Difference between revisions of "Gene Interaction"

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'links to relevant pages''<br>
 
'links to relevant pages''<br>
 
[[Caltech documentation]] <br>
 
[[Caltech documentation]] <br>
 +
 +
Archived Interaction documentation may be found [[Gene_Interaction/archive | here]]
  
 
[https://bitbucket.org/xdwang/ggi_oa/wiki/Home  OA link]<br>
 
[https://bitbucket.org/xdwang/ggi_oa/wiki/Home  OA link]<br>
Line 8: Line 10:
 
==Pipeline==
 
==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**
 
−
# cd to directory on tazendra: /home/acedb/xiaodong/textpresso_ggi
 
−
# mkdir directionay_name (eg 20110106)
 
−
# cd directory_name (eg 20110106)
 
−
# get Arun's result file (35225-35725.txt in the directory)
 
−
# 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)
 
−
# 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===
 
===dump .ace file from OA for upload===
Line 50: Line 24:
 
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.
 
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.
  
 +
Updated for WS261 - '''CG 7-21-2017'''
  
 
<pre>
 
<pre>
−
?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  ?PCR_product #Interactor_info // PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments
 
−
Sequence_interactor  ?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
 
−
Rearrangement    ?Rearrangement    XREF  Interactor  #Interactor_info   // Rearrangement 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
+
?Interaction Interaction_type Physical UNIQUE ProteinProtein
−
Origin From_laboratory UNIQUE ?Laboratory // A library generated at an academic laboratory
+
                                              ProteinDNA
−
From_company UNIQUE ?Text // A library generated at a company
+
                                              ProteinRNA
−
 
+
                              Predicted
−
//Genetic interaction-specific tags
+
                              Regulatory Change_of_localization
−
 
+
                                        Change_of_expression_level
−
Deviation_from_expectation Text // A text description of the way in which the phenotype deviated from expectation in genetic interactions
+
                              Genetic Genetic_interaction
−
+
                                      Neutral_genetic
−
Neutrality_function UNIQUE Multiplicative // The multiplicative neutrality function defines expectation as the product of two quantified phenotypes (relative to wild type)
+
                                      Synthetic
−
Additive // The additive neutrality function defines expectation as the sum of two quantified phenotypes (relative to wild type)
+
                                      Enhancement
−
Minimal // The minimal neutrality function defines expectation as the most severe of two quantified phenotypes (relative to wild type)
+
                                      Unilateral_enhancement
−
 
+
                                      Mutual_enhancement
−
//Gene regulation-specific tags
+
                                      Positive_genetic
−
 
+
                                      Suppression
−
Regulation_level Transcriptional // Regulation occurs at the transcriptional level
+
                                      Complete_suppression
−
Post_transcriptional // Regulation occurs at the post-transcriptional level
+
                                      Partial_suppression
−
Post_translational // Regulation occurs at the post-translational level
+
                                      Unilateral_suppression
−
 
+
                                      Complete_unilateral_suppression
−
Interaction_associated_feature ?Feature XREF Associated_with_gene_regulation #Evidence //to curate sequence feature connection [ar2]
+
                                      Partial_unilateral_suppression
−
 
+
                                      Mutual_suppression
−
Regulation_result Positive_regulate #GR_condition
+
                                      Complete_mutual_suppression
−
Negative_regulate #GR_condition
+
                                      Partial_mutual_suppression
−
Does_not_regulate #GR_condition // added to capture negative data [040220 krb]
+
                                      Suppression_enhancement
−
 
+
                                      Asynthetic
−
//General tags
+
                                      Negative_genetic
−
 
+
                                      Oversuppression
−
Confidence Description Text // Free text description of the confidence, e.g. "Core" vs "Noncore" (Vidal Interactome terms)
+
                                      Unilateral_oversuppression
−
P_value   UNIQUE Float // P-value confidence of interaction, if given
+
                                      Mutual_oversuppression
−
Log_likelihood_score   UNIQUE Float // Only used for Predicted interactions
+
                                      Oversuppression_enhancement
−
 
+
                                      Phenotype_bias
−
 
+
                                      No_interaction // Negative data; no interaction was observed after testing
−
Throughput UNIQUE High_throughput //See BioGRID curation criteria for discussion:  http://www.yeastgenome.org/help/BiogridCuration.html
+
                                      Epistasis
−
Low_throughput
+
                                      Positive_epistasis
−
Interaction_RNAi ?RNAi XREF Interaction // RNAi experiment associated with the interaction
+
                                      Maximal_epistasis
−
Interaction_phenotype ?Phenotype XREF Interaction // Phenotype associated with a genetic interaction
+
                                      Minimal_epistasis
−
Unaffiliated_variation   ?Variation   // As opposed to Variations affiliated directly with an interacting gene, these are unaffiliated variations that somehow play a role in the interaction
+
                                      Neutral_epistasis
−
Unaffiliated_transgene   ?Transgene   // As opposed to Transgenes affiliated directly with an interacting gene, these are unaffiliated Transgenes that somehow play a role in the interaction
+
                                      Qualitative_epistasis
−
Unaffiliated_antibody   ?Antibody   // As opposed to Antibodies affiliated directly with an interacting gene, these are unaffiliated Antibodies that somehow play a role in the interaction
+
                                      Opposing_epistasis
−
Unaffiliated_expr_pattern   ?Expr_pattern   // As opposed to Expression Patterns affiliated directly with an interacting gene, these are unaffiliated Expression Patterns that somehow play a role in the interaction
+
                                      Quantitative_epistasis
−
                Antibody_remark    ?Text      // Free text description of the antibody used to detect a regulation event //removed XREF from proposal
+
                              GI_module_one A_phenotypic
−
WBProcess ?WBProcess XREF Interaction // WormBase biological process associated with the interaction
+
                                            Mono_phenotypic
−
DB_info Database ?Database ?Database_field ?Accession_number // Any database reference to the interaction outside of WormBase, e.g. BioGRID, Interactome
+
                                            Cis_phenotypic
−
Paper ?Paper XREF Interaction
+
                                            Iso_phenotypic
−
Remark ?Text #Evidence
+
                                            Trans_phenotypic
 +
                              GI_module_two Enhancing
 +
                                            Suppressing
 +
                                            All_suppressing
 +
                                            Super_suppressing
 +
                                            Sub_suppressing
 +
                                            Inter_suppressing
 +
                                            Semi_suppressing
 +
                                            Co_suppressing
 +
                                            Masking
 +
                              GI_module_three Neutral
 +
                                              Non_neutral
 +
                                              Positive
 +
                                              Negative
 +
                                              Converging
 +
                                              Diverging
 +
            Interactor PCR_interactor ?PCR_product XREF Interaction #Interactor_info      // PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments
 +
                        Sequence_interactor ?Sequence XREF Interaction #Interactor_info    // Sequence of the interacting gene or protein
 +
                        Interactor_overlapping_CDS ?CDS XREF Interaction #Interactor_info  // CDS of the interacting gene or protein (or related sequence)
 +
                        Interactor_overlapping_gene ?Gene XREF Interaction #Interactor_info // Gene (or portion of gene) involved in the interaction
 +
                        Interactor_overlapping_protein ?Protein XREF Interaction #Interactor_info    // Protein (or portion of protein) involved in the interaction
 +
                        Molecule_interactor ?Molecule XREF Interaction #Interactor_info    // Molecule that regulates a gene or protein (ported from Gene_regulation Class) Modified Chris WS244
 +
                        Other_interactor  ?Text #Interactor_info
 +
                        Rearrangement ?Rearrangement XREF Interactor #Interactor_info
 +
                        Feature_interactor ?Feature XREF Associated_with_Interaction #Interactor_info
 +
                        Variation_interactor ?Variation XREF Interactor #Interactor_info
 +
            Interaction_summary ?Text #Evidence
 +
            Detection_method Affinity_capture_luminescence // A physical interaction detection technique
 +
                              Affinity_capture_MS          // A physical interaction detection technique
 +
                              Affinity_capture_RNA          // A physical interaction detection technique
 +
                              Affinity_capture_Western      // A physical interaction detection technique
 +
                              Chromatin_immunoprecipitation // Chris WS244
 +
                              Cofractionation              // A physical interaction detection technique
 +
                              Colocalization                // A physical interaction detection technique
 +
                              Construct
 +
                              Copurification                // A physical interaction detection technique
 +
                              DNase_I_footprinting          //
 +
                              Fluorescence_resonance_energy_transfer  // A physical interaction detection technique
 +
                              Protein_fragment_complementation_assay  // A physical interaction detection technique
 +
                              Yeast_two_hybrid                        // A physical interaction detection technique (Protein-protein)
 +
                              Biochemical_activity                    // A physical interaction detection technique
 +
                              Cocrystal_structure                    // A physical interaction detection technique
 +
                              Far_western                            // A physical interaction detection technique
 +
                              Protein_peptide                        // A physical interaction detection technique
 +
                              Protein_RNA                            // A physical interaction detection technique
 +
                              Reconstituted_complex                  // A physical interaction detection technique
 +
                              Electrophoretic_mobility_shift_assay    // A physical interaction detection technique
 +
                              Yeast_one_hybrid                        // A physical interaction detection technique (Protein-DNA)
 +
                              Directed_yeast_one_hybrid              // A physical interaction detection technique (Protein-DNA)
 +
                              Antibody                                // A regulatory interaction detection technique; Antibody name and details captured in Interactor_info hash
 +
                              Reporter_gene ?Text                    // A regulatory interaction detection technique
 +
                              Transgene                              // A regulatory interaction detection technique; Trasnsgene name and details captured in Interactor_info hash
 +
                              In_situ Text                            // A regulatory interaction detection technique
 +
                              Northern Text                          // A regulatory interaction detection technique
 +
                              Western Text                            // A regulatory interaction detection technique
 +
                              RT_PCR Text                            // A regulatory interaction detection technique
 +
                              Other_method ?Text                      // A regulatory interaction detection technique
 +
            Library_info Library_screened Text INT                   // In the context of Y2H or YH screens, for example, the library may have been cDNA library or a pool of clones
 +
                          Origin From_laboratory UNIQUE ?Laboratory   // A library generated at an academic laboratory
 +
                                From_company UNIQUE ?Text           // A library generated at a company
 +
            Regulation_level Transcriptional                         // Regulation occurs at the transcriptional level
 +
                              Post_transcriptional                   // Regulation occurs at the post-transcriptional level
 +
                              Post_translational                     // Regulation occurs at the post-translational level
 +
            Regulation_result Positive_regulate #GR_condition
 +
                              Negative_regulate #GR_condition
 +
                              Does_not_regulate #GR_condition       // added to capture negative data [040220 krb]
 +
            Confidence Description Text                             // Free text description of the confidence, e.g. "Core" vs "Noncore" (Vidal Interactome terms)
 +
                        P_value UNIQUE Float                         // P-value confidence of interaction, if given
 +
                        Log_likelihood_score UNIQUE Float             // Only used for Predicted interactions
 +
            Throughput UNIQUE High_throughput                       // See BioGRID curation criteria for discussion
 +
                              Low_throughput
 +
            Interaction_RNAi ?RNAi XREF Interaction                 // RNAi experiment associated with the interaction
 +
            Interaction_phenotype ?Phenotype XREF Interaction       // Phenotype associated with a genetic interaction
 +
            Unaffiliated_variation ?Variation
 +
            Unaffiliated_transgene ?Transgene
 +
            Unaffiliated_antibody ?Antibody
 +
            Unaffiliated_expr_pattern ?Expr_pattern
 +
            Unaffiliated_construct ?Construct
 +
            WBProcess ?WBProcess XREF Interaction                   // WormBase biological process associated with the interaction
 +
            DB_info Database ?Database ?Database_field ?Text        // Any database reference to the interaction outside of WormBase, e.g. BioGRID, Interactome
 +
            Paper ?Paper XREF Interaction
 +
            Antibody_remark ?Text
 +
            Historical_gene ?Gene Text
 +
Remark ?Text #Evidence
  
 
</pre>
 
</pre>
−
 
  
  
Line 186: Line 171:
 
      Cis_regulated   // A gene regulated in cis, e.g. by an enhancer element
 
      Cis_regulated   // A gene regulated in cis, e.g. by an enhancer element
 
      Expr_pattern ?Expr_pattern   // An expression pattern altered to indicate  
 
      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
 
−
      Intragenic_effector_variation  ?Variation  XREF  Interactor // An effector variation that interacts with another variation from the same gene
 
−
      Intragenic_affected_variation  ?Variation  XREF  Interactor // An affected variation that interacts with another variation from the same gene
 
 
      Transgene ?Transgene XREF Interactor   // Transgene XREF Interactor that carries an interacting gene //removed XREF from proposal
 
      Transgene ?Transgene XREF Interactor   // Transgene XREF Interactor that carries an interacting gene //removed XREF from proposal
−
      Antibody ?Antibody XREF Interactor   // Antibody used to detect a regulation event
+
      Construct ?Construct XREF Interactor
−
      Remark ?Text #Evidence   // Info about reagents that the model can't capture (e.g. co_suppression, RNA_reagent, etc.)
+
      Antibody ?Antibody XREF Interactor   // Free text description of the antibody used to detect a regulation event //removed XREF from proposal
 +
      Inferred_automatically Text                 // a script has updated this connection
  
 
</pre>
 
</pre>
Line 197: Line 180:
  
 
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.
 
