Difference between revisions of "Gene Interaction"

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***'''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'''
 
***'''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"
 
**Effected Variation      //WBGene, WBVar, multiontology, autocomplete on Variation, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar"
***'''In new OA, all variations will go into the Variation(s) field'''
+
***'''In new OA, all variations will go into the Variation(s) field.  merge both effector + effected.'''
 
**Effected Transgene_Name  //ontology, autocomplete  transgene object name, eg iaIs3.
 
**Effected Transgene_Name  //ontology, autocomplete  transgene object name, eg iaIs3.
***'''In new OA, all transgenes will go into the Transgene(s) field'''
+
***'''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.   
 
**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'''
 
***'''In new OA, all transgenes will automatically be mapped to their associated genes'''
Line 559: Line 559:
 
***'''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'''
 
***'''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.
 
**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, all variations will go into the Variation(s) field'''
+
***'''In new OA, all variations will go into the Variation(s) field.  merge both effector + effected.'''
 
**Effector Transgene_Name  //autocomplete name, ontology  
 
**Effector Transgene_Name  //autocomplete name, ontology  
***'''In new OA, all transgenes will go into the Transgene(s) field'''
+
***'''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.
 
**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'''
 
***'''In new OA, all transgenes will automatically be mapped to their associated genes'''

Revision as of 22:20, 5 April 2012

'links to relevant pages
Caltech documentation
Interaction
OA link


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.

dump .ace file from OA for upload

  • on tazendra: /home/acedb/xiaodong/oa_interactions_dumper
  • run script by calling: ./use_package.pl
  • error file will be spitted out in the same directory after every run. inform curators to check the errors.

Interaction Models

Current Models

The current ?Interaction model now consolidates ?Gene_regulation objects, ?YH objects, and ?Interaction objects into a single class, ?Interaction. The proposed ?Physical_interaction model has also been consolidated into this larger model. Note that #Interaction_info and #Interaction_type have been deprecated.


?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



#Interactor_info       Interactor_type Non_directional		   // An interactor that has no inherent directionality
				       Bait			   // The interactor of interest or focus; the focus/starting point of an interaction screen
				       Target			   // The discovered interactor; interactors found as a result of an interaction screen
				       Effector			   // In a genetic interaction, the perturbation that affects the phenotype of the other perturbation
				       Affected			   // In a genetic interaction, the perturbation whose phenotype is affected by the other perturbation
				       Trans_regulator		   // A trans-acting regulator, e.g. a transcription factor
				       Cis_regulator		   // A cis-acting regulator, e.g. an enhancer element
				       Trans_regulated		   // A gene regulated in trans, e.g. by a transcription factor
				       Cis_regulated		   // A gene regulated in cis, e.g. by an enhancer element
		       Expr_pattern ?Expr_pattern		   // An expression pattern altered to indicate 
		       Variation ?Variation XREF Interactor	   // (allele, polymorphism, etc.) involved in the interaction //removed XREF from proposal
		       Transgene ?Transgene XREF Interactor	   // Transgene XREF Interactor that carries an interacting gene //removed XREF from proposal
		       Antibody ?Text				   // Antibody used to detect a regulation event
		       Antibody_info ?Antibody XREF Interactor	   // Free text description of the antibody used to detect a regulation event //removed XREF from proposal
		       Remark ?Text #Evidence			   // Info about reagents that the model can't capture (e.g. co_suppression, RNA_reagent, etc.)


In the adoption of this new ?Interaction model in WS231, we have consolidated the ?YH and ?Gene_regulation class into the ?Interaction class. As of WS231, there were 3831 ?Gene_regulation objects, which were then converted to ?Interaction objects with IDs WBInteraction000501384 through WBInteraction000505214. As of WS231, there were 11,993 ?YH objects, which were then converted to ?Interaction objects with IDs WBInteraction000505215 through WBInteraction000517207.

Old Models

?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
///////////////////////////////////////////////////////////////////////////////////

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

Gene_gene Interaction OA

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.
      • 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, all variations will go into the Variation(s) field. merge both effector + effected.
    • 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
    • Effected Other Type //dropdown list of 'Chemicals' and 'Transgene'
      • In new OA, these will be moved to the 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.
      • two fields above will be dumped in remark field.
      • In new OA, these will be moved to the 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, all variations will go into the Variation(s) field. merge both effector + effected.
    • 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
    • Effector Other Type //dropdown list of 'Chemicals' and 'Transgene'
      • In new OA, these will be moved to the Remark
    • Effector Other //free text field
      • two fields above will be dumped in remark field.
      • In new OA, these will be moved to the 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 fiel In new OA, this RNAi object will fill the "Interaction RNAi" field
    • Phenotype//multiontology In new OA, this Phenotype object will fill the "Interaction phenotype" field
    • 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

