Difference between revisions of "Gene Interaction/archive"

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(Created page with "=Interaction Curation= ==Pipeline== ===semi-automatic curation with textpresso extracted sentences=== *There are 2138 sentences (actually 2133 sentences) in the sourcefile...")
 
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**To run :  ./parse_ace_interaction_oa.pl gary_RNAi.ace WBPerson1823  
 
**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.
 
** where gary_RNAi.ace is the <inputfile>,the first argument, and WBPerson# is the second argument.
 +
 +
 +
 +
===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====
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 +
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

Revision as of 23:09, 18 September 2014

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

?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
Retrieved from "https://wiki.wormbase.org/index.php?title=Gene_Interaction/archive&oldid=24871"