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''' ==
 
== '''Gene_gene Interaction OA''' ==
−
 
−
==='''OA interface'''===
 
−
 
−
[[File:tab1.png]]
 
−
 
−
* Tab 1
 
−
**PGID  '''Same in new OA'''
 
−
**Interaction ID
 
−
***A new interaction ID is generated by clicking on 'new'. when 'duplicate', the ID from old entry will be in the field, but need to be deleted in order to get an new ID.
 
−
*** Interaction ID will be assigned by cronjob daily at 4 am. This is for curators who would like to use 'Duplicate' to generate new objects with similar field entries and erase the Interaction IDs to let the cron job add new IDs overnight.  The cronjob is at /home/acedb/xiaodong/assigning_interaction_ids/assign_interaction_ids.pl and '''we need to change it based on the new table structure -- J'''
 
−
*** interaction field autocompletes now key off of the int_index table used by the interaction_ticket.cgi, it no longer keys off of the int_name table from this field in the interaction OA, which makes the rest of this line obsolete.  (OBSOLETE If you mistakenly make a typo and assign a correct ID's value to some other ID, you will _not_ be able to bring it back (because it's an ontology) without going to postgres directly and editing the int_name and int_name_hst tables by pgid (in postgres called joinkey).  You'll have to note the pgid and then manually change it in postgres. end obsolete)
 
−
**Non_directional  In new OA, there will be a separate field for each interactor type: Gene, Sequence, CDS, PCR_Product, or Protein. Since "old" interaction objects only contain genes, any genes that are part of Interaction obejcts in which the Non_directional toggle was activated will need to move to the "Non-directional Gene(s)" field. '''if toggle is on, move all effector + effected genes to the new non-directional gene field.  get rid of this field in new OA'''
 
−
***toggle OFF (default), means interaction is directional. there is effected/effector parties involve in the object.
 
−
***toggle ON (color change to red by click) means interaction is non_directional
 
−
**Interaction Type//dropdown list with 11 types showing in .ace template
 
−
***'''In the new OA, these 11 types will be mapped as follows:'''
 
−
***'''"Genetic" will become "Genetic - Genetic Interaction"
 
−
***'''"Regulatory" will remain "Regulatory"'''
 
−
***'''"No_interaction" will become "Genetic - No_interaction"
 
−
***'''"Predicted_interaction" will become "Predicted"
 
−
***'''"Physical_interaction" will become "Physical"'''
 
−
***'''"Suppression" will become "Genetic - Suppression"'''
 
−
***'''"Enhancement" will become "Genetic - Enhancement"'''
 
−
***'''"Synthetic" will become "Genetic - Synthetic"'''
 
−
***'''"Epistasis" will become "Genetic - Epistasis"'''
 
−
***'''"Mutual_enhancement" will become "Genetic - Mutual_enhancement"'''
 
−
***'''"Mutual_suppression" will become "Genetic - Mutual_suppression"'''
 
−
 
−
**Effected Gene      //autocomplete WBGene, multiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors
 
−
***'''In new OA, this field will be called "Affected Gene(s)" -- C  If non-directional is on, move to non-directional gene, otherwise leave here'''
 
−
**Effected Variation      //WBGene, WBVar, multiontology, autocomplete on Variation, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar"
 
−
***'''In new OA, this field will be called "Affected Variation(s)"; the dumping script will attempt to map these variations to their respetive genes and place the variation in that gene's interactor_info hash -- C'''
 
−
***'''In new OA, the gene(s) affiliated with this variation will become the "Affected Gene(s)" for this interaction.
 
−
**Effected Transgene_Name  //ontology, autocomplete  transgene object name, eg iaIs3.
 
−
***'''In new OA, all transgenes will go into the Transgene(s) field.  merge both effector + effected.'''
 
−
**Effected Transgene_Gene //  multi-ontology, autocomplete WBGene->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id. One wbgene for each .ace line ?  Make sure you really want it this way, we can go with product/promoter if that's what you want, just make sure it's what you want.  It matters having extra fields and scrolling and so forth.  You'll see when the text fields become multi-ontology and ontology. 
 
−
***'''In new OA, all transgenes will automatically be mapped to their associated genes based on all genes in the transgene OA's gene + driven_by_gene field.  remove this field.'''
 
−
***'''In new OA, genes from the "Effected Transgene Gene" field will move to the "Affected Gene" field.'''
 
−
**Effected Other Type //dropdown list of 'Chemicals' and 'Transgene'
 
−
***'''In new OA, these will be named "Affected Other Type" and dump as remark.'''
 
−
**Effected Other //free text field now, however, when entering chemicals make sure to enter common names followed by mesh IDs in parenthesis for later ontologinization.
 
−
***'''In new OA, these will be named "Affected Other" and dump as remark.'''
 
−
**Effector Gene      //autocomplete WBGene, multiontology. corresponding to interactor in .ace file. order does not matter when dump to interactors
 
−
***'''In new OA, these genes will all go in the "Effector Gene(s)" field.  If non-directional is on, move to non-directional gene, otherwise leave here'''
 
−
**Effector Variation      //WBGene, WBVar, autocomplete multiontology on variation, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar". use name server to map variation to gene, or the file Karen gave you to map variation to gene for variation OA.
 
−
***'''In new OA, this field will be the same; the dumping script will attempt to map these variations to their respetive genes and place the variation in that gene's interactor_info hash -- C'''
 
−
***'''In new OA, the gene(s) affiliated with this variation will become the "Effector Gene(s)" for this interaction.
 
−
**Effector Transgene_Name  //autocomplete name, ontology
 
−
***'''In new OA, all transgenes will go into the Transgene(s) field.  merge both effector + effected.'''
 
−
**Effector Transgene_Gene //  autocomplete WBGene, multi-ontology, ->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id.
 
−
***'''In new OA, all transgenes will automatically be mapped to their associated genes based on all genes in the transgene OA's gene + driven_by_gene field.  remove this field.'''
 
−
***'''In new OA, genes from the "Effector Transgene Gene" field will move to the "Effector Gene" field.'''
 
−
**Effector Other Type //dropdown list of 'Chemicals' and 'Transgene'
 
−
***'''In new OA, these will stay the same and dump as Remark'''
 
−
**Effector Other //free text field
 
−
***two fields above will be dumped in remark field.
 
−
***'''In new OA, these will stay the same and dump as Remark'''
 
−
 
−
'''Note: Gene, Variation, and Transgene_Gene all refer to different genes. There is no pairing problem.'''
 
−
 
−
 
−
[[File:tab2.png]]
 
−
*Tab 2
 
−
**Curator//dropdown list  '''Same in new OA'''
 
−
**Paper//ontology  '''Same in new OA'''
 
−
**RNAi ID//free text field  '''In new OA, this RNAi object will fill the "RNAi" field if it is not from WBPaper00029258 (hence large scale); if it is from WBPaper00029258, this will go in the "Large scale RNAi" field as free text'''
 
−
**Phenotype//multiontology  '''In new OA, this Phenotype object will fill the "Interaction phenotype" field.  keep OA field the same, change dumper.'''
 
−
**Remark//big text  '''Same in new OA'''
 
−
**Sentence ID//sentence shows in term info  '''Same in new OA'''
 
−
**False Positive//toggle, will not give an id or no dump if the sentence is false positive, containing no interaction info  '''Same in new OA'''
 
  
 
=== Postgres Table Names ===
 
=== Postgres Table Names ===
Line 609: Line 197:
  
 
'Interaction Type'             = int_type
 
'Interaction Type'             = int_type
 +
 +
'GI Module 1'                  = int_gimoduleone
 +
 +
'GI Module 2'                  = int_gimoduletwo
 +
 +
'GI Module 3'                  = int_gimodulethree
  
 
'Interaction Summary'          = int_summary
 
'Interaction Summary'          = int_summary
Line 633: Line 227:
  
 
'Non-directional Sequence(s)'  = int_sequencenondir
 
'Non-directional Sequence(s)'  = int_sequencenondir
 +
 +
'Feature Bait'                = int_featurebait
 +
 +
'Feature Target'                = int_featuretarget
  
 
'Bait overlapping CDS'        = int_cdsbait
 
'Bait overlapping CDS'        = int_cdsbait
Line 666: Line 264:
 
'Affected Rearrangement(s)'    = int_rearrtwo
 
'Affected Rearrangement(s)'    = int_rearrtwo
  
−
'Effector Other Type'         = int_otheronetype
+
'Non-Directional Other'       = int_othernondir
−
 
 
−
'Effector Other'              = int_otherone
 
  
−
'Affected Other Type'         = int_othertwotype    
+
'Effector Other'               = int_otherone    
  
 
'Affected Other'              = int_othertwo
 
'Affected Other'              = int_othertwo
−
 
−
'Deviation from expectation'  = int_deviation
 
−
 
−
'Neutrality function'          = int_neutralityfxn
 
  
 
'Large scale RNAi'            = int_lsrnai
 
'Large scale RNAi'            = int_lsrnai
Line 692: Line 284:
 
'Affected Variation(s)'        = int_variationtwo
 
'Affected Variation(s)'        = int_variationtwo
  
−
'Intragenic Effector Variation(s)' = int_intravariationone
+
'Non-directional Molecule(s)' = int_moleculenondir
 +
 
 +
'Effector Molecule(s)'       = int_moleculeone
  
−
'Intragenic Affected Variation(s)' = int_intravariationtwo
+
'Affected Molecule(s)'       = int_moleculetwo
  
 
'Transgene(s)'                = int_transgene
 
'Transgene(s)'                = int_transgene
 +
 +
'Construct'                    = int_construct 
  
 
'Person'                       = int_person  
 
'Person'                       = int_person  
Line 706: Line 302:
 
'Log-likelihood score'        = int_loglikelihood
 
'Log-likelihood score'        = int_loglikelihood
  
−
'High_hroughput'                  = int_throughput
+
'High_throughput'                  = int_throughput
  
 
'Sentence ID'                  = int_sentid        
 
'Sentence ID'                  = int_sentid        
  
 
'False Positive'               = int_falsepositive
 
'False Positive'               = int_falsepositive
−
 
−
 
−
'''Old Table Names'''
 
−
 
−
<strike>
 
−
 
−
'Non_directional'      = int_nondirectional 
 
−
 
−
'Effector Transgene Name' = int_transgeneone
 
−
 
−
'Effector Transgene Gene'      = int_transgeneonegene           
 
−
 
−
'Affected Transgene Name'      = int_transgenetwo   
 
−
 
−
'Affected Transgene Gene'      = int_transgenetwogene
 
−
 
−
</strike>
 
−
 
−
==='''.ace template: (OUTDATED)'''===
 
−
<strike>
 
−
<br>
 
−
* Interaction      :      ""
 
−
<br>
 
−
* Interactor                "WBGene"        Variation            ""
 
−
* Interactor                "WBGene"        Transgene        ""
 
−
* Interactor                "WBGene"
 
−
<br>
 
−
* Interaction_type                          Genetic                                      Effector  ""
 
−
* Interaction_type                          Genetic                                      Effected  ""
 
−
* Interaction_type                          Genetic                                      Non_directional    ""
 
−
* Interaction_type                          Genetic                                      Interaction_RNAi    ""
 
−
* Interaction_type                            Genetic                                    Interaction_phenotype    ""
 
−
<br>
 
−
* Interaction_type                            Regulatory                              Effector  ""
 
−
* Interaction_type                            Regulatory                              Effected  ""
 
−
* Interaction_type                            Regulatory                              Non_directional    ""
 
−
* Interaction_type                            Regulatory                              Interaction_RNAi    ""
 
−
* Interaction_type                            Regulatory                              Interaction_phenotype    ""
 
−
<br>
 
−
* 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    ""
 
−
<br>
 
−
* Interaction_type                            Predicted_interaction              Non_directional    ""
 
−
* Interaction_type                            Predicted_interaction              Interaction_RNAi    ""
 
−
* Interaction_type                            Predicted_interaction              Interaction_phenotype    ""
 
−
<br>
 
−
* Interaction_type                Physical_interaction                Effector  ""
 
−
* Interaction_type                Physical_interaction                Effected  "" 
 
