Gene Interaction/archive

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Interaction Curation

Pipeline

semi-automatic curation with textpresso extracted sentences

  • There are 2138 sentences (actually 2133 sentences) in the sourcefile /home/postgres/work/pgpopulation/genegeneinteraction/20091002-xiaodong/ggi_20091002
    • paper starts at WBPaper00028425, ends at WBPaper00035225
  • .ace dumper at /home/acedb/xiaodong/gene_gene_interaction/dump_ggi_ace.pl
    • go to the directory and do: ./dump_ggi_ace.pl > some_file.ace
  • Populate textpresso data in tazendra OA: done on 20110110 -X**
  1. cd to directory on tazendra: /home/acedb/xiaodong/textpresso_ggi
  2. mkdir directionay_name (eg 20110106)
  3. cd directory_name (eg 20110106)
  4. get Arun's result file (35225-35725.txt in the directory)
  5. run script: ./populate_textpresso_ggi_to_OA.pl 20110106/35225-35725.txt WBPerson4793 > 20110106/35225-35725.pg (with first argument file_name as input file, and second argument WBPersonID, then output file)
  6. after running, '20110106/35225-35725.pg' should be in '20111106' directory.

upload Gary and Chris RNAi-based interaction objects into OA

  • Reading file created by Igor's script into aceDB
    • you can use the empty database by ssh -X citpub@spica.caltech.edu
    • then cd CitaceMirror
    • then type 'ts' to launch an empty acedb
  • Dumping no-worry .ace file
  • Then parse into OA
    • scp ace file to same directory as below
    • ssh acedb@tazendra.caltech.edu (directory xiaodong/interaction_ace_parsing)
    • To run : ./parse_ace_interaction_oa.pl gary_RNAi.ace WBPerson1823
    • where gary_RNAi.ace is the <inputfile>,the first argument, and WBPerson# is the second argument.


Old Models

Updated for WS249 - CG 4-2-2015

?Interaction	Interaction_type Physical
				 Predicted
				 Regulatory Change_of_localization
					    Change_of_expression_level
				 Genetic Genetic_interaction
					 Neutral_genetic
					 Synthetic
					 Enhancement
					 Unilateral_enhancement
					 Mutual_enhancement
					 Positive_genetic
					 Suppression
					 Complete_suppression
					 Partial_suppression
					 Unilateral_suppression
					 Complete_unilateral_suppression
					 Partial_unilateral_suppression
					 Mutual_suppression
					 Complete_mutual_suppression
					 Partial_mutual_suppression
					 Suppression_enhancement
					 Asynthetic
					 Negative_genetic
					 Oversuppression	
					 Unilateral_oversuppression
					 Mutual_oversuppression		
					 Oversuppression_enhancement
       					 Phenotype_bias				
					 No_interaction				// Negative data; no interaction was observed after testing
					 Epistasis
					 Positive_epistasis
					 Maximal_epistasis
					 Minimal_epistasis
					 Neutral_epistasis
					 Qualitative_epistasis
					 Opposing_epistasis
					 Quantitative_epistasis
		Interactor PCR_interactor ?PCR_product  XREF Interaction #Interactor_info	// PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments
			   Sequence_interactor ?Sequence  XREF Interaction #Interactor_info	// Sequence of the interacting gene or protein
			   Feature_interactor ?Feature  XREF Associated_with_Interaction  #Interactor_info
			   Interactor_overlapping_CDS ?CDS XREF Interaction #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_interactor ?Molecule XREF Interaction #Interactor_info	  // Molecule that interacts with a gene or protein (ported from Gene_regulation Class)
			   Other_interactor ?Text #Interactor_info	// Free text describing an interactor entity or condition that does not fall into a standard WormBase category
			   Rearrangement  ?Rearrangement XREF Interactor #Interactor_info
			   Variation_interactor  ?Variation  XREF  Interactor  #Interactor_info   // Added WS248; allele involved in genetic interaction
		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
				 Chromatin_immunoprecipitation	      	      // A physical interaction detection technique
				 Cofractionation		      	      // A physical interaction detection technique
				 Colocalization				      // A physical interaction detection technique
				 Copurification				      // A physical interaction detection technique
				 DNase_I_footprinting    		      // 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
				 Electrophoretic_mobility_shift_assay         // 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
		Library_info Library_screened Text INT			  // In the context of Y2H or YH screens, for example, the library may have been cDNA library or a 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
		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
		Regulation_result Positive_regulate #GR_condition
				  Negative_regulate #GR_condition
				  Does_not_regulate #GR_condition // added to capture negative data [040220 krb]
		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
				  Low_throughput
		Interaction_RNAi ?RNAi XREF Interaction			// RNAi experiment associated with the interaction
		Interaction_phenotype ?Phenotype XREF Interaction	// Phenotype associated with a genetic interaction
		Unaffiliated_variation   ?Variation
		Unaffiliated_transgene   ?Transgene
		Unaffiliated_antibody    ?Antibody
		Unaffiliated_expr_pattern   ?Expr_pattern
		Unaffiliated_construct   ?Construct
		WBProcess ?WBProcess XREF Interaction			// WormBase biological process associated with the interaction
		DB_info Database ?Database ?Database_field ?Text	// Any database reference to the interaction outside of WormBase, e.g. BioGRID, Interactome
		Paper ?Paper XREF Interaction
		Antibody_remark ?Text
		Historical_gene   ?Gene Text
		Remark ?Text #Evidence