.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 ""


interaction objects source file

File:Example.jpg

  • 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

  • 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)
  • directories on tazendra related to gene_gene_interaction (home/acedb/xiaodong)
    • assigning_interaction_ids
    • textpresso_ggi
    • interaction_ace_parsing
    • oa_interactions_dumper
  • 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


The new Interaction OA, March 2012

  • Tab1
    • PGID
    • Interaction ID
    • Curator - Curator
    • Process - ?WBProcess (MultiOntology)
    • Database - ?Database ?Database_field ?Accession_number
    • Paper - ?Paper
    • Interaction Type - Text (Multiple-Dropdown)
      • The options for Interaction Type will include:
        • Physical
        • Predicted
        • Genetic - Genetic interaction
        • Genetic - Negative genetic
        • Genetic - Synthetic
        • Genetic - Enhancement
        • Genetic - Unilateral enhancement
        • Genetic - Mutual enhancement
        • Genetic - Suppression
        • Genetic - Unilateral suppression
        • Genetic - Mutual suppression
        • Genetic - Asynthetic
        • Genetic - Suppression/Enhancement
        • Genetic - Epistasis
        • Genetic - Maximal epistasis
        • Genetic - Minimal epistasis
        • Genetic - Suppression/Epistasis
        • Genetic - Agonistic epistasis
        • Genetic - Antagonistic epistasis
        • Genetic - Oversuppression
        • Genetic - Unilateral oversuppression
        • Genetic - Mutual oversuppression
        • Genetic - Complex oversuppression
        • Genetic - Oversuppression/Enhancement
        • Genetic - Phenotype bias
        • Genetic - Biased suppression
        • Genetic - Biased enhancement
        • Genetic - Complex phenotype bias
        • Genetic - No interaction
    • Interaction Summary - Big Text
    • Remark - Big text


  • Tab2
    • Physical interaction detection method (Multi-dropdown)
      • The detection method options are:
        • Affinity capture luminescence
        • Affinity capture MS
        • Affinity capture RNA
        • Affinity capture Western
        • Biochemical activity
        • Cocrystal structure
        • Cofractionation
        • Colocalization
        • Copurification
        • Far western
        • Fluorescence resonance energy transfer
        • Protein fragment complementation assay
        • Protein peptide
        • Protein RNA
        • Reconstituted complex
        • Yeast two hybrid
        • Chromatin IP
        • Yeast one hybrid
        • Directed yeast one hybrid
    • Library screened - Text Text (First text then an integer)
    • From Laboratory - ?Laboratory (ontology)
    • From Company - Text
    • PCR Bait - ?PCR_product (Ontology)
    • PCR Target(s) - ?PCR_product (MultiOntology)
    • Non-directional PCR(s) - ?PCR_product (MultiOntology)
    • Sequence Bait - ?Sequence (Ontology)
    • Sequence Target(s) - ?Sequence (MultiOntology)
    • Non-directional Sequence(s) - ?Sequence (MultiOntology)
    • Bait overlapping CDS - ?CDS (Ontology)
    • Target overlapping CDS(s) - ?CDS (MultiOntology)
    • Non-directional overlapping CDS(s) - ?CDS (MultiOntology)
    • Bait overlapping protein - ?Protein (Ontology)
    • Target overlapping protein(s) - ?Protein (MultiOntology)
    • Non-directional overlapping protein(s) - ?Protein (MultiOntology)
    • Bait overlapping gene - ?Gene (Ontology)
    • Target overlapping gene(s) - ?Gene (MultiOntology)
    • Antibody - ?Antibody (MultiOntology)
    • Antibody remark - Big Text


  • Tab3
    • Non-directional Gene(s) - ?Gene (MultiOntology)
    • Effector Gene(s) - ?Gene (MultiOntology)
    • Affected Gene(s) - ?Gene (MultiOntology)
    • Deviation from expectation - Big text
    • Neutrality function - (Dropdown) options are: Multiplicative, Additive, Minimal
    • Interaction RNAi - ?RNAi (Ontology)
    • Interaction phenotype(s) - ?Phenotype (MultiOntology)
    • Expression pattern(s) - ?Expr_pattern (MultiOntology)
    • Variation(s) - ?Variation (MultiOntology)
    • Transgene(s) - ?Transgene (MultiOntology)


  • Tab4
    • Confidence description - Text
    • P-value - Text (Float)
    • Log-likelihood score - Text (Float)
    • Throughput - (Dropdown) options are: High throughput, Low throughput
    • 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