−
* Interaction_type                Physical_interaction                Interaction_RNAi    ""
 
−
* Interaction_type                Physical_interaction                Interaction_phenotype    ""
 
−
<br>
 
−
* Interaction_type                  Suppression                            Effector  ""
 
−
* Interaction_type                  Suppression                            Effected  "" 
 
−
* Interaction_type                  Suppression                            Interaction_RNAi    ""
 
−
* Interaction_type                  Suppression                            Interaction_phenotype    ""
 
−
<br>
 
−
* Interaction_type                  Enhancement                          Effector  ""
 
−
* Interaction_type                  Enhancement                          Effected  "" 
 
−
* Interaction_type                  Enhancement                          Interaction_RNAi    ""                                                     
 
−
* Interaction_type                  Enhancement                          Interaction_phenotype    ""
 
−
<br>
 
−
* Interaction_type                    Synthetic                                Non_directional      ""
 
−
* Interaction_type                    Synthetic                                Interaction_RNAi    ""
 
−
* Interaction_type                    Synthetic                                Interaction_phenotype    ""
 
−
<br>
 
−
* Interaction_type                    Epistasis                                Effector  ""
 
−
* Interaction_type                    Epistasis                                Effected  "" 
 
−
* Interaction_type                    Epistasis                                Interaction_RNAi    ""
 
−
* Interaction_type                    Epistasis                                Interaction_phenotype    ""
 
−
<br>
 
−
* Interaction_type                    Mutual_enhancement            Non_directional  ""
 
−
* Interaction_type                    Mutual_enhancement            Interaction_RNAi    ""
 
−
* Interaction_type                    Mutual_enhancement            Interaction_phenotype    ""
 
−
<br>
 
−
* Interaction_type                  Mutual_suppression                Non_directional    ""
 
−
* Interaction_type                  Mutual_suppression                Interaction_RNAi    ""
 
−
* Interaction_type                  Mutual_suppression                Interaction_phenotype    ""
 
−
<br>
 
−
*Paper                        ""
 
−
*Remark                    ""
 
−
<br>
 
−
</strike>
 
−
 
−
==='''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 ==
 
== Some Notes for gene_gene_interaction ==
Line 846: Line 338:
 
The above file needs to be checked for dead genes before every upload by running the "historicGeneReplacementLSInteraction.pl" script in the same directory. Before running the script, make sure that the output file is appropriately named. The script prints all dead genes to the screen, so when running the script you may want to redirect the script output into a file so you can read the results later.
 
The above file needs to be checked for dead genes before every upload by running the "historicGeneReplacementLSInteraction.pl" script in the same directory. Before running the script, make sure that the output file is appropriately named. The script prints all dead genes to the screen, so when running the script you may want to redirect the script output into a file so you can read the results later.
  
−
 
−
==== Outdated notes on large scale interaction files ====
 
−
*<strike> ready_to_upload large scale data file: Large_scale_interactions_WS231.ace  is located on tazendra: /home/acedb/xiaodong/oa_interactions_dumper should be uploaded for every upload
 
−
* large scale .ace file needs to be checkd again dead genes for each upload using scripts in the same directory: find_invalid_genes_largescale.pl*  - 08/31/2012 for upload WS234
 
−
**before run, change source file (in file) to latest large scale .ace version (in scripts)
 
−
**dead/merged genes will appear on screen. replace merged genes, leave dead/dead genes for now
 
−
**change large scale.ace file name to latest upload version
 
−
**then upload </strike>
 
  
 
=== Directories on tazendra related to gene_gene_interaction (home/acedb/xiaodong) ===
 
=== Directories on tazendra related to gene_gene_interaction (home/acedb/xiaodong) ===
Line 860: Line 344:
 
*interaction_ace_parsing
 
*interaction_ace_parsing
 
*oa_interactions_dumper
 
*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 ==
 
== The new Interaction OA, March 2012 ==
Line 884: Line 356:
 
**'''If there are multiple entries, data to be entered like this: "Database 1" "Field 1" "Accession number 1" | "Database 2" "Field 2" "Accession number 2"'''
 
**'''If there are multiple entries, data to be entered like this: "Database 1" "Field 1" "Accession number 1" | "Database 2" "Field 2" "Accession number 2"'''
 
*Paper - ?Paper (Ontology)  int_paper  '''Dumps as: Paper <Paper>'''
 
*Paper - ?Paper (Ontology)  int_paper  '''Dumps as: Paper <Paper>'''
 +
*Person - ?Person (MultiOntology)  int_person  '''Dumps as: Remark  <Remark_text>  Person_evidence  <Person>'''
 +
**'''If there is no Remark entry, dumps as: Remark "See Person Evidence"  Person_evidence  <Person>'''
 
*Interaction Type - Text (Multiple-Dropdown)  int_type
 
*Interaction Type - Text (Multiple-Dropdown)  int_type
 
**The options for Interaction Type will include:
 
**The options for Interaction Type will include:
−
***Physical  '''Dumps as: Physical'''
+
** <span style="color: red;"> '''NOTE: The Curation Status Form infers that genetic interaction(s) have been curated if the type is NOT physical or predicted''' </span>
−
***Predicted  '''Dumps as: Predicted'''
+
**Physical  '''Dumps as: Physical'''
−
***Genetic - Genetic interaction  '''Dumps as: Genetic_interaction'''
+
**Predicted  '''Dumps as: Predicted'''
−
***Genetic - Negative genetic  '''Dumps as: Negative_genetic'''
+
**Genetic - Genetic interaction  '''Dumps as: Genetic_interaction'''
−
***Genetic - Synthetic  '''Dumps as: Synthetic'''
+
**Genetic - Negative genetic  '''Dumps as: Negative_genetic'''
−
***Genetic - Enhancement  '''Dumps as: Enhancement'''
+
**Genetic - Synthetic  '''Dumps as: Synthetic'''
−
***Genetic - Unilateral enhancement  '''Dumps as: Unilateral_enhancement'''
+
**Genetic - Enhancement  '''Dumps as: Enhancement'''
−
***Genetic - Mutual enhancement  '''Dumps as: Mutual_enhancement'''
+
**Genetic - Unilateral enhancement  '''Dumps as: Unilateral_enhancement'''
−
***Genetic - Suppression  '''Dumps as: Suppression'''
+
**Genetic - Mutual enhancement  '''Dumps as: Mutual_enhancement'''
−
***Genetic - Complete suppression  '''Dumps as: Complete_suppression'''  ''NEW  CG 9-3-2013''
+
**Genetic - Positive genetic  '''Dumps as: Positive_genetic'''
−
***Genetic - Partial suppression  '''Dumps as: Partial_suppression'''  ''NEW  CG 9-3-2013''
+
**Genetic - Suppression  '''Dumps as: Suppression'''
−
***Genetic - Unilateral suppression  '''Dumps as: Unilateral_suppression'''
+
**Genetic - Complete suppression  '''Dumps as: Complete_suppression'''
−
***Genetic - Complete unilateral suppression  '''Dumps as: Complete_unilateral_suppression'''  ''NEW  CG 9-3-2013''
+
**Genetic - Partial suppression  '''Dumps as: Partial_suppression'''
−
***Genetic - Partial unilateral suppression  '''Dumps as: Partial_unilateral_suppression'''  ''NEW  CG 9-3-2013''
+
**Genetic - Unilateral suppression  '''Dumps as: Unilateral_suppression'''
−
***Genetic - Mutual suppression  '''Dumps as: Mutual_suppression'''
+
**Genetic - Complete unilateral suppression  '''Dumps as: Complete_unilateral_suppression'''
−
***Genetic - Complete mutual suppression  '''Dumps as: Complete_mutual_suppression'''  ''NEW  CG 9-3-2013''
+
**Genetic - Partial unilateral suppression  '''Dumps as: Partial_unilateral_suppression'''
−
***Genetic - Partial mutual suppression  '''Dumps as: Partial_mutual_suppression'''  ''NEW  CG 9-3-2013''
+
**Genetic - Mutual suppression  '''Dumps as: Mutual_suppression'''
−
***Genetic - Asynthetic  '''Dumps as: Asynthetic'''
+
**Genetic - Complete mutual suppression  '''Dumps as: Complete_mutual_suppression'''
−
***Genetic - Suppression/Enhancement  '''Dumps as: Suppression_enhancement'''
+
**Genetic - Partial mutual suppression  '''Dumps as: Partial_mutual_suppression'''
−
***Genetic - Epistasis  '''Dumps as: Epistasis'''
+
**Genetic - Asynthetic  '''Dumps as: Asynthetic'''
−
***Genetic - Positive epistasis  '''Dumps as: Positive_epistasis'''  ''NEW  CG 9-3-2013''
+
**Genetic - Suppression/Enhancement  '''Dumps as: Suppression_enhancement'''
−
***Genetic - Maximal epistasis  '''Dumps as: Maximal_epistasis'''
+
**Genetic - Epistasis  '''Dumps as: Epistasis'''
−
***Genetic - Minimal epistasis  '''Dumps as: Minimal_epistasis'''
+
**Genetic - Positive epistasis  '''Dumps as: Positive_epistasis'''
−
***Genetic - Neutral epistasis  '''Dumps as: Neutral_epistasis'''  ''NEW  CG 9-3-2013''
+
**Genetic - Maximal epistasis  '''Dumps as: Maximal_epistasis'''
−
***Genetic - Qualitative epistasis  '''Dumps as: Qualitative_epistasis'''  ''NEW  CG 9-3-2013''
+
**Genetic - Minimal epistasis  '''Dumps as: Minimal_epistasis'''
−
***Genetic - Opposing epistasis  '''Dumps as: Opposing_epistasis'''  ''NEW  CG 9-3-2013''
+
**Genetic - Neutral epistasis  '''Dumps as: Neutral_epistasis'''
−
***Genetic - Quantitative epistasis  '''Dumps as: Quantitative_epistasis'''  ''NEW  CG 9-3-2013''
+
**Genetic - Qualitative epistasis  '''Dumps as: Qualitative_epistasis'''
−
<pre style="color: red">
+
**Genetic - Opposing epistasis  '''Dumps as: Opposing_epistasis'''
−
***<strike>Genetic - Suppression/Epistasis '''Dumps as: Suppression_epistasis'''</strike> ''CG 9-3-2013''
+
**Genetic - Quantitative epistasis  '''Dumps as: Quantitative_epistasis'''
−
***<strike>Genetic - Agonistic epistasis '''Dumps as: Agonistic_epistasis'''</strike> ''CG 9-3-2013''
+
**Genetic - Neutral genetic '''Dumps as: Neutral_genetic'''
−
***<strike>Genetic - Antagonistic epistasis '''Dumps as: Antagonistic_epistasis'''</strike> ''CG 9-3-2013''
+
**Genetic - Oversuppression '''Dumps as: Oversuppression'''
−
</pre>
+
**Genetic - Unilateral oversuppression '''Dumps as: Unilateral_oversuppression'''
−
***Genetic - Neutral genetic  '''Dumps as: Neutral_genetic''' ''NEW  CG 9-3-2013''
+
**Genetic - Mutual oversuppression '''Dumps as: Mutual_oversuppression'''
−
***Genetic - Oversuppression  '''Dumps as: Oversuppression'''
+
**Genetic - Oversuppression/Enhancement '''Dumps as: Oversuppression_enhancement'''
−
***Genetic - Unilateral oversuppression '''Dumps as: Unilateral_oversuppression'''
+
**Genetic - Phenotype bias '''Dumps as: Phenotype_bias'''
−
***Genetic - Mutual oversuppression  '''Dumps as: Mutual_oversuppression'''
+
**Genetic - No interaction '''Dumps as: No_interaction'''
−
***<strike>Genetic - Complex oversuppression  '''Dumps as: Complex_oversuppression'''</strike>  ''CG 9-3-2013''
+
*GI Module 1 - Text (Dropdown)  int_gimoduleone
−
***Genetic - Oversuppression/Enhancement  '''Dumps as: Oversuppression_enhancement'''
+
** GI Module 1 options are:
−
***Genetic - Phenotype bias  '''Dumps as: Phenotype_bias'''
+
** A_phenotypic '''Dumps as: A_phenotypic'''
−
***<strike>Genetic - Biased suppression  '''Dumps as: Biased_suppression'''</strike>  ''CG 9-3-2013''
+
** Mono_phenotypic '''Dumps as: Mono_phenotypic'''
−
***<strike>Genetic - Biased enhancement '''Dumps as: Biased_enhancement'''</strike>  ''CG 9-3-2013''
+
** Cis_phenotypic '''Dumps as: Cis_phenotypic'''
−
***<strike>Genetic - Complex phenotype bias  '''Dumps as: Complex_phenotype_bias'''</strike>  ''CG 9-3-2013''
+
** Iso_phenotypic '''Dumps as: Iso_phenotypic'''
−
***Genetic - No interaction  '''Dumps as: No_interaction'''
+
** Trans_phenotypic '''Dumps as: Trans_phenotypic'''
 +
*GI Module 2 - Text (Dropdown) int_gimoduletwo
 +
** GI Module 2 options are:
 +
** Enhancing '''Dumps as: Enhancing'''
 +
** Suppressing '''Dumps as: Suppressing'''
 +
** Sub_suppressing '''Dumps as: Sub_suppressing'''
 +
** Inter_suppressing '''Dumps as: Inter_suppressing'''
 +
** Semi_suppressing '''Dumps as: Semi_suppressing'''
 +
** Co_suppressing '''Dumps as: Co_suppressing'''
 +
** All_suppressing '''Dumps as: All_suppressing'''
 +
** Super_suppressing '''Dumps as: Super_suppressing'''
 +
** Masking '''Dumps as: Masking'''
 +
*GI Module 3 - Text (Dropdown) int_gimodulethree
 +
** GI Module 3 options are:
 +
** Neutral '''Dumps as: Neutral'''
 +
** Non_neutral '''Dumps as: Non_neutral'''
 +
** Positive '''Dumps as: Positive'''
 +
** Negative '''Dumps as: Negative'''
 +
** Converging '''Dumps as: Converging'''
 +
** Diverging '''Dumps as: Diverging'''
 