?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 //directional and non_directional
                 Physical_interaction
                 Regulation
                 No_interaction
                 Synthetic//non_directional
                 Epistasis
                 Enhancement
                 Suppression
                 Predicted  //addition for WeiWei, non_direactional
                 Mutual_enhancement//non_directional
                 Mutual_suprression//non_directional
///////////////////////////////////////////////////////////////////////////////////

Tags removed for WS248

From ?Interaction model

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)

From #Interactor_info model

Intragenic_effector_variation   ?Variation   XREF   Interactor
Intragenic_affected_variation   ?Variation   XREF   Interactor
Variation ?Variation XREF Interactor	   // (allele, polymorphism, etc.) involved in the interaction //removed XREF from proposal

New Model Proposals

Physical Interactions

Physical Interaction Model v1.3

    ?Physical_interaction   Evidence #Evidence
            Interactor   Non_directional_interactor PCR_non_directional_interactor UNIQUE  ?PCR_product  XREF to?  ?Species 
                                                    Sequence_non_directional_interactor  UNIQUE  ?Sequence  XREF to?  ?Species
                                                    Non_directional_interactor_overlapping_CDS  ?CDS  XREF to? ?Species  #Evidence
                                                    Non_directional_interactor_overlapping_gene  ?Gene  XREF to ? ?Species #Evidence
                                                    Non_directional_interactor_DB_info ?Database ?Database_field UNIQUE ?Accession_number //BioGRID, BioGRIDID, Numerical Value
                         Bait    PCR_bait  UNIQUE  ?PCR_product  XREF to? ?Species
                                 Sequence_bait  UNIQUE  ?Sequence  XREF to? ?Species 
                                 Bait_overlapping_CDS  ?CDS  XREF to? ?Species #Evidence 
                                 Bait_overlapping_gene  ?Gene XREF to? ?Species #Evidence
                                 Bait_DB_info ?Database ?Database_field UNIQUE ?Accession_number //BioGRID, BioGRIDID, Numerical Value 
                         Target  PCR_target UNIQUE  ?PCR_product  XREF to? ?Species
                                 Sequence_target  UNIQUE  ?Sequence  XREF to? ?Species 
                                 Target_overlapping_CDS  ?CDS  XREF to? ?Species  #Evidence
                                 Target_overlapping_gene  ?Gene  XREF to? ?Species  #Evidence
                                 Target_DB_info ?Database ?Database_field UNIQUE ?Accession_number //BioGRID, BioGRIDID, Numerical Value
             Experimental_System UNIQUE Affinity_capture-luminescence  //Experimental_system includes WormBase tags values as well as BioGRID values
                                        Affinity_capture-MS
                                        Affinity_capture-RNA
                                        Affinity_capture-Western
                                        Co-fractionation
                                        Co-localization
                                        Co-purification
                                        FRET
                                        PCA
                                        Two-hybrid
                                        Biochemical_activity
                                        Co-crystal_structure
                                        Far_western
                                        Protein_peptide 
                                        Protein_RNA 
                                        Reconstituted_complex
                                        Y1H  //BioGRID is not curating protein-DNA interactions.  WB has both Y1H data and GO MF data.
                                        Directed_Y1H  Text
                                        Protein_DNA 
              Throughput  UNIQUE  High_throughput //See BioGRID curation criteria for discussion:  http://www.yeastgenome.org/help/BiogridCuration.html
                                  Low_throughput 
              Library_info     Library_screened  UNIQUE  ?Library //This could also just be ?Text.  Doesn't look like ?Library class is used.
                               Origin From_laboratory  UNIQUE  ?Laboratory  //XREF by making a Reagents tag in the ?Laboratory model?
                                      From_company UNIQUE  ?Text //We don't currently have a ?Company class.  Should we?
              Confidence     ?Text //Not currently captured by BioGRID, but this tag can accommodate the legacy YH data.
              Paper     ?Paper XREF to ?               
              Remark    ?Text  #Evidence //How would remarks coming from BioGRID be attributed? Person_evidence? Curator_confirmed? Accession_evidence?  Person or Curator would require a change to the dumping file from BioGRID.

