_info	// PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments
				Sequence_interactor UNIQUE ?Sequence 	#Interactor_info	// Sequence of the interacting gene or protein
				Interactor_overlapping_CDS ?CDS		#Interactor_info	// CDS of the interacting gene or protein (or related sequence)
				Interactor_overlapping_gene ?Gene XREF Interaction #Interactor_info	// Gene (or portion of gene) involved in the interaction
				Interactor_overlapping_protein ?Protein XREF Interaction 	#Interactor_info	// Protein (or portion of protein) involved in the interaction
				Molecule_regulator      ?Molecule  XREF    Interaction	#Interactor_info	// Molecule that regulates a gene or protein (ported from Gene_regulation class)
				Other_regulator         ?Text	#Interactor_info	// Free text describing a regulator entity or condition that does not fall into a standard WormBase category
				Other_regulated         ?Text	#Interactor_info	// Free text describing a regulated entity or condition that does not fall into a standard WormBase category

		Interaction_summary ?Text #Evidence

		Detection_method		Affinity_capture_luminescence			// A physical interaction detection technique
						Affinity_capture_MS				// A physical interaction detection technique
						Affinity_capture_RNA				// A physical interaction detection technique
						Affinity_capture_Western			// A physical interaction detection technique
						Cofractionation					// A physical interaction detection technique
						Colocalization					// A physical interaction detection technique
						Copurification					// A physical interaction detection technique
						Fluorescence_resonance_energy_transfer		// A physical interaction detection technique
						Protein_fragment_complementation_assay		// A physical interaction detection technique
						Yeast_two_hybrid				// A physical interaction detection technique (Protein-protein)
						Biochemical_activity				// A physical interaction detection technique
						Cocrystal_structure				// A physical interaction detection technique
						Far_western					// A physical interaction detection technique
						Protein_peptide 				// A physical interaction detection technique
						Protein_RNA 					// A physical interaction detection technique
						Reconstituted_complex				// A physical interaction detection technique
						Yeast_one_hybrid  				// A physical interaction detection technique (Protein-DNA)
						Directed_yeast_one_hybrid			// A physical interaction detection technique (Protein-DNA)
						Antibody			// A regulatory interaction detection technique; Antibody name and details captured in Interactor_info hash
						Reporter_gene  ?Text		// A regulatory interaction detection technique
						Transgene			// A regulatory interaction detection technique; Trasnsgene name and details captured in Interactor_info hash
						In_situ        Text		// A regulatory interaction detection technique
						Northern       Text		// A regulatory interaction detection technique
						Western        Text		// A regulatory interaction detection technique
						RT_PCR         Text		// A regulatory interaction detection technique
						Other_method   ?Text		// A regulatory interaction detection technique

//Physical interaction-specific tag

		Library_info 	Library_screened Text INT	// In the context of Yeast Two Hybrid or Yeast One Hybrid screens, for example, the library may have been cDNA library or some other pool of clones
				Origin  From_laboratory UNIQUE ?Laboratory 	// A library generated at an academic laboratory
					From_company UNIQUE ?Text		// A library generated at a company

//Genetic interaction-specific tags

		Deviation_from_expectation	Text	// A text description of the way in which the phenotype deviated from expectation in genetic interactions
			
		Neutrality_function UNIQUE	Multiplicative		// The multiplicative neutrality function defines expectation as the product of two quantified phenotypes (relative to wild type) 
						Additive		// The additive neutrality function defines expectation as the sum of two quantified phenotypes (relative to wild type) 
						Minimal			// The minimal neutrality function defines expectation as the most severe of two quantified phenotypes (relative to wild type) 

//Gene regulation-specific tags

		Regulation_level	Transcriptional		// Regulation occurs at the transcriptional level
					Post_transcriptional	// Regulation occurs at the post-transcriptional level
					Post_translational	// Regulation occurs at the post-translational level

		Interaction_associated_feature ?Feature XREF Associated_with_gene_regulation #Evidence //to curate sequence feature connection [ar2]

		Regulation_result	Positive_regulate #GR_condition
					Negative_regulate #GR_condition
					Does_not_regulate #GR_condition // added to capture negative data [040220 krb]

//General tags

		Confidence	Description	Text		// Free text description of the confidence, e.g. "Core" vs "Noncore" (Vidal Interactome terms)
				P_value		  UNIQUE Float	// P-value confidence of interaction, if given
				Log_likelihood_score    UNIQUE Float	// Only used for Predicted interactions


		Throughput	UNIQUE	High_throughput //See BioGRID curation criteria for discussion:  http://www.yeastgenome.org/help/BiogridCuration.html
					Low_throughput
		Interaction_RNAi	?RNAi XREF Interaction		// RNAi experiment associated with the interaction
		Interaction_phenotype	?Phenotype XREF Interaction	// Phenotype associated with a genetic interaction
		WBProcess	?WBProcess	XREF	Interaction	// WormBase biological process associated with the interaction
		DB_info 	Database 	?Database 	?Database_field 	?Accession_number	// Any database reference to the interaction outside of WormBase, e.g. BioGRID, Interactome
		Paper 		?Paper		XREF	Interaction
		Remark 		?Text 		#Evidence

Proposed Changes

Unused tags

Evidence

Confidence_level

P_value

DB_info Database