*Interaction Summary - bigtext '''int_summary''' '''Dumps as: Interaction_summary <Big_Text>'''
 
*Interaction Summary - bigtext '''int_summary''' '''Dumps as: Interaction_summary <Big_Text>'''
 
*Remark - bigtext  int_remark  '''Dumps as: Remark <Big_Text>'''
 
*Remark - bigtext  int_remark  '''Dumps as: Remark <Big_Text>'''
 +
*Interaction phenotype(s) - ?Phenotype (MultiOntology)  int_phenotype  '''Dumps as: Interaction_phenotype <Phenotype>'''
 +
 +
 +
Each interaction type can be considered necessarily directional, necessarily non-directional, or ambiguous. The OA dumping script will check to make sure that the correct interactor types (Non-directional, Effector, or Affected) are listed in each case and notify the curator during the dump in the error output file. Here are the directionalities for each interaction type:
 +
 +
'''Necessarily Directional:'''
 +
*Enhancement
 +
*Unilateral enhancement
 +
*Suppression
 +
*Complete suppression
 +
*Partial suppression
 +
*Unilateral suppression
 +
*Complete unilateral suppression
 +
*Partial unilateral suppression
 +
*Epistasis
 +
*Positive epistasis
 +
*Maximal epistasis
 +
*Minimal epistasis
 +
*Neutral epistasis
 +
*Qualitative epistasis
 +
*Opposing epistasis
 +
*Quantitative epistasis
 +
*Oversuppression
 +
*Unilateral oversuppression
 +
*Phenotype_bias
 +
 +
 +
'''Necessarily Non-directional:'''
 +
*Predicted
 +
*Synthetic
 +
*Asynthetic
 +
*Mutual enhancement
 +
*Mutual suppression
 +
*Complete mutual suppression
 +
*Partial mutual suppression
 +
*Mutual oversuppression
 +
*Suppression enhancement
 +
*Oversuppression enhancement
 +
*No interaction
 +
 +
 +
'''Ambiguous (ignore in dumping script):'''
 +
*Physical
 +
*Genetic interaction
 +
*Negative genetic
 +
*Positive genetic
 +
*Neutral genetic
  
 
=== TAB2 ===
 
=== TAB2 ===
Line 939: Line 479:
 
***Affinity_capture_RNA  '''Dumps as: Affinity_capture_RNA'''
 
***Affinity_capture_RNA  '''Dumps as: Affinity_capture_RNA'''
 
***Affinity_capture_Western  '''Dumps as: Affinity_capture_Western'''
 
***Affinity_capture_Western  '''Dumps as: Affinity_capture_Western'''
 +
***Chromatin_immunoprecipitation  '''Dumps as: Chromatin_immunoprecipitation'''
 
***Cofractionation  '''Dumps as: Cofractionation'''
 
***Cofractionation  '''Dumps as: Cofractionation'''
 
***Colocalization  '''Dumps as: Colocalization'''
 
***Colocalization  '''Dumps as: Colocalization'''
 
***Copurification  '''Dumps as: Copurification'''
 
***Copurification  '''Dumps as: Copurification'''
 +
***DNase_I_footprinting  '''Dumps as: DNase_I_footprinting'''
 
***Fluorescence_resonance_energy_transfer  '''Dumps as: Fluorescence_resonance_energy_transfer'''
 
***Fluorescence_resonance_energy_transfer  '''Dumps as: Fluorescence_resonance_energy_transfer'''
 
***Protein_fragment_complementation_assay  '''Dumps as: Protein_fragment_complementation_assay'''
 
***Protein_fragment_complementation_assay  '''Dumps as: Protein_fragment_complementation_assay'''
Line 953: Line 495:
 
***Yeast_one_hybrid  '''Dumps as: Yeast_one_hybrid'''
 
***Yeast_one_hybrid  '''Dumps as: Yeast_one_hybrid'''
 
***Directed_yeast_one_hybrid  '''Dumps as: Directed_yeast_one_hybrid'''
 
***Directed_yeast_one_hybrid  '''Dumps as: Directed_yeast_one_hybrid'''
−
***Electrophoretic_mobility_shift_assay_(EMSA) '''Dumps as: Electrophoretic_mobility_shift_assay_(EMSA)'''  ''NEW CG 9-3-2013''
+
***Electrophoretic_mobility_shift_assay '''Dumps as: Electrophoretic_mobility_shift_assay'''
  
 
*Library screened/Times found - Text Text(Integer) '''int_library'''; separate multiple entries with pipes ('|') '''int_library''' '''Dumps as: Library_screened <Text> INT'''
 
*Library screened/Times found - Text Text(Integer) '''int_library'''; separate multiple entries with pipes ('|') '''int_library''' '''Dumps as: Library_screened <Text> INT'''
Line 969: Line 511:
 
*Sequence Target(s) - ?Sequence (Free Text); separate multiple entries with pipes ('|')  '''int_sequencetarget''' '''Dumps as: Sequence_interactor <Sequence> Target'''
 
*Sequence Target(s) - ?Sequence (Free Text); separate multiple entries with pipes ('|')  '''int_sequencetarget''' '''Dumps as: Sequence_interactor <Sequence> Target'''
 
*Non-directional Sequence(s) - ?Sequence (Free Text); separate multiple entries with pipes ('|')  '''int_sequencenondir''' '''Dumps as: Sequence_interactor <Sequence> Non_directional'''
 
*Non-directional Sequence(s) - ?Sequence (Free Text); separate multiple entries with pipes ('|')  '''int_sequencenondir''' '''Dumps as: Sequence_interactor <Sequence> Non_directional'''
−
 
+
*Feature Bait - ?Feature (MultiOntology)  '''int_featurebait'''  '''Dumps as: Feature_interactor <Feature> Bait'''
 +
*Feature Target - ?Feature (MultiOntology)  '''int_featuretarget'''  '''Dumps as: Feature_interactor <Feature> Target'''
 
*Bait overlapping CDS - ?CDS (Free Text) '''int_cdsbait''' '''Dumps as: Interactor_overlapping_CDS <CDS> Bait'''
 
*Bait overlapping CDS - ?CDS (Free Text) '''int_cdsbait''' '''Dumps as: Interactor_overlapping_CDS <CDS> Bait'''
 
*Target overlapping CDS(s) - ?CDS (Free Text); separate multiple entries with pipes ('|')  '''int_cdstarget''' '''Dumps as: Interactor_overlapping_CDS <CDS> Target'''
 
*Target overlapping CDS(s) - ?CDS (Free Text); separate multiple entries with pipes ('|')  '''int_cdstarget''' '''Dumps as: Interactor_overlapping_CDS <CDS> Target'''
Line 987: Line 530:
  
 
=== TAB3 ===
 
=== TAB3 ===
−
*Non-directional Gene(s) - ?Gene (MultiOntology) '''int_genenondir''' '''Dumps as: Interactor_overlapping_gene <Gene> Non_directional'''
+
*Non-directional Gene(s) - ?Gene (MultiOntology) int_genenondir '''Dumps as: Interactor_overlapping_gene <Gene> Non_directional'''
 
*Effector Gene(s) - ?Gene (MultiOntology)  int_geneone  '''Dumps as: Interactor_overlapping_gene <Gene> Effector'''
 
*Effector Gene(s) - ?Gene (MultiOntology)  int_geneone  '''Dumps as: Interactor_overlapping_gene <Gene> Effector'''
 
*Affected Gene(s) - ?Gene (MultiOntology)  int_genetwo  '''Dumps as: Interactor_overlapping_gene <Gene> Affected'''
 
*Affected Gene(s) - ?Gene (MultiOntology)  int_genetwo  '''Dumps as: Interactor_overlapping_gene <Gene> Affected'''
  
 
*Non-directional Variation(s) - ?Variation (MultiOntology)  int_variationnondir
 
*Non-directional Variation(s) - ?Variation (MultiOntology)  int_variationnondir
 +
**'''Dumps as: Variation_interactor <Variation> Non_directional'''
 
**'''Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
 
**'''Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
−
**'''Dumps as: (Line 1) Interactor_overlapping_gene <Mapped Gene> Variation <Variation>'''
+
**'''Dumps as: Interactor_overlapping_gene <Mapped Gene> Non_directional'''
−
**'''Dumps as: (Line 2) Interactor_overlapping_gene <Mapped Gene> Non_directional'''
+
**Variations that don't map to a gene will need to be assigned a gene at the ACEDB build stage; these objects will be indicated as such in the OA-dumper error output file
−
**'''For Variations that don't map to a gene, Dump as: Unaffiliated_variation <Variation>'''
 
  
 
*Effector Variation(s) - ?Variation (MultiOntology)  int_variationone
 
*Effector Variation(s) - ?Variation (MultiOntology)  int_variationone
 +
**'''Dumps as: Variation_interactor <Variation> Effector'''
 
**'''Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
 
**'''Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
−
**'''Dumps as: (Line 1) Interactor_overlapping_gene <Mapped Gene> Variation <Variation>'''
+
**'''Dumps as: Interactor_overlapping_gene <Mapped Gene> Effector'''
−
**'''Dumps as: (Line 2) Interactor_overlapping_gene <Mapped Gene> Effector'''
+
**Variations that don't map to a gene will need to be assigned a gene at the ACEDB build stage; these objects will be indicated as such in the OA-dumper error output file
−
**'''For Variations that don't map to a gene, Dump as: Unaffiliated_variation <Variation>'''
 
  
 
*Affected Variation(s) - ?Variation (MultiOntology)  int_variationtwo
 
*Affected Variation(s) - ?Variation (MultiOntology)  int_variationtwo
 +
**'''Dumps as: Variation_interactor <Variation> Affected'''
 
**'''Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
 
**'''Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
−
**'''Dumps as: (Line 1) Interactor_overlapping_gene <Mapped Gene> Variation <Variation>'''
+
**'''Dumps as: Interactor_overlapping_gene <Mapped Gene> Affected'''
−
**'''Dumps as: (Line 2) Interactor_overlapping_gene <Mapped Gene> Affected'''
+
**Variations that don't map to a gene will need to be assigned a gene at the ACEDB build stage; these objects will be indicated as such in the OA-dumper error output file
−
**'''For Variations that don't map to a gene in the interaction, Dump as: Unaffiliated_variation <Variation>'''
+
*Non-directional Molecule(s) - ?Molecule (MultiOntology) int_moleculenondir '''Dumps as: Molecule_interactor <Molecule> Non_directional'''
−
 
+
*Effector Molecule(s) - ?Molecule (MultiOntology)  int_moleculeone  '''Dumps as: Molecule_interactor <Molecule> Effector'''
−
*Intragenic Effector Variation(s) - ?Variation (MultiOntology) '''int_intravariationone'''
+
*Affected Molecule(s) - ?Molecule (MultiOntology) int_moleculetwo  '''Dumps as: Molecule_interactor <Molecule> Affected'''
−
**'''Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
 
−
**'''Dumps as: Interactor_overlapping_gene <Mapped Gene> Intragenic_effector_variation <Variation>'''
 
−
**'''For Variations that don't map to a gene in the interaction, Dump as: Unaffiliated_variation <Variation>'''
 
−
 
 
−
*Intragenic Affected Variation(s) - ?Variation (MultiOntology) '''int_intravariationtwo'''
 
−
**'''Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
 
−
**'''Dumps as: Interactor_overlapping_gene <Mapped Gene> Intragenic_affected_variation <Variation>'''
 
−
**'''For Variations that don't map to a gene in the interaction, Dump as: Unaffiliated_variation <Variation>'''
 