Physical Interaction Model v1.2

The revised v1 includes: 1) a ?Species tag, 2) a slot to capture Non-directional interactors (for curating things like protein complexes purified over sedimentation gradients, i.e. where there is no clear Bait or Target directionality), and 3) change ?Confidence from a specific list of phrases or statistical methods to a ?Text tag since this information is expressed in many different ways in the literature so including specific text here doesn't seem practical. If we change this to ?Text, then I'd also remove the specific Interactome_core tag.

Also, current XREF tags in the ?YH model are YH_bait and YH_target. What would be a more appropriate name? Model below has Interaction_target, etc. but I think that's not clear enough. What about Physical_interaction_target?

Also, CDS and Gene, when overlapping, have #Evidence, but the PCR and Sequence do not. Why is this? Does it have to do with needing to indicate how a CDS or Gene was selected without a corresponding sequence?


 ?Physical_interaction   Evidence #Evidence
              Species UNIQUE ?Species
              Interactor   Non_directional_interactor PCR_non_directional_interactor UNIQUE  ?PCR_product  XREF ? 
                                                      Sequence_non_directional_interactor  UNIQUE  ?Sequence  XREF  ?
                                                      Non_directional_interactor_overlapping_CDS  ?CDS  XREF  ?  #Evidence
                                                      Non_directional_interactor_overlapping_gene  ?Gene  XREF ? #Evidence
                           Bait    PCR_bait  UNIQUE  ?PCR_product  XREF  ?
                                   Sequence_bait  UNIQUE  ?Sequence  XREF  ?  
                                   Bait_overlapping_CDS  ?CDS  XREF  ?  #Evidence 
                                   Bait_overlapping_gene  ?Gene XREF  ? #Evidence 
                           Target  PCR_target UNIQUE  ?PCR_product  XREF ?
                                   Sequence_target  UNIQUE  ?Sequence  XREF ?
                                   Target_overlapping_CDS  ?CDS  XREF  ?  #Evidence
                                   Target_overlapping_gene  ?Gene  XREF  ?  #Evidence
              Experiment_type      Affinity_capture-luminescence
                                   Affinity_capture-MS
                                   Affinity_capture-RNA
                                   Affinity_capture-Western
                                   Co-fractionation
                                   Co-localization
                                   Co-purification
                                   FRET
                                   PCA
                                   Two-hybrid
                                   Biochemical_activity
                                   Co-crystal_structure
                                   Far_western
                                   Protein_peptide
                                   Protein_RNA
                                   Reconstituted_complex
                                   Y1H
                                   Directed_Y1H  Text
                                   Protein_DNA
              Throughput  UNIQUE  High_throughput //Need to define in context of physical interactions
                                  Low_throughput //Same as above
              Library_info     Library  UNIQUE  ?Library //This could also just be ?Text.  Doesn't look like ?Library class is used.
                               Origin From_laboratory  UNIQUE  ?Laboratory  //XREF by making a Reagents tag in the ?Laboratory model?
                                      From_company UNIQUE  ?Text //We don't currently have a ?Company class.  Should we?
              Confidence     ?Text //This can accommodate the great variety of language used to expressed this, if curated.           
              Paper     ?Paper XREF Interaction //Should this XREF also be updated to Physical_interaction?
              Remark    ?Text  #Evidence

Physical Interaction Model v1

This version of the model treats each instance of a physical interaction as a separate entity.

