WormBase Model:Interaction
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Old Model
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//
// ?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.
//
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?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