−
 
 
  
 
=== TAB4 ===
 
=== TAB4 ===
−
*Deviation from expectation - Big text '''int_deviation''' '''Dumps as: Deviation_from_expectation <Big_Text>'''
 
−
 
−
*Neutrality function - (Dropdown) '''int_neutralityfxn''' options are:
 
−
**Multiplicative  '''Dumps as: Multiplicative'''
 
−
**Additive  '''Dumps as: Additive'''
 
−
**Minimal  '''Dumps as: Minimal'''
 
  
 
*Non-directional Rearrangement(s) - ?Rearrangement (MultiOntology)  '''int_rearrnondir''' '''Dumps as: Rearrangement <Rearrangement> Non_directional'''
 
*Non-directional Rearrangement(s) - ?Rearrangement (MultiOntology)  '''int_rearrnondir''' '''Dumps as: Rearrangement <Rearrangement> Non_directional'''
 
*Effector Rearrangement(s) - ?Rearrangement (MultiOntology)  '''int_rearrone''' '''Dumps as: Rearrangement <Rearrangement> Effector'''
 
*Effector Rearrangement(s) - ?Rearrangement (MultiOntology)  '''int_rearrone''' '''Dumps as: Rearrangement <Rearrangement> Effector'''
 
*Affected Rearrangement(s) - ?Rearrangement (MultiOntology)  '''int_rearrtwo''' '''Dumps as: Rearrangement <Rearrangement> Affected'''
 
*Affected Rearrangement(s) - ?Rearrangement (MultiOntology)  '''int_rearrtwo''' '''Dumps as: Rearrangement <Rearrangement> Affected'''
−
 
−
*Effector Other Type  - (Dropdown) int_otheronetype    options are: Chemical or Transgene, int_otheronetype '''Dumps as (see next line)'''
 
−
*Effector Other - ?Text  int_otherone  '''Dumps as: Remark "Effector <Effector Other Type>: <Text>"'''
 
−
*Affected Other Type  - (Dropdown) int_othertwotype    options are: Chemical or Transgene, int_othertwotype '''Dumps as (see next line)'''
 
−
*Affected Other - ?Text  int_othertwo    '''Dumps as: Remark "Affected <Affected Other Type>: <Text>"'''
 
  
 
*RNAi - (MultiOntology) int_rnai  '''Dumps as: Interaction_RNAi <RNAi>'''
 
*RNAi - (MultiOntology) int_rnai  '''Dumps as: Interaction_RNAi <RNAi>'''
 
*Large scale RNAi - Free Text; separate multiple entries with pipes ('|')  '''int_lsrnai''' (all large scale RNAi that doesn't match ontology)  '''Dumps as: Interaction_RNAi <RNAi>'''
 
*Large scale RNAi - Free Text; separate multiple entries with pipes ('|')  '''int_lsrnai''' (all large scale RNAi that doesn't match ontology)  '''Dumps as: Interaction_RNAi <RNAi>'''
−
 
−
*Interaction phenotype(s) - ?Phenotype (MultiOntology)  int_phenotype  '''Dumps as: Interaction_phenotype <Phenotype>'''
 
  
 
*Expression pattern(s) - ?Expr_pattern (MultiOntology) '''int_exprpattern''' '''Dumps as: Interactor_overlapping_gene <Mapped Gene> Expr_pattern <Expr_pattern>'''
 
*Expression pattern(s) - ?Expr_pattern (MultiOntology) '''int_exprpattern''' '''Dumps as: Interactor_overlapping_gene <Mapped Gene> Expr_pattern <Expr_pattern>'''
Line 1,047: Line 569:
  
 
*Transgene(s) - ?Transgene (MultiOntology) '''int_transgene''' '''Dumps as: Interactor_overlapping_gene <Mapped Gene> Transgene <Transgene> ''AND'' Transgene (on new line)'''
 
*Transgene(s) - ?Transgene (MultiOntology) '''int_transgene''' '''Dumps as: Interactor_overlapping_gene <Mapped Gene> Transgene <Transgene> ''AND'' Transgene (on new line)'''
−
**'''When mapping transgenes to genes, compare transgene-affiliated genes (from the Driven_by_gene, Gene, and 3'UTR fields) with those in the Non-directional Gene(s), Effector Gene(s), Affected Gene(s), Bait Overlapping Gene and Target Overlapping Gene fields'''
+
**'''When mapping transgenes to genes, compare transgene-affiliated genes (from the Driven_by_gene, Gene, and 3'UTR fields of the associated ?Construct in the Construct OA) with those in the Non-directional Gene(s), Effector Gene(s), Affected Gene(s), Bait Overlapping Gene and Target Overlapping Gene fields'''
 
**'''For Transgenes that don't map to a gene in the interaction, Dump as: Unaffiliated_transgene <Transgene>'''
 
**'''For Transgenes that don't map to a gene in the interaction, Dump as: Unaffiliated_transgene <Transgene>'''
  
 +
*Construct - ?Construct (MultiOntology) '''int_construct''' '''Dumps as: Interactor_overlapping_gene <Mapped Gene> Construct <Construct>'''
 +
**'''When mapping constructs to genes, compare construct-affiliated genes (from the Driven_by_gene, Gene, and 3'UTR fields of the ?Construct in the Construct OA) with those in the Non-directional Gene(s), Effector Gene(s), Affected Gene(s), Bait Overlapping Gene and Target Overlapping Gene fields'''
 +
**'''For Constructs that don't map to a gene in the interaction, Dump as: Unaffiliated_construct <Construct>'''
 +
 +
*Non-Directional Other - ?Text  int_othernondir  '''Dumps as: Other_interactor <Text> Non_directional'''
 +
*Effector Other - ?Text  int_otherone  '''Dumps as: Other_interactor <Text> Effector'''
 +
*Affected Other - ?Text  int_othertwo    '''Dumps as: Other_interactor <Text> Affected'''
  
 
=== TAB5 ===
 
=== TAB5 ===
−
*Person - ?Person  int_person  '''Dumps as: Remark  <Remark_text>  Person_evidence  <Person>'''
 
−
**'''If there is no Remark entry, dumps as: Remark "See Person Evidence"  Person_evidence  <Person>'''
 
 
*Confidence description - Text '''int_confidence''' '''Dumps as: Description <Text>'''
 
*Confidence description - Text '''int_confidence''' '''Dumps as: Description <Text>'''
 
*P-value - Text (Float) '''int_pvalue''' '''Dumps as: P_value FLOAT'''
 
*P-value - Text (Float) '''int_pvalue''' '''Dumps as: P_value FLOAT'''
Line 1,062: Line 589:
 
*Sentence ID - (Ontology) sentence shows in term info;  int_sentid  '''Dumps as: N/A'''
 
*Sentence ID - (Ontology) sentence shows in term info;  int_sentid  '''Dumps as: N/A'''
 
*False Positive - toggle, will not give an id or no dump if the sentence is false positive, containing no interaction info; int_falsepositive  '''Dumps as: N/A'''
 
*False Positive - toggle, will not give an id or no dump if the sentence is false positive, containing no interaction info; int_falsepositive  '''Dumps as: N/A'''
−
 
+
*Community Curator - int_communitycurator
 +
*Community Curator Email - int_communitycuratoremail
 +
*Needs Review - (Toggle) int_needsreview (Flagging only)
  
 
== To go live on tazendra ==
 
== To go live on tazendra ==
Line 1,182: Line 711:
 
=== TAB 3 ===
 
=== TAB 3 ===
  
−
9) '''Effector Variation(s)''', '''Affected Variation(s)''', and '''Non-directional Variation(s)''' fields are for variations that implicate an affiliated gene as an effector or affected interactor in a directional genetic interaction or non-directional interactors in a non-directional interaction. These fields can be populated without the need to populate the respective gene in the relevant gene field, as the dumping script will make the appropriate associations.
+
9) '''Effector Variation(s)''', '''Affected Variation(s)''', and '''Non-directional Variation(s)''' fields are for variations that implicate an affiliated gene as an effector or affected interactor in a directional genetic interaction or non-directional interactors in a non-directional interaction. These fields can be populated without the need to populate the respective gene in the relevant gene field, as the dumping script (or build process) will make the appropriate associations.
−
 
 
−
 
 
−
10) The '''Intragenic Effector Variation(s)''' and '''Intragenic Affected Variation(s)''' fields are reserved for genetic interactions between two variations within the same gene, for example intragenic suppression events. The lack of a "Non-directional" field assumes that all of these interactions will be directional.
 
−
 
 
  
 
=== TAB 4 ===
 
=== TAB 4 ===
  
−
 
+
10) The '''RNAi''' fields: There are two fields for references to RNAi objects: "RNAi" and "Large scale RNAi". The reason for two fields is that one field ("RNAi") is an ontology field reading off of RNAi experiments that live in the RNAi OA and Postgres. As RNAi experiments from papers containing 2,000 or more RNAi experiments (WBPaper00029258 for example) were excluded from the RNAi OA for performance reasons, any RNAi experiments from such papers will not be recognized by the "RNAi" ontology field, and therefore must be entered as free-text in the "Large scale RNAi" field.
−
11) '''Deviation from expectation''' is a free-text field where, at the curator's discretion, a curator can describe why a genetic interaction is an interaction, i.e. why it is an unexpected result warranting an interaction. This could be as simple as "The life spans were synergistic" or "Neither mutation alone exhibited a phenotype".
 
−
 
 
−
 
 
−
12) '''Neutrality function''' is closely related to the "Deviation from expectation" field, where the curator can decide, if applicable, which "Neutrality function" applies to this genetic interaction. The choices in this drop down field are "Multiplicative", "Additive", and "Minimal". "Multiplicative" means that the authors expected to see a quantifiable phenotype in the double mutant that was the mathematical product of the quantified phenotypes of the individual mutations. For example, one mutant extends life span by 20%, and another extends it by 30%. With a multiplicative neutrality function, we would expect the double mutant to have (1.2 * 1.3 = 1.56) about 56% extended life span. Alternatively, in the "Additive" neutrality function, the authors might expect the sum of the effects (A + B - 1) or (1.2 + 1.3 - 1 = 1.5) or a 50% extended life span. The "Minimal" neutrality function assumes that the double mutant will be as severe as the most severe single mutant, in this case (1.3) or 30% extended. Therefore, any life span extension beyond 30%, for example, in the double mutant would be considered "surprising" and therefore, an interaction.
 
−
 
 
−
 
 
−
13) The '''RNAi''' fields: There are two fields for references to RNAi objects: "RNAi" and "Large scale RNAi". The reason for two fields is that one field ("RNAi") is an ontology field reading off of RNAi experiments that live in the RNAi OA and Postgres. As RNAi experiments from papers containing 2,000 or more RNAi experiments (WBPaper00029258 for example) were excluded from the RNAi OA for performance reasons, any RNAi experiments from such papers will not be recognized by the "RNAi" ontology field, and therefore must be entered as free-text in the "Large scale RNAi" field.
 
  
  
−
14) The '''Transgene(s)''' field is for transgenes involved in the interaction, regardless of whether it is related to an "Effector" gene or "Affected" gene or the interaction is Non-directional. The dumping script will automatically associate the transgene with the appropriate interacting gene and dump in .ACE format accordingly.
+
11) The '''Transgene(s)''' field is for transgenes involved in the interaction, regardless of whether it is related to an "Effector" gene or "Affected" gene or the interaction is Non-directional. The dumping script will automatically associate the transgene with the appropriate interacting gene and dump in .ACE format accordingly.
  
  
−
15) '''Effector/Affected Other Type''' and '''Effector/Affected Other''' fields: these fields allow for the curation of Chemicals, Transgenes, or other entities that don't exists as proper WormBase/ACEDB objects, for example transgenes that only express human proteins. The "Other Type" fields allow for the selection of "Chemical" or "Transgene", the identity of which would go into the "Other" fields. This, ideally, will get phased out as chemicals are generated in the Molecule OA and transgenes in the Transgene OA, thereby allowing them to be entered into ontology-based "Transgene" or "Molecule" fields.
+
12) '''Non-Directional Other''', '''Effector Other''', and '''Affected Other''' fields: these fields allow for the curation of entities that don't exists as proper WormBase/ACEDB objects, for example transgenes that only express human proteins, or experimental conditions or treatments (e.g. "Ionizing radiation") that are interactors
−
 
 
  
 
=== TAB 5 ===
 
=== TAB 5 ===
  
  
−
16) '''Confidence description''': This field will capture free-text descriptions of the confidence the authors suggest they have for this interaction. In the Yeast Two Hybrid experiments, for example, the interaction may be described as "Interactome Core 1", "Interactome Core 2", or "Interactome Noncore" referring to the varying degrees of confidence for those interactions.
+
13) '''Confidence description''': This field will capture free-text descriptions of the confidence the authors suggest they have for this interaction. In the Yeast Two Hybrid experiments, for example, the interaction may be described as "Interactome Core 1", "Interactome Core 2", or "Interactome Noncore" referring to the varying degrees of confidence for those interactions.
  