 ?Physical_interaction   Evidence #Evidence
              Interactor     Bait  PCR_bait  UNIQUE  ?PCR_product  XREF  Interaction_bait //Change XREF tag to Physical...
                                   Sequence_bait  UNIQUE  ?Sequence  XREF  Interaction_bait  
                                   Bait_overlapping_CDS  ?CDS  XREF  Interaction_bait  #Evidence 
                                   Bait_overlapping_gene  ?Gene XREF  Interaction_bait #Evidence 
                           Target  PCR_target UNIQUE  ?PCR_product  XREF Interaction_target //Change Target to Hit? Also change XREF as above?
                                   Sequence_target  UNIQUE  ?Sequence  XREF  Interaction_target
                                   Target_overlapping_CDS  ?CDS  XREF  Interaction_target  #Evidence
                                   Target_overlapping_gene  ?Gene  XREF  Interaction_target  #Evidence
              Experiment_type      Affinity_capture-luminescence
                                   Affinity_capture-MS
                                   Affinity_capture-RNA
                                   Affinity_capture-Western
                                   Co-fractionation
                                   Co-localization
                                   Co-purification
                                   FRET
                                   PCA
                                   Two-hybrid
                                   Biochemical_activity
                                   Co-crystal_structure
                                   Far_western
                                   Protein_peptide
                                   Protein_RNA
                                   Reconstituted_complex
                                   Y1H
                                   Directed_Y1H  Text
                                   Protein_DNA
              Throughput  UNIQUE  High_throughput //Need to define in context of physical interactions
                                  Low_throughput //Same as above
              Library_info     Library  UNIQUE  ?Library //This could also just be ?Text.  Doesn't look like ?Library class is used.
                               Origin Species UNIQUE  ?Species
                                      From_laboratory  UNIQUE  ?Laboratory  //XREF by making a Reagents tag in the ?Laboratory model?
                                      From_company UNIQUE  ?Text //We don't currently have a ?Company class.  Should we?
              Confidence     Confidence_level  UNIQUE  Float //Do we need this in the ?Physical_interaction model?
                             P_value  UNIQUE  Float  //Same as above.
                             Log_likelihood_score  UNIQUE  Float  //Same as above.
                             Interaction_frequency  UNIQUE  Int //This would hold the Int data in the existing Library_screened tag.
                             Interactome_type  UNIQUE  Interactome_core_1 //As defined in Li et al., 2004
                                                       Interactome_core_2
                                                       Interactome_core_3			           
              Paper     ?Paper XREF Interaction //Should this XREF also be updated to Physical_interaction?
              Remark    ?Text  #Evidence

Physical Interaction Model v2

This version of the model gives a single interaction ID to two interacting entities, but each instance, or evidence for the interaction, is added in the #Interaction_info under the corresponding Experiment_type.

