Difference between revisions of "Gene Interaction"
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− | == ''' | + | 'links to relevant pages''<br> |
+ | [[Caltech documentation]] <br> | ||
+ | [[Interaction]]<br> | ||
+ | ---- | ||
+ | ==Interaction Curation== | ||
+ | |||
+ | ==Pipeline== | ||
+ | |||
+ | |||
+ | ==Interaction Model== | ||
+ | |||
+ | //////////////////////////////////////////////////////////////////////////////////// | ||
+ | ?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 | ||
+ | |||
+ | #Interactor_info Variation ?Variation XREF Interactor | ||
+ | Transgene ?Transgene XREF Interactor | ||
+ | Remark ?Text #Evidence //info about the reagents that the model can't capture goes here (e.g. co_suppression, RNA_reagent, etc.) | ||
+ | |||
+ | #Interaction_info Interaction_RNAi ?RNAi XREF Interaction | ||
+ | Effector ?Gene //master, upstream | ||
+ | Effected ?Gene //subject, downstream | ||
+ | Non_directional ?Gene //e.g. synthetic interactions - Igor | ||
+ | Interaction_phenotype ?Phenotype XREF Interaction | ||
+ | Confidence Confidence_level UNIQUE Float | ||
+ | P_value UNIQUE Float | ||
+ | |||
+ | |||
+ | #Interaction_type Genetic | ||
+ | Regulation | ||
+ | No_interaction | ||
+ | Predicted //addition for WeiWei | ||
+ | /////////////////////////////////////////////////////////////////////////////////// | ||
+ | |||
+ | == '''Gene_gene Interaction OA''' == | ||
'''OA interface''' | '''OA interface''' | ||
− | [[File: | + | [[File:tab1.png]] |
* Tab 1 | * Tab 1 | ||
Line 14: | Line 65: | ||
<br> | <br> | ||
− | [[File: | + | [[File:tab2.png]] |
*Tab 2 | *Tab 2 | ||
**Curator//dropdown list | **Curator//dropdown list |
Revision as of 22:35, 29 September 2010
'links to relevant pages
Caltech documentation
Interaction
Interaction Curation
Pipeline
Interaction Model
////////////////////////////////////////////////////////////////////////////////////
?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
- Interactor_info Variation ?Variation XREF Interactor
Transgene ?Transgene XREF Interactor Remark ?Text #Evidence //info about the reagents that the model can't capture goes here (e.g. co_suppression, RNA_reagent, etc.)
- Interaction_info Interaction_RNAi ?RNAi XREF Interaction
Effector ?Gene //master, upstream Effected ?Gene //subject, downstream Non_directional ?Gene //e.g. synthetic interactions - Igor Interaction_phenotype ?Phenotype XREF Interaction Confidence Confidence_level UNIQUE Float P_value UNIQUE Float
- Interaction_type Genetic
Regulation No_interaction Predicted //addition for WeiWei ///////////////////////////////////////////////////////////////////////////////////
Gene_gene Interaction OA
OA interface
- Tab 1
- PGID
- Interaction ID//generate automatically per entry
- Non_directional //toggle on (default), off (color change by click) means effected/effector on.
- Interaction Type//dropdown list with 11 types showing in .ace template
- Effected Gene/Variation/Transgene//WBGene, WBVar, etc. Imultiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors
- Effector Gene/Variation/Transgene//WBGene, WBVar, etc. multiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors
- Tab 2
- Curator//dropdown list
- Paper//ontology
- RNAi ID//free text fiel
- Phenotype//multiontology
- Remark//big text
- Sentence ID//sentence shows in term info
- False Positive//toggle, will not give an id or no dump if the sentence is false positive, containing no interaction info
- next sentence button
.ace template:
- Interaction : ""
- Interactor "WBGene" Variation ""
- Interactor "WBGene" Transgene ""
- Interactor "WBGene"
- Interaction_type Genetic Effector ""
- Interaction_type Genetic Effected ""
- Interaction_type Genetic Non_directional ""
- Interaction_type Genetic Interaction_RNAi ""
- Interaction_type Genetic Interaction_phenotype ""
- Interaction_type Regulatory Effector ""
- Interaction_type Regulatory Effected ""
- Interaction_type Regulatory Non_directional ""
- Interaction_type Regulatory Interaction_RNAi ""
- Interaction_type Regulatory Interaction_phenotype ""
- Interaction_type No_interaction Effector ""
- Interaction_type No_interaction Effected ""
- Interaction_type No_interaction Non_directional ""
- Interaction_type No_interaction Interaction_RNAi ""
- Interaction_type No_interaction Interaction_phenotype ""
- Interaction_type Predicted_interaction Non_directional ""
- Interaction_type Predicted_interaction Interaction_RNAi ""
- Interaction_type Predicted_interaction Interaction_phenotype ""
- Interaction_type Physical_interaction Effector ""
- Interaction_type Physical_interaction Effected ""
- Interaction_type Physical_interaction Interaction_RNAi ""
- Interaction_type Physical_interaction Interaction_phenotype ""
- Interaction_type Suppression Effector ""
- Interaction_type Suppression Effected ""
- Interaction_type Suppression Interaction_RNAi ""
- Interaction_type Suppression Interaction_phenotype ""
- Interaction_type Enhancement Effector ""
- Interaction_type Enhancement Effected ""
- Interaction_type Enhancement Interaction_RNAi ""
- Interaction_type Enhancement Interaction_phenotype ""
- Interaction_type Synthetic Non_directional ""
- Interaction_type Synthetic Interaction_RNAi ""
- Interaction_type Synthetic Interaction_phenotype ""
- Interaction_type Epistasis Effector ""
- Interaction_type Epistasis Effected ""
- Interaction_type Epistasis Interaction_RNAi ""
- Interaction_type Epistasis Interaction_phenotype ""
- Interaction_type Mutual_enhancement Non_directional ""
- Interaction_type Mutual_enhancement Interaction_RNAi ""
- Interaction_type Mutual_enhancement Interaction_phenotype ""
- Interaction_type Mutual_suppression Non_directional ""
- Interaction_type Mutual_suppression Interaction_RNAi ""
- Interaction_type Mutual_suppression Interaction_phenotype ""
- Paper ""
- Remark ""
== Some Notes for gene_gene_interaction ==
- two large scale papers
- WBPaper00027155 (Weiwei's science paper) has 23128 objects, starting from WBInteraction0008637 and ending at WBInteraction0050578 (blank ids in between)
- WBPaper00031465 (Lee's Nature Genetics paper) has 375491 objects, starting from WBInteraction 0100001, ending at WBInteraction0475491 (which is the largest WBInteraction id in acedb)