WormBase Model:RNAi

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Contents 1 Curator Comments/Description 2 Model 3 Proposed Changes

WormBase Models

Curator Comments/Description

//////////////////////////////////////////////////////////////////
//
// ?RNAi class
// 
// Initially from Lincoln Stein December, 2000
//
// Heavily modified by Igor November, 2004
//
//////////////////////////////////////////////////////////////////

Model

?RNAi   Evidence #Evidence
        History_name UNIQUE ?Text
        Homol Homol_homol ?Homol_data XREF RNAi_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
        Sequence_info   DNA_text Text UNIQUE Text //stores actual probe sequence for automated mapping
						  // 1st Text is DNA, 2nd is probe name
                        Sequence ?Sequence XREF RNAi  //links to a real Sequence object used in the experiment 
						      // such as yk clone; not UNIQUE anymore
                        PCR_product ?PCR_product XREF RNAi // links to a PCR_product object used in 
							   // the experiment; not UNIQUE anymore
        Uniquely_mapped  //boolean; if present, signifies that ?RNAi object has a unique sequence 
			// which maps to a single place in the genome
        Experiment      Laboratory ?Laboratory
                        Author ?Author
                        Date UNIQUE DateType
                        Strain UNIQUE ?Strain
                        Genotype UNIQUE ?Text   //used when no Strain object exists
                        Treatment UNIQUE ?Text
                        Life_stage UNIQUE ?Life_stage
                        Temperature UNIQUE Int
                        Delivered_by UNIQUE Bacterial_feeding      //RL [010327]
                                            Injection              //RL [010327]
                                            Soaking                //RL [010327]
                                            Transgene_expression   //RL [010327]
        Inhibits        Predicted_gene ?CDS XREF RNAi_result #Evidence // "gene" parent (unreliable)
                        Gene ?Gene   XREF RNAi_result #Evidence           //RL [010327]
                        Transcript ?Transcript XREF RNAi_result #Evidence // [021126 krb]
                        Pseudogene ?Pseudogene XREF RNAi_result #Evidence // [030801 krb]
        Supporting_data Movie ?Movie XREF RNAi    // Lincoln, krb [010807]
                        Picture ?Picture XREF RNAi
	DB_info    Database ?Database ?Database_field ?Accession_number //to link out to Phenobank ar2 02-DEC-05 //removed UNIQUE as reqs multiple connections
	Species UNIQUE ?Species
	Gene_regulation ?Gene_regulation XREF RNAi  // this tag is used when an RNAi experiment describes gene regulation ar2 29-MAR-06 for igor
	Interaction ?Interaction
        Reference UNIQUE ?Paper XREF RNAi //[070215 ar2] made reference unique so Paper sort of equates to a Study class for Will S
        Phenotype ?Phenotype XREF RNAi #Phenotype_info
        Expr_profile ?Expr_profile XREF RNAi_result // connection added during build [030106 krb]
        Remark ?Text #Evidence
	Method UNIQUE ?Method

Proposed Changes