 ?Physical_interaction   Evidence #Evidence
              Interactor     Bait  PCR_bait  UNIQUE  ?PCR_product  XREF  Interaction_bait //Change XREF tag to Physical...
                                   Sequence_bait  UNIQUE  ?Sequence  XREF  Interaction_bait  
                                   Bait_overlapping_CDS  ?CDS  XREF  Interaction_bait  #Evidence 
                                   Bait_overlapping_gene  ?Gene XREF  Interaction_bait #Evidence 
                           Target  PCR_target UNIQUE  ?PCR_product  XREF Interaction_target //Change Target to Hit? Also change XREF as above?
                                   Sequence_target  UNIQUE  ?Sequence  XREF  Interaction_target
                                   Target_overlapping_CDS  ?CDS  XREF  Interaction_target  #Evidence
                                   Target_overlapping_gene  ?Gene  XREF  Interaction_target  #Evidence
              Experiment_type      Affinity_capture-luminescence  #Interaction_info
                                   Affinity_capture-MS            #Interaction_info
                                   Affinity_capture-RNA           #Interaction_info
                                   Affinity_capture-Western       #Interaction_info
                                   Co-fractionation               #Interaction_info
                                   Co-localization                #Interaction_info
                                   Co-purification                #Interaction_info
                                   FRET                           #Interaction_info
                                   PCA                            #Interaction_info
                                   Two-hybrid                     #Interaction_info
                                   Biochemical_activity           #Interaction_info
                                   Co-crystal_structure           #Interaction_info
                                   Far_western                    #Interaction_info
                                   Protein_peptide                #Interaction_info
                                   Protein_RNA                    #Interaction_info
                                   Reconstituted_complex          #Interaction_info
                                   Y1H                            #Interaction_info
                                   Directed_Y1H  Text             #Interaction_info
                                   Protein_DNA                    #Interaction_info
              Remark ?Text #Evidence


 #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
                    Throughput  UNIQUE  High_throughput
                                        Low_throughput
                    Library_info  Library UNIQUE ?Library
                                  Origin  Species  UNIQUE  ?Species
                                          From_laboratory  UNIQUE  ?Laboratory
                                          From_company ?Text
                    Confidence    Confidence_level UNIQUE Float
                                  P_value UNIQUE Float
                                  Log_likelihood UNIQUE Float
                                  Interaction_frequency UNIQUE Int
                                  Interactome_type UNIQUE Interactome_core_1
                                                          Interactome_core_2
                                                          Interactome_noncore
                    Paper ?Paper XREF Interaction

Physical Interaction Model v3

This model keeps the physical interaction as part of the general ?Interaction model with the details again going into the #Interaction_info. The #Interaction_info would now contain the information about bait/hit directionality.

 ?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
              DB_info      Database ?Database ?Database_field ?Accession_number
              Remark      ?Text   #Evidence


 #Interaction_info  Interaction_RNAi ?RNAi XREF Interaction    
                    Effector ?Gene //master, upstream
                    Effected ?Gene //subject, downstream
                    Bait  PCR_bait  UNIQUE  ?PCR_product  XREF  Interaction_bait //Change XREF tag to Physical...
                          Sequence_bait  UNIQUE  ?Sequence  XREF  Interaction_bait  
                          Bait_overlapping_CDS  ?CDS  XREF  Interaction_bait  #Evidence 
                          Bait_overlapping_gene  ?Gene XREF  Interaction_bait #Evidence 
                    Target  PCR_target UNIQUE  ?PCR_product  XREF Interaction_target //Change Target to Hit? Also change XREF as above?
                            Sequence_target  UNIQUE  ?Sequence  XREF  Interaction_target
                            Target_overlapping_CDS  ?CDS  XREF  Interaction_target  #Evidence
                            Target_overlapping_gene  ?Gene  XREF  Interaction_target  #Evidence
                    Experiment_type      Affinity_capture-luminescence
                                         Affinity_capture-MS
                                         Affinity_capture-RNA
                                         Affinity_capture-Western
                                         Co-fractionation
                                         Co-localization
                                         Co-purification
                                         FRET
                                         PCA
                                         Two-hybrid
                                         Biochemical_activity
                                         Co-crystal_structure
                                         Far_western
                                         Protein_peptide
                                         Protein_RNA
                                         Reconstituted_complex
                                         Y1H
                                         Directed_Y1H  Text
                                         Protein_DNA
                    Throughput  UNIQUE  High_throughput 
                                        Low_throughput 
                    Library_info  Library  UNIQUE  ?Library //This could also just be ?Text.  Doesn't look like ?Library class is used.
                                  Origin Species UNIQUE  ?Species
                                         From_laboratory  UNIQUE  ?Laboratory  //XREF by making a Reagents tag in the ?Laboratory model?
                                         From_company UNIQUE  ?Text //We don't currently have a ?Company class.  Should we?
                    Confidence    Confidence_level  UNIQUE  Float  
                                  P_value  UNIQUE  Float   
                                  Log_likelihood_score  UNIQUE  Float   
                                  Interaction_frequency  UNIQUE  Int //This would hold the Int data in the existing Library_screened tag.
                                  Interactome_type  UNIQUE  Interactome_core_1 //As defined in Li et al., 2004
                                                       Interactome_core_2
                                                       Interactome_core_3			           
                    Paper     ?Paper XREF Interaction //Should this XREF also be updated to Physical_interaction?
                    Remark    ?Text  #Evidence