  
−
17) The '''P-value''' and '''Log-likelihood score''' fields are mostly to capture confidence values for predicted interactions that have been reported.
+
14) The '''P-value''' and '''Log-likelihood score''' fields are mostly to capture confidence values for predicted interactions that have been reported.
  
  
−
18) '''High_throughput''' toggle field is intended to capture whether or not the interaction was observed as one of several (50 - 1000s) interactions and thus should be interpreted with caution, or at least acknowledged as from a large scale experiment. The default is OFF and indicates that the experiment is low throughput.
+
15) '''High_throughput''' toggle field is intended to capture whether or not the interaction was observed as one of several (50 - 1000s) interactions and thus should be interpreted with caution, or at least acknowledged as from a large scale experiment. The default is OFF and indicates that the experiment is low throughput.
  
  
−
19) The '''Sentence ID''' and '''False Positve''' fields are exclusively for Textpresso sentence-based curation
+
16) The '''Sentence ID''' and '''False Positve''' fields are exclusively for Textpresso sentence-based curation
−
 
 
  
 
== Nightly Cron Job to Assign New Interaction IDs ==
 
== Nightly Cron Job to Assign New Interaction IDs ==
Line 1,262: Line 778:
 
b) There is at least one "Effector" and one "Affected" entry OR
 
b) There is at least one "Effector" and one "Affected" entry OR
  
−
c) There is at least two "Non-directional" entries OR
+
c) There is at least two "Non-directional" entries
−
 
 
−
d) There is at least one "Intragenic Effector Variation" and at least one "Intragenic Affected Variation" entry
 
  
 
If none of these conditions hold true, then an error message will be printed in tab-delimited format like this:
 
If none of these conditions hold true, then an error message will be printed in tab-delimited format like this:
Line 1,421: Line 935:
 
The dumper script will now (as of May, 2013) run an automatic check for dead genes in any gene field. Any genes that are considered dead that are referenced in an Interaction object in the OA will be handled in the following manner:
 
The dumper script will now (as of May, 2013) run an automatic check for dead genes in any gene field. Any genes that are considered dead that are referenced in an Interaction object in the OA will be handled in the following manner:
  
−
1) If there is a replacement for the gene (i.e. the gene has merged into another gene), the dead gene will be dumped into a "Historical_gene" field in the .ACE file, the replacement gene will fill the original gene field. A comment will be added to the Historical_gene field via the #Evidence hash. The original gene field (now with the updated gene reference) will be printed with an "Inferred_automatically" tag after the gene. So, for example, if WBGene00001234 is now a dead gene that has been merged into WBGene00002345:
+
1) If there is a replacement for the gene (i.e. the gene has merged into another gene), the dead gene will be dumped into a "Historical_gene" field in the .ACE file, the replacement gene will fill the original gene field. A comment will be added to the Historical_gene field via a 'Text' tag (updated as of 3-18-2015). The original gene field (now with the updated gene reference) will be printed with an "Inferred_automatically" tag after the gene. So, for example, if WBGene00001234 is now a dead gene that has been merged into WBGene00002345:
  
 
<pre>
 
<pre>
Line 1,431: Line 945:
 
<pre>
 
<pre>
 
Gene  "WBGene00002345"  Inferred_automatically
 
Gene  "WBGene00002345"  Inferred_automatically
−
Historical_gene  "WBGene00001234" Remark "Note: This object originally referred to WBGene00001234.
+
Historical_gene  "WBGene00001234"  "Note: This object originally referred to WBGene00001234.
 
WBGene00001234 is now considered dead and has been merged into WBGene00002345. WBGene00002345 has  
 
WBGene00001234 is now considered dead and has been merged into WBGene00002345. WBGene00002345 has  
 
replaced WBGene00001234 accordingly."
 
replaced WBGene00001234 accordingly."
Line 1,438: Line 952:
 
Also, since Antibodies, Transgenes, Expression patterns, Variations are mapped to an interactor where possible (or else they are dumped as "Unaffiliated"), this mapping will now occur to only the newest genes that the interactor refers to.
 
Also, since Antibodies, Transgenes, Expression patterns, Variations are mapped to an interactor where possible (or else they are dumped as "Unaffiliated"), this mapping will now occur to only the newest genes that the interactor refers to.
  
−
2) If there is no replacement for the gene, we would dump the following:
+
2) If there is no replacement for the gene (Dead or Suppressed), we would dump the following:
  
 
<pre>
 
<pre>
−
Historical_gene  "WBGene00001234" Remark "Note: This object originally referred to an interacting gene
+
Gene  "WBGene00001234"
 +
Historical_gene  "WBGene00001234"  "Note: This object originally referred to a gene
 
  (WBGene00001234) that is now considered dead. Please interpret with discretion."
 
  (WBGene00001234) that is now considered dead. Please interpret with discretion."
 +
</pre>
 +
 +
OR
 +
 +
<pre>
 +
Gene  "WBGene00001234"
 +
Historical_gene  "WBGene00001234"  "Note: This object originally referred to a gene
 +
(WBGene00001234) that has been suppressed. Please interpret with discretion."
 
</pre>
 
</pre>
  
 
and lastly,
 
and lastly,
  
−
3) If the gene has undergone a split, such genes will be printed out in the error output file of the dumping script for a curator to go back and manually change according to best judgement.
+
3) If the gene has undergone a split, such genes will be dumped as:
 +
 
 +
<pre>
 +
Gene  "WBGene00001234"
 +
Historical_gene  "WBGene00001234"  "Note: This object originally referred to a gene
 +
(WBGene00001234) that is now considered split. Please interpret with discretion."
 +
</pre>
 +
 
 +
and also printed out in the error output file of the dumping script for a curator to go back and manually change according to best judgement.
 +
 
 +
 
 +
Gene Examples:<br>
 +
A split gene: WBGene00012507<br>
 +
A merged gene: WBGene00007524<br>
 +
A dead gene: WBGene00007814<br>
 +
A suppressed gene: WBGene00015490<br>

Latest revision as of 20:51, 7 March 2019

'links to relevant pages
 Caltech documentation

Archived Interaction documentation may be found here

OA link

Interaction Curation

Pipeline

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.
  • Old dumper outputs (err* and interaction* files) will now be archived in the following directory:
    • /home/acedb/xiaodong/oa_interactions_dumper/Interaction_OA_Dumper_Output_Archive -- CG 10-31-2012

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.

Updated for WS261 - CG 7-21-2017 


?Interaction Interaction_type Physical UNIQUE ProteinProtein
                                              ProteinDNA
                                              ProteinRNA
                              Predicted
                              Regulatory Change_of_localization
                                         Change_of_expression_level
                              Genetic Genetic_interaction
                                      Neutral_genetic
                                      Synthetic
                                      Enhancement
                                      Unilateral_enhancement
                                      Mutual_enhancement
                                      Positive_genetic
                                      Suppression
                                      Complete_suppression
                                      Partial_suppression
                                      Unilateral_suppression
                                      Complete_unilateral_suppression
                                      Partial_unilateral_suppression
                                      Mutual_suppression
                                      Complete_mutual_suppression
                                      Partial_mutual_suppression
                                      Suppression_enhancement
                                      Asynthetic
                                      Negative_genetic
                                      Oversuppression
                                      Unilateral_oversuppression
                                      Mutual_oversuppression
                                      Oversuppression_enhancement
                                      Phenotype_bias
                                      No_interaction // Negative data; no interaction was observed after testing
                                      Epistasis
                                      Positive_epistasis
                                      Maximal_epistasis
                                      Minimal_epistasis
                                      Neutral_epistasis
                                      Qualitative_epistasis
                                      Opposing_epistasis
                                      Quantitative_epistasis
                              GI_module_one A_phenotypic
                                            Mono_phenotypic
                                            Cis_phenotypic
                                            Iso_phenotypic
                                            Trans_phenotypic
                              GI_module_two Enhancing
                                            Suppressing
                                            All_suppressing
                                            Super_suppressing
                                            Sub_suppressing
                                            Inter_suppressing
                                            Semi_suppressing
                                            Co_suppressing
                                            Masking
                              GI_module_three Neutral
                                              Non_neutral
                                              Positive
                                              Negative
                                              Converging
                                              Diverging
             Interactor PCR_interactor ?PCR_product XREF Interaction #Interactor_info       // PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments
                        Sequence_interactor ?Sequence XREF Interaction #Interactor_info     // Sequence of the interacting gene or protein
                        Interactor_overlapping_CDS ?CDS XREF Interaction #Interactor_info   // CDS of the interacting gene or protein (or related sequence)
                        Interactor_overlapping_gene ?Gene XREF Interaction #Interactor_info // Gene (or portion of gene) involved in the interaction
                        Interactor_overlapping_protein ?Protein XREF Interaction #Interactor_info    // Protein (or portion of protein) involved in the interaction
                        Molecule_interactor ?Molecule XREF Interaction #Interactor_info     // Molecule that regulates a gene or protein (ported from Gene_regulation Class) Modified Chris WS244
                        Other_interactor  ?Text #Interactor_info
                        Rearrangement ?Rearrangement XREF Interactor #Interactor_info
                        Feature_interactor ?Feature XREF Associated_with_Interaction #Interactor_info
                        Variation_interactor ?Variation XREF Interactor #Interactor_info
             Interaction_summary ?Text #Evidence
             Detection_method Affinity_capture_luminescence // A physical interaction detection technique
                              Affinity_capture_MS           // A physical interaction detection technique
                              Affinity_capture_RNA          // A physical interaction detection technique
                              Affinity_capture_Western      // A physical interaction detection technique
                              Chromatin_immunoprecipitation // Chris WS244
                              Cofractionation               // A physical interaction detection technique
                              Colocalization                // A physical interaction detection technique
                              Construct
                              Copurification                // A physical interaction detection technique
                              DNase_I_footprinting          //
                              Fluorescence_resonance_energy_transfer  // A physical interaction detection technique
                              Protein_fragment_complementation_assay  // A physical interaction detection technique
                              Yeast_two_hybrid                        // A physical interaction detection technique (Protein-protein)
                              Biochemical_activity                    // A physical interaction detection technique
                              Cocrystal_structure                     // A physical interaction detection technique
                              Far_western                             // A physical interaction detection technique
                              Protein_peptide                         // A physical interaction detection technique
                              Protein_RNA                             // A physical interaction detection technique
                              Reconstituted_complex                   // A physical interaction detection technique
                              Electrophoretic_mobility_shift_assay    // A physical interaction detection technique
                              Yeast_one_hybrid                        // A physical interaction detection technique (Protein-DNA)
                              Directed_yeast_one_hybrid               // A physical interaction detection technique (Protein-DNA)
                              Antibody                                // A regulatory interaction detection technique; Antibody name and details captured in Interactor_info hash
                              Reporter_gene ?Text                     // A regulatory interaction detection technique
                              Transgene                               // A regulatory interaction detection technique; Trasnsgene name and details captured in Interactor_info hash
                              In_situ Text                            // A regulatory interaction detection technique
                              Northern Text                           // A regulatory interaction detection technique
                              Western Text                            // A regulatory interaction detection technique
                              RT_PCR Text                             // A regulatory interaction detection technique
                              Other_method ?Text                      // A regulatory interaction detection technique
             Library_info Library_screened Text INT                   // In the context of Y2H or YH screens, for example, the library may have been cDNA library or a pool of clones
                          Origin From_laboratory UNIQUE ?Laboratory   // A library generated at an academic laboratory
                                 From_company UNIQUE ?Text            // A library generated at a company
             Regulation_level Transcriptional                         // Regulation occurs at the transcriptional level
                              Post_transcriptional                    // Regulation occurs at the post-transcriptional level
                              Post_translational                      // Regulation occurs at the post-translational level
             Regulation_result Positive_regulate #GR_condition
                               Negative_regulate #GR_condition
                               Does_not_regulate #GR_condition        // added to capture negative data [040220 krb]
             Confidence Description Text                              // Free text description of the confidence, e.g. "Core" vs "Noncore" (Vidal Interactome terms)
                        P_value UNIQUE Float                          // P-value confidence of interaction, if given
                        Log_likelihood_score UNIQUE Float             // Only used for Predicted interactions
             Throughput UNIQUE High_throughput                        // See BioGRID curation criteria for discussion
                               Low_throughput
             Interaction_RNAi ?RNAi XREF Interaction                  // RNAi experiment associated with the interaction
             Interaction_phenotype ?Phenotype XREF Interaction        // Phenotype associated with a genetic interaction
             Unaffiliated_variation ?Variation
             Unaffiliated_transgene ?Transgene
             Unaffiliated_antibody ?Antibody
             Unaffiliated_expr_pattern ?Expr_pattern
             Unaffiliated_construct ?Construct
             WBProcess ?WBProcess XREF Interaction                    // WormBase biological process associated with the interaction
             DB_info Database ?Database ?Database_field ?Text         // Any database reference to the interaction outside of WormBase, e.g. BioGRID, Interactome
             Paper ?Paper XREF Interaction
             Antibody_remark ?Text
             Historical_gene ?Gene Text
Remark ?Text #Evidence





#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 
		       Transgene ?Transgene XREF Interactor	   // Transgene XREF Interactor that carries an interacting gene //removed XREF from proposal
		       Construct ?Construct XREF Interactor
		       Antibody ?Antibody XREF Interactor	   // Free text description of the antibody used to detect a regulation event //removed XREF from proposal
		       Inferred_automatically Text                 // a script has updated this connection


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.

