Difference between revisions of "RNAi"
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== RNAi Data Model == | == RNAi Data Model == | ||
+ | |||
+ | ////////////////////////////////////////////////////////////////// | ||
+ | // | ||
+ | // ?RNAi class | ||
+ | // | ||
+ | ////////////////////////////////////////////////////////////////// | ||
+ | |||
+ | |||
+ | ?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 | ||
+ | Phenotype_not_observed ?Phenotype XREF Not_in_RNAi #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes | ||
+ | Expr_profile ?Expr_profile XREF RNAi_result // connection added during build [030106 krb] | ||
+ | Remark ?Text #Evidence | ||
+ | Method UNIQUE ?Method | ||
== RNAi Curation Standard Operating Procedure (SOP) == | == RNAi Curation Standard Operating Procedure (SOP) == |
Revision as of 19:26, 8 September 2011
Contents
RNAi Curation Mission Summary
The term "RNAi" stands for "RNA-interference" and refers to the targeted silencing of gene expression of a "target gene" via introduction of double stranded RNA (dsRNA) containing high degrees of sequence identity to the "target gene". In C. elegans, sequences of dsRNA may be introduced into the worm by a variety of different methods including direct micro-injection, soaking of worms in solution containing dsRNA, feeding worms bacteria that express dsRNA from a plasmid, and transgenic expression (within the worm) of dsRNA. For efficient and specific knockdown of gene expression, the dsRNA must have a minimum sequence identity with the target gene sequence. Any phenotype(s) resulting from the RNAi-mediated knockdown of a particular gene is thought to directly reflect the phenotype of a loss-of-function mutation in that gene, hence providing evidence as to the gene's biological function.
The goal of RNAi curation is to associate RNAi-mediated phenotypes with the target genes knocked down in RNAi experiments, as found in the literature pertaining to C. elegans and related species.
RNAi Data Model
////////////////////////////////////////////////////////////////// // // ?RNAi class // //////////////////////////////////////////////////////////////////
?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
Phenotype_not_observed ?Phenotype XREF Not_in_RNAi #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes
Expr_profile ?Expr_profile XREF RNAi_result // connection added during build [030106 krb] Remark ?Text #Evidence
Method UNIQUE ?Method