OA interface

Tab1.png

  • Tab 1
    • PGID Same in new OA
    • Interaction ID
      • A new interaction ID is generated by clicking on 'new'. when 'duplicate', the ID from old entry will be in the field, but need to be deleted in order to get an new ID.
      • Interaction ID will be assigned by cronjob daily at 4 am. This is for curators who would like to use 'Duplicate' to generate new objects with similar field entries and erase the Interaction IDs to let the cron job add new IDs overnight. The cronjob is at /home/acedb/xiaodong/assigning_interaction_ids/assign_interaction_ids.pl and we need to change it based on the new table structure -- J
      • interaction field autocompletes now key off of the int_index table used by the interaction_ticket.cgi, it no longer keys off of the int_name table from this field in the interaction OA, which makes the rest of this line obsolete. (OBSOLETE If you mistakenly make a typo and assign a correct ID's value to some other ID, you will _not_ be able to bring it back (because it's an ontology) without going to postgres directly and editing the int_name and int_name_hst tables by pgid (in postgres called joinkey). You'll have to note the pgid and then manually change it in postgres. end obsolete)
    • Non_directional In new OA, there will be a separate field for each interactor type: Gene, Sequence, CDS, PCR_Product, or Protein. Since "old" interaction objects only contain genes, any genes that are part of Interaction obejcts in which the Non_directional toggle was activated will need to move to the "Non-directional Gene(s)" field. if toggle is on, move all effector + effected genes to the new non-directional gene field. get rid of this field in new OA
      • toggle OFF (default), means interaction is directional. there is effected/effector parties involve in the object.
      • toggle ON (color change to red by click) means interaction is non_directional
    • Interaction Type//dropdown list with 11 types showing in .ace template
      • In the new OA, these 11 types will be mapped as follows:
      • "Genetic" will become "Genetic - Genetic Interaction"
      • "Regulatory" will remain "Regulatory"
      • "No_interaction" will become "Genetic - No_interaction"
      • "Predicted_interaction" will become "Predicted"
      • "Physical_interaction" will become "Physical"
      • "Suppression" will become "Genetic - Suppression"
      • "Enhancement" will become "Genetic - Enhancement"
      • "Synthetic" will become "Genetic - Synthetic"
      • "Epistasis" will become "Genetic - Epistasis"
      • "Mutual_enhancement" will become "Genetic - Mutual_enhancement"
      • "Mutual_suppression" will become "Genetic - Mutual_suppression"
    • Effected Gene //autocomplete WBGene, multiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors
      • In new OA, this field will be called "Affected Gene(s)" -- C If non-directional is on, move to non-directional gene, otherwise leave here
    • Effected Variation //WBGene, WBVar, multiontology, autocomplete on Variation, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar"
      • In new OA, this field will be called "Affected Variation(s)"; the dumping script will attempt to map these variations to their respetive genes and place the variation in that gene's interactor_info hash -- C
      • In new OA, the gene(s) affiliated with this variation will become the "Affected Gene(s)" for this interaction.
    • Effected Transgene_Name //ontology, autocomplete transgene object name, eg iaIs3.
      • In new OA, all transgenes will go into the Transgene(s) field. merge both effector + effected.
    • Effected Transgene_Gene // multi-ontology, autocomplete WBGene->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id. One wbgene for each .ace line ? Make sure you really want it this way, we can go with product/promoter if that's what you want, just make sure it's what you want. It matters having extra fields and scrolling and so forth. You'll see when the text fields become multi-ontology and ontology.
      • In new OA, all transgenes will automatically be mapped to their associated genes based on all genes in the transgene OA's gene + driven_by_gene field. remove this field.
      • In new OA, genes from the "Effected Transgene Gene" field will move to the "Affected Gene" field.
    • Effected Other Type //dropdown list of 'Chemicals' and 'Transgene'
      • In new OA, these will be named "Affected Other Type" and dump as remark.
    • Effected Other //free text field now, however, when entering chemicals make sure to enter common names followed by mesh IDs in parenthesis for later ontologinization.
      • In new OA, these will be named "Affected Other" and dump as remark.
    • Effector Gene //autocomplete WBGene, multiontology. corresponding to interactor in .ace file. order does not matter when dump to interactors
      • In new OA, these genes will all go in the "Effector Gene(s)" field. If non-directional is on, move to non-directional gene, otherwise leave here
    • Effector Variation //WBGene, WBVar, autocomplete multiontology on variation, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar". use name server to map variation to gene, or the file Karen gave you to map variation to gene for variation OA.
      • In new OA, this field will be the same; the dumping script will attempt to map these variations to their respetive genes and place the variation in that gene's interactor_info hash -- C
      • In new OA, the gene(s) affiliated with this variation will become the "Effector Gene(s)" for this interaction.
    • Effector Transgene_Name //autocomplete name, ontology
      • In new OA, all transgenes will go into the Transgene(s) field. merge both effector + effected.
    • Effector Transgene_Gene // autocomplete WBGene, multi-ontology, ->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id.
      • In new OA, all transgenes will automatically be mapped to their associated genes based on all genes in the transgene OA's gene + driven_by_gene field. remove this field.
      • In new OA, genes from the "Effector Transgene Gene" field will move to the "Effector Gene" field.
    • Effector Other Type //dropdown list of 'Chemicals' and 'Transgene'
      • In new OA, these will stay the same and dump as Remark
    • Effector Other //free text field
      • two fields above will be dumped in remark field.
      • In new OA, these will stay the same and dump as Remark