Gene_gene Interaction OA

Postgres Table Names

'Interaction ID'               = int_name

'Curator' = int_curator

'Process' = int_process

'Database Field Accession Number' = int_database

'Paper' = int_paper

'Interaction Type'             = int_type

'GI Module 1' = int_gimoduleone

'GI Module 2' = int_gimoduletwo

'GI Module 3' = int_gimodulethree

'Interaction Summary' = int_summary

'Remark' = int_remark

'Physical interaction detection method' = int_detectionmethod

'Library screened and times found' = int_library

'From Laboratory' = int_laboratory

'From Company' = int_company

'PCR Bait' = int_pcrbait

'PCR Target(s)' = int_pcrtarget

'Non-directional PCR(s) = int_pcrnondir

'Sequence Bait' = int_sequencebait

'Sequence Target(s)' = int_sequencetarget

'Non-directional Sequence(s)' = int_sequencenondir

'Feature Bait' = int_featurebait

'Feature Target' = int_featuretarget

'Bait overlapping CDS' = int_cdsbait

'Target overlapping CDS(s)' = int_cdstarget

'Non-directional overlapping CDS(s)' = int_cdsnondir

'Bait overlapping protein' = int_proteinbait

'Target overlapping protein' = int_proteintarget

'Non-directional overlapping protein' = int_proteinnondir

'Bait overlapping gene' = int_genebait

'Target overlapping gene' = int_genetarget

'Antibody' = int_antibody

'Antibody remark' = int_antibodyremark

'Non-directional Gene(s)' = int_genenondir

'Effector Gene(s)'             = int_geneone

'Affected Gene(s)' = int_genetwo

'Non-directional Rearrangement(s)' = int_rearrnondir

'Effector Rearrangement(s)' = int_rearrone

'Affected Rearrangement(s)' = int_rearrtwo

'Non-Directional Other' = int_othernondir

'Effector Other' = int_otherone

'Affected Other' = int_othertwo

'Large scale RNAi' = int_lsrnai

'RNAi' = int_rnai

'Interaction Phenotype(s)' = int_phenotype

'Expression pattern(s)' = int_exprpattern

'Non-directional Variation(s)' = int_variationnondir

'Effector Variation(s)'        = int_variationone

'Affected Variation(s)' = int_variationtwo

'Non-directional Molecule(s)' = int_moleculenondir

'Effector Molecule(s)' = int_moleculeone

'Affected Molecule(s)' = int_moleculetwo

'Transgene(s)' = int_transgene

'Construct' = int_construct

'Person'                       = int_person  

'Confidence description' = int_confidence

'P-value' = int_pvalue

'Log-likelihood score' = int_loglikelihood

'High_throughput' = int_throughput

'Sentence ID'                  = int_sentid        

'False Positive'               = int_falsepositive

Some Notes for gene_gene_interaction

Two Large Scale Interaction Data Sets

  • Files and scripts for these large scale datasets have been moved into a new directory:
/home/acedb/xiaodong/oa_interactions_dumper/Large_Scale_Interactions

-- CG 10-31-2012


  • WBPaper00027155 (Weiwei's science paper) has 23,128 objects, starting from WBInteraction000008637 and ending at WBInteraction000050578 (blank ids from WBInteraction000050579 to 000100000)
    • Original .ACE file (in old .ACE interaction format) on Tazendra here:
/home/acedb/xiaodong/oa_interactions_dumper/Large_Scale_Interactions/Original_Files/27155_interaction.ace
  • WBPaper00031465 (Lee's Nature Genetics paper) has 375,491 objects, starting from WBInteraction000100001, ending at WBInteraction000475491
    • Original .ACE file (in old .ACE interaction format) on Tazendra here:
/home/acedb/xiaodong/oa_interactions_dumper/Large_Scale_Interactions/Original_Files/31465_interaction.ace
  • The two large scale data sets have now been updated to the new interaction format (as of May 2013) and consolidated into a single file on Tazendra here:
/home/acedb/xiaodong/oa_interactions_dumper/Large_Scale_Interactions/Original_Large_Scale_Interactions_new_format.ace

The above file needs to be checked for dead genes before every upload by running the "historicGeneReplacementLSInteraction.pl" script in the same directory. Before running the script, make sure that the output file is appropriately named. The script prints all dead genes to the screen, so when running the script you may want to redirect the script output into a file so you can read the results later.


Directories on tazendra related to gene_gene_interaction (home/acedb/xiaodong)

  • assigning_interaction_ids
  • textpresso_ggi
  • interaction_ace_parsing
  • oa_interactions_dumper

The new Interaction OA, March 2012

TAB1

  • PGID Dumps as: N/A
  • Interaction ID (Ontology) int_name Dumps as: Interaction: <Interaction ID>
  • Curator - (Dropdown) int_curator Dumps as: N/A
  • Process - ?WBProcess (MultiOntology) int_process Dumps as: WBProcess <WBProcess>
  • Database, Field, & Accession Number - ?Database, Field, Accession_number (Free Text) int_database Dumps as: Database <Database> <Database_field> <Accession_number>
    • For single entries, surround the Database, Field, and Accession number entries with double quotes and separate them with spaces like so: "Database" "Database Field" "Accession Number"
    • If there are multiple entries, data to be entered like this: "Database 1" "Field 1" "Accession number 1" | "Database 2" "Field 2" "Accession number 2"
  • Paper - ?Paper (Ontology) int_paper Dumps as: Paper <Paper>
  • Person - ?Person (MultiOntology) int_person Dumps as: Remark <Remark_text> Person_evidence <Person>
    • If there is no Remark entry, dumps as: Remark "See Person Evidence" Person_evidence <Person>
  • Interaction Type - Text (Multiple-Dropdown) int_type
    • The options for Interaction Type will include:
    • NOTE: The Curation Status Form infers that genetic interaction(s) have been curated if the type is NOT physical or predicted
    • Physical Dumps as: Physical
    • Predicted Dumps as: Predicted
    • Genetic - Genetic interaction Dumps as: Genetic_interaction
    • Genetic - Negative genetic Dumps as: Negative_genetic
    • Genetic - Synthetic Dumps as: Synthetic
    • Genetic - Enhancement Dumps as: Enhancement
    • Genetic - Unilateral enhancement Dumps as: Unilateral_enhancement
    • Genetic - Mutual enhancement Dumps as: Mutual_enhancement
    • Genetic - Positive genetic Dumps as: Positive_genetic
    • Genetic - Suppression Dumps as: Suppression
    • Genetic - Complete suppression Dumps as: Complete_suppression
    • Genetic - Partial suppression Dumps as: Partial_suppression
    • Genetic - Unilateral suppression Dumps as: Unilateral_suppression
    • Genetic - Complete unilateral suppression Dumps as: Complete_unilateral_suppression
    • Genetic - Partial unilateral suppression Dumps as: Partial_unilateral_suppression
    • Genetic - Mutual suppression Dumps as: Mutual_suppression
    • Genetic - Complete mutual suppression Dumps as: Complete_mutual_suppression
    • Genetic - Partial mutual suppression Dumps as: Partial_mutual_suppression
    • Genetic - Asynthetic Dumps as: Asynthetic
    • Genetic - Suppression/Enhancement Dumps as: Suppression_enhancement
    • Genetic - Epistasis Dumps as: Epistasis
    • Genetic - Positive epistasis Dumps as: Positive_epistasis
    • Genetic - Maximal epistasis Dumps as: Maximal_epistasis
    • Genetic - Minimal epistasis Dumps as: Minimal_epistasis
    • Genetic - Neutral epistasis Dumps as: Neutral_epistasis
    • Genetic - Qualitative epistasis Dumps as: Qualitative_epistasis
    • Genetic - Opposing epistasis Dumps as: Opposing_epistasis
    • Genetic - Quantitative epistasis Dumps as: Quantitative_epistasis
    • Genetic - Neutral genetic Dumps as: Neutral_genetic
    • Genetic - Oversuppression Dumps as: Oversuppression
    • Genetic - Unilateral oversuppression Dumps as: Unilateral_oversuppression
    • Genetic - Mutual oversuppression Dumps as: Mutual_oversuppression
    • Genetic - Oversuppression/Enhancement Dumps as: Oversuppression_enhancement
    • Genetic - Phenotype bias Dumps as: Phenotype_bias
    • Genetic - No interaction Dumps as: No_interaction
  • GI Module 1 - Text (Dropdown) int_gimoduleone
    • GI Module 1 options are:
    • A_phenotypic Dumps as: A_phenotypic
    • Mono_phenotypic Dumps as: Mono_phenotypic
    • Cis_phenotypic Dumps as: Cis_phenotypic
    • Iso_phenotypic Dumps as: Iso_phenotypic
    • Trans_phenotypic Dumps as: Trans_phenotypic
  • GI Module 2 - Text (Dropdown) int_gimoduletwo
    • GI Module 2 options are:
    • Enhancing Dumps as: Enhancing
    • Suppressing Dumps as: Suppressing
    • Sub_suppressing Dumps as: Sub_suppressing
    • Inter_suppressing Dumps as: Inter_suppressing
    • Semi_suppressing Dumps as: Semi_suppressing
    • Co_suppressing Dumps as: Co_suppressing
    • All_suppressing Dumps as: All_suppressing
    • Super_suppressing Dumps as: Super_suppressing
    • Masking Dumps as: Masking
  • GI Module 3 - Text (Dropdown) int_gimodulethree
    • GI Module 3 options are:
    • Neutral Dumps as: Neutral
    • Non_neutral Dumps as: Non_neutral
    • Positive Dumps as: Positive
    • Negative Dumps as: Negative
    • Converging Dumps as: Converging
    • Diverging Dumps as: Diverging
  • Interaction Summary - bigtext int_summary Dumps as: Interaction_summary <Big_Text>
  • Remark - bigtext int_remark Dumps as: Remark <Big_Text>
  • Interaction phenotype(s) - ?Phenotype (MultiOntology) int_phenotype Dumps as: Interaction_phenotype <Phenotype>


Each interaction type can be considered necessarily directional, necessarily non-directional, or ambiguous. The OA dumping script will check to make sure that the correct interactor types (Non-directional, Effector, or Affected) are listed in each case and notify the curator during the dump in the error output file. Here are the directionalities for each interaction type:

Necessarily Directional:

  • Enhancement
  • Unilateral enhancement
  • Suppression
  • Complete suppression
  • Partial suppression
  • Unilateral suppression
  • Complete unilateral suppression
  • Partial unilateral suppression
  • Epistasis
  • Positive epistasis
  • Maximal epistasis
  • Minimal epistasis
  • Neutral epistasis
  • Qualitative epistasis
  • Opposing epistasis
  • Quantitative epistasis
  • Oversuppression
  • Unilateral oversuppression
  • Phenotype_bias


Necessarily Non-directional:

  • Predicted
  • Synthetic
  • Asynthetic
  • Mutual enhancement
  • Mutual suppression
  • Complete mutual suppression
  • Partial mutual suppression
  • Mutual oversuppression
  • Suppression enhancement
  • Oversuppression enhancement
  • No interaction


Ambiguous (ignore in dumping script):

  • Physical
  • Genetic interaction
  • Negative genetic
  • Positive genetic
  • Neutral genetic