Note: Gene, Variation, and Transgene_Gene all refer to different genes. There is no pairing problem.


Tab2.png

  • Tab 2
    • Curator//dropdown list Same in new OA
    • Paper//ontology Same in new OA
    • RNAi ID//free text field In new OA, this RNAi object will fill the "RNAi" field if it is not from WBPaper00029258 (hence large scale); if it is from WBPaper00029258, this will go in the "Large scale RNAi" field as free text
    • Phenotype//multiontology In new OA, this Phenotype object will fill the "Interaction phenotype" field. keep OA field the same, change dumper.
    • Remark//big text Same in new OA
    • Sentence ID//sentence shows in term info Same in new OA
    • False Positive//toggle, will not give an id or no dump if the sentence is false positive, containing no interaction info Same in new OA


Old Table Names


'Non_directional' = int_nondirectional

'Effector Transgene Name' = int_transgeneone

'Effector Transgene Gene' = int_transgeneonegene

'Affected Transgene Name' = int_transgenetwo

'Affected Transgene Gene' = int_transgenetwogene

'Deviation from expectation' = int_deviation

'Neutrality function' = int_neutralityfxn

'Intragenic Effector Variation(s)' = int_intravariationone

'Intragenic Affected Variation(s)' = int_intravariationtwo

'Effector Other Type' = int_otheronetype

'Affected Other Type' = int_othertwotype

Removed OA fields

  • As of 2-19-2015

TAB3

  • Intragenic Effector Variation(s) - ?Variation (MultiOntology) int_intravariationone
    • Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
    • Dumps as: Interactor_overlapping_gene <Mapped Gene> Intragenic_effector_variation <Variation>
    • For Variations that don't map to a gene in the interaction, Dump as: Unaffiliated_variation <Variation>
  • Intragenic Affected Variation(s) - ?Variation (MultiOntology) int_intravariationtwo
    • Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
    • Dumps as: Interactor_overlapping_gene <Mapped Gene> Intragenic_affected_variation <Variation>
    • For Variations that don't map to a gene in the interaction, Dump as: Unaffiliated_variation <Variation>


TAB4

  • Deviation from expectation - Big text int_deviation Dumps as: Deviation_from_expectation <Big_Text>
  • Neutrality function - (Dropdown) int_neutralityfxn options are:
    • Multiplicative Dumps as: Multiplicative
    • Additive Dumps as: Additive
    • Minimal Dumps as: Minimal
  • Effector Other Type - (Dropdown) int_otheronetype options are: Chemical or Transgene, int_otheronetype Dumps as (see next line)
  • Affected Other Type - (Dropdown) int_othertwotype options are: Chemical or Transgene, int_othertwotype Dumps as (see next line)

How to use:

Deviation from expectation is a free-text field where, at the curator's discretion, a curator can describe why a genetic interaction is an interaction, i.e. why it is an unexpected result warranting an interaction. This could be as simple as "The life spans were synergistic" or "Neither mutation alone exhibited a phenotype".

Neutrality function is closely related to the "Deviation from expectation" field, where the curator can decide, if applicable, which "Neutrality function" applies to this genetic interaction. The choices in this drop down field are "Multiplicative", "Additive", and "Minimal". "Multiplicative" means that the authors expected to see a quantifiable phenotype in the double mutant that was the mathematical product of the quantified phenotypes of the individual mutations. For example, one mutant extends life span by 20%, and another extends it by 30%. With a multiplicative neutrality function, we would expect the double mutant to have (1.2 * 1.3 = 1.56) about 56% extended life span. Alternatively, in the "Additive" neutrality function, the authors might expect the sum of the effects (A + B - 1) or (1.2 + 1.3 - 1 = 1.5) or a 50% extended life span. The "Minimal" neutrality function assumes that the double mutant will be as severe as the most severe single mutant, in this case (1.3) or 30% extended. Therefore, any life span extension beyond 30%, for example, in the double mutant would be considered "surprising" and therefore, an interaction.


Effector/Affected Other Type and Effector/Affected Other fields: these fields allow for the curation of Chemicals, Transgenes, or other entities that don't exists as proper WormBase/ACEDB objects, for example transgenes that only express human proteins. The "Other Type" fields allow for the selection of "Chemical" or "Transgene", the identity of which would go into the "Other" fields. This, ideally, will get phased out as chemicals are generated in the Molecule OA and transgenes in the Transgene OA, thereby allowing them to be entered into ontology-based "Transgene" or "Molecule" fields.

.ace template: (OUTDATED)


  • 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 ""


interaction objects source file

  • there are 9242 interaction objects dumped from WS220 on Monday, 10/01/2010
  • Juancarlos's parse results from this file:

/home/postgres/work/pgpopulation/interaction/20101004_xiaodong_start/out

There are two interactions in postgres, but not the .ace file : In postgres, no ace WBInteraction0008637 In postgres, no ace WBInteraction0008638//will be OA

There are 1290 interactions in .ace file not in postgres (so I imagine these are what we should read in ?)//these are RNAi based interaction objects, we want to include them in OA

There are >40000 interactions that have a ticket and are in neither .ace nor postgres.//these 398,619 interactions are from two large scale papers

Also there are interaction data in postgres without an interaction ID//will be assigned id from WBInteraction0500001.

Some Notes for gene_gene_interaction

Outdated notes on large scale interaction files

  • ready_to_upload large scale data file: Large_scale_interactions_WS231.ace is located on tazendra: /home/acedb/xiaodong/oa_interactions_dumper should be uploaded for every upload
  • large scale .ace file needs to be checkd again dead genes for each upload using scripts in the same directory: find_invalid_genes_largescale.pl* - 08/31/2012 for upload WS234
    • before run, change source file (in file) to latest large scale .ace version (in scripts)
    • dead/merged genes will appear on screen. replace merged genes, leave dead/dead genes for now
    • change large scale.ace file name to latest upload version
    • then upload


Citace upload notes

  • 2011.1.27
    • caught-up at acedb reading: WBInteraction0500069 (Karen), new line in remark field. fixed in .ace file.
    • some confusion on ids. found out ticket issuer was using sandbox data. fixed.
  • 2011.5.4
    • Karen needed to update variation_wbgene file on tazendra: /home/acedb/jolene/WS_AQL_queries/Variation_gene.txt
    • Juancarlos changed the dumper to ignore line breaks and double spaces in remark field for dumping ace file