TAB2

  • Physical interaction detection method (Multi-dropdown) int_detectionmethod
    • The detection method options are:
      • Affinity_capture_luminescence Dumps as: Affinity_capture_luminescence
      • Affinity_capture_MS Dumps as: Affinity_capture_MS
      • Affinity_capture_RNA Dumps as: Affinity_capture_RNA
      • Affinity_capture_Western Dumps as: Affinity_capture_Western
      • Chromatin_immunoprecipitation Dumps as: Chromatin_immunoprecipitation
      • Cofractionation Dumps as: Cofractionation
      • Colocalization Dumps as: Colocalization
      • Copurification Dumps as: Copurification
      • DNase_I_footprinting Dumps as: DNase_I_footprinting
      • Fluorescence_resonance_energy_transfer Dumps as: Fluorescence_resonance_energy_transfer
      • Protein_fragment_complementation_assay Dumps as: Protein_fragment_complementation_assay
      • Yeast_two_hybrid Dumps as: Yeast_two_hybrid
      • Biochemical_activity Dumps as: Biochemical_activity
      • Cocrystal_structure Dumps as: Cocrystal_structure
      • Far_western Dumps as: Far_western
      • Protein_peptide Dumps as: Protein_peptide
      • Protein_RNA Dumps as: Protein_RNA
      • Reconstituted_complex Dumps as: Reconstituted_complex
      • Yeast_one_hybrid Dumps as: Yeast_one_hybrid
      • Directed_yeast_one_hybrid Dumps as: Directed_yeast_one_hybrid
      • Electrophoretic_mobility_shift_assay Dumps as: Electrophoretic_mobility_shift_assay
  • Library screened/Times found - Text Text(Integer) int_library; separate multiple entries with pipes ('|') int_library Dumps as: Library_screened <Text> INT
    • For single entries, surround the 'Library screened' entry with double quotes and separate the number with a space like so: "Library screened" 3
    • For multiple entries, data should be entered as such: "Library screened 1" INT | "Library screened 2" INT
  • From Laboratory - ?Laboratory (ontology) int_laboratory Dumps as: From_laboratory <Laboratory>
  • From Company - Text; separate multiple entries with pipes ('|') int_company Dumps as: From_company <Text>
  • PCR Bait - ?PCR_product (Ontology) int_pcrbait Dumps as: PCR_interactor <PCR_product> Bait
  • PCR Target(s) - ?PCR_product (MultiOntology) int_pcrtarget Dumps as: PCR_interactor <PCR_product> Target
  • Non-directional PCR(s) - ?PCR_product (MultiOntology) int_pcrnondir Dumps as: PCR_interactor <PCR_product> Non_directional
  • Sequence Bait - ?Sequence (Free Text) int_sequencebait Dumps as: Sequence_interactor <Sequence> Bait
  • Sequence Target(s) - ?Sequence (Free Text); separate multiple entries with pipes ('|') int_sequencetarget Dumps as: Sequence_interactor <Sequence> Target
  • Non-directional Sequence(s) - ?Sequence (Free Text); separate multiple entries with pipes ('|') int_sequencenondir Dumps as: Sequence_interactor <Sequence> Non_directional
  • Feature Bait - ?Feature (MultiOntology) int_featurebait Dumps as: Feature_interactor <Feature> Bait
  • Feature Target - ?Feature (MultiOntology) int_featuretarget Dumps as: Feature_interactor <Feature> Target
  • Bait overlapping CDS - ?CDS (Free Text) int_cdsbait Dumps as: Interactor_overlapping_CDS <CDS> Bait
  • Target overlapping CDS(s) - ?CDS (Free Text); separate multiple entries with pipes ('|') int_cdstarget Dumps as: Interactor_overlapping_CDS <CDS> Target
  • Non-directional overlapping CDS(s) - ?CDS (Free Text); separate multiple entries with pipes ('|') int_cdsnondir Dumps as: Interactor_overlapping_CDS <CDS> Non_directional
  • Bait overlapping protein - ?Protein (Free Text) int_proteinbait Dumps as: Interactor_overlapping_protein <Protein> Bait
  • Target overlapping protein(s) - ?Protein (Free Text); separate multiple entries with pipes ('|') int_proteintarget Dumps as: Interactor_overlapping_protein <Protein> Target
  • Non-directional overlapping protein(s) - ?Protein (Free Text); separate multiple entries with pipes ('|') int_proteinnondir Dumps as: Interactor_overlapping_protein <Protein> Non_directional
  • Bait overlapping gene - ?Gene (Ontology) int_genebait Dumps as: Interactor_overlapping_gene <Gene> Bait
  • Target overlapping gene(s) - ?Gene (MultiOntology) int_genetarget Dumps as: Interactor_overlapping_gene <Gene> Target
  • Antibody - ?Antibody (MultiOntology) int_antibody Dumps as: Interactor_overlapping_gene <Mapped Gene> Antibody <Antibody> AND Antibody (on new line)
    • When mapping antibodies to genes, compare antibody-affiliated genes with those in the Non-directional Gene(s), Effector Gene(s), Affected Gene(s), Bait Overlapping Gene and Target Overlapping Gene fields
    • For Antibodies that don't map to a gene in the interaction, Dump as: Unaffiliated_antibody <Antibody>
  • Antibody remark - Big Text int_antibodyremark Dumps as: Antibody_remark <Big_Text>

TAB3

  • Non-directional Gene(s) - ?Gene (MultiOntology) int_genenondir Dumps as: Interactor_overlapping_gene <Gene> Non_directional
  • Effector Gene(s) - ?Gene (MultiOntology) int_geneone Dumps as: Interactor_overlapping_gene <Gene> Effector
  • Affected Gene(s) - ?Gene (MultiOntology) int_genetwo Dumps as: Interactor_overlapping_gene <Gene> Affected
  • Non-directional Variation(s) - ?Variation (MultiOntology) int_variationnondir
    • Dumps as: Variation_interactor <Variation> Non_directional
    • Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
    • Dumps as: Interactor_overlapping_gene <Mapped Gene> Non_directional
    • Variations that don't map to a gene will need to be assigned a gene at the ACEDB build stage; these objects will be indicated as such in the OA-dumper error output file
  • Effector Variation(s) - ?Variation (MultiOntology) int_variationone
    • Dumps as: Variation_interactor <Variation> Effector
    • Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
    • Dumps as: Interactor_overlapping_gene <Mapped Gene> Effector
    • Variations that don't map to a gene will need to be assigned a gene at the ACEDB build stage; these objects will be indicated as such in the OA-dumper error output file
  • Affected Variation(s) - ?Variation (MultiOntology) int_variationtwo
    • Dumps as: Variation_interactor <Variation> Affected
    • Genes for this field need to be mapped to a gene at the dump stage; Genes that map to the variation will be dumped as the "Interactor_overlapping_gene" as follows:
    • Dumps as: Interactor_overlapping_gene <Mapped Gene> Affected
    • Variations that don't map to a gene will need to be assigned a gene at the ACEDB build stage; these objects will be indicated as such in the OA-dumper error output file
  • Non-directional Molecule(s) - ?Molecule (MultiOntology) int_moleculenondir Dumps as: Molecule_interactor <Molecule> Non_directional
  • Effector Molecule(s) - ?Molecule (MultiOntology) int_moleculeone Dumps as: Molecule_interactor <Molecule> Effector
  • Affected Molecule(s) - ?Molecule (MultiOntology) int_moleculetwo Dumps as: Molecule_interactor <Molecule> Affected

TAB4

  • Non-directional Rearrangement(s) - ?Rearrangement (MultiOntology) int_rearrnondir Dumps as: Rearrangement <Rearrangement> Non_directional
  • Effector Rearrangement(s) - ?Rearrangement (MultiOntology) int_rearrone Dumps as: Rearrangement <Rearrangement> Effector
  • Affected Rearrangement(s) - ?Rearrangement (MultiOntology) int_rearrtwo Dumps as: Rearrangement <Rearrangement> Affected
  • RNAi - (MultiOntology) int_rnai Dumps as: Interaction_RNAi <RNAi>
  • Large scale RNAi - Free Text; separate multiple entries with pipes ('|') int_lsrnai (all large scale RNAi that doesn't match ontology) Dumps as: Interaction_RNAi <RNAi>
  • Expression pattern(s) - ?Expr_pattern (MultiOntology) int_exprpattern Dumps as: Interactor_overlapping_gene <Mapped Gene> Expr_pattern <Expr_pattern>
    • When mapping Expression patterns to genes, compare Expr-affiliated genes with those in the Non-directional Gene(s), Effector Gene(s), Affected Gene(s), Bait Overlapping Gene and Target Overlapping Gene fields
    • For Expression patterns that don't map to a gene in the interaction, Dump as: Unaffiliated_expr_pattern <Expr_pattern>
  • Transgene(s) - ?Transgene (MultiOntology) int_transgene Dumps as: Interactor_overlapping_gene <Mapped Gene> Transgene <Transgene> AND Transgene (on new line)
    • When mapping transgenes to genes, compare transgene-affiliated genes (from the Driven_by_gene, Gene, and 3'UTR fields of the associated ?Construct in the Construct OA) with those in the Non-directional Gene(s), Effector Gene(s), Affected Gene(s), Bait Overlapping Gene and Target Overlapping Gene fields
    • For Transgenes that don't map to a gene in the interaction, Dump as: Unaffiliated_transgene <Transgene>
  • Construct - ?Construct (MultiOntology) int_construct Dumps as: Interactor_overlapping_gene <Mapped Gene> Construct <Construct>
    • When mapping constructs to genes, compare construct-affiliated genes (from the Driven_by_gene, Gene, and 3'UTR fields of the ?Construct in the Construct OA) with those in the Non-directional Gene(s), Effector Gene(s), Affected Gene(s), Bait Overlapping Gene and Target Overlapping Gene fields
    • For Constructs that don't map to a gene in the interaction, Dump as: Unaffiliated_construct <Construct>
  • Non-Directional Other - ?Text int_othernondir Dumps as: Other_interactor <Text> Non_directional
  • Effector Other - ?Text int_otherone Dumps as: Other_interactor <Text> Effector
  • Affected Other - ?Text int_othertwo Dumps as: Other_interactor <Text> Affected

TAB5

  • Confidence description - Text int_confidence Dumps as: Description <Text>
  • P-value - Text (Float) int_pvalue Dumps as: P_value FLOAT
  • Log-likelihood score - Text (Float) int_loglikelihood Dumps as: Log_likelihood_score FLOAT
  • High_throughput - (Toggle) int_throughput:
    • If ON, dumps as: High_throughput
    • If OFF (default), dumps as: Low_throughput
  • Sentence ID - (Ontology) sentence shows in term info; int_sentid Dumps as: N/A
  • False Positive - toggle, will not give an id or no dump if the sentence is false positive, containing no interaction info; int_falsepositive Dumps as: N/A
  • Community Curator - int_communitycurator
  • Community Curator Email - int_communitycuratoremail
  • Needs Review - (Toggle) int_needsreview (Flagging only)

To go live on tazendra

To create new interaction tables on tazendra : /home/postgres/work/pgpopulation/interaction/20120527_OA_newModel/create_datatype_tables.pl

Backup relevant tables : /home/postgres/work/pgpopulation/interaction/20120527_OA_newModel/backupTable.pl

To transfer data from old interaction model tables to new interaction model tables and table formats : /home/postgres/work/pgpopulation/interaction/20120527_OA_newModel/transfer_int_data.pl


Instructions on How to Use the New OA

The new Interaction OA is intended to be used by curators for curating physical, predicted and genetic interactions. This is an overview of the key points to keep in mind while curating with the Interaction OA.

1) TAB 1 is for general information, TAB 2 is for physical interactions, TAB 3 & TAB 4 are for genetic and predicted interactions, and TAB5 is for detailed (and rarely used) information


TAB 1

2) Interaction IDs are generated automatically when the "New" button is clicked; new Postgres IDs (PGIDs) are generated automatically as well. If you would like to duplicate objects (because you are generating several similar interaction objects) and assign new IDs to them, select the interaction to duplicate and click the "Duplicate" button; this will generate a new PGID and OA row, but carry the same Interaction ID over from the duplicated interaction. If the new row should be a distinct interaction, delete the interaction ID from the Interaction ID field, and a cron job will assign an Interaction ID to that row the following evening. Note that if you leave any rows without an Interaction ID overnight, they will be each assigned a unique (and new) Interaction ID.


3) Entering Database information: Database information is typically provided with three pieces of information: the Database, the Database field name, and the Database Accession number for the interaction in question. These must be each entered surrounded by double quotes (") and separated with spaces. So for example: 

"Database" "Database Field" "Accession Number"

If mulitiple database references are to be made, split on pipes ("|") like this: 

"Database 1" "Database Field 1" "Accession Number 1"   |   "Database 2" "Database Field 2" "Accession Number 2"

In the (unlikely) event that any of the field entries have double quotes (") in the name itself, then the 'inner' double quotes will need to be escaped with a backslash ("\") like this: 

"Database \"Supreme!!!!\""   "Database \"Field\""   "Accession \"Number\""

so that it will be read in ACEDB as: 

Database "Supreme!!!!"     Database "Field"     Accession "Number"


4) The Person field is for Person evidence, when no other reference (such as a WormBase paper) is supplied as a reference. This will be dumped as a hash/supplement to the "Remark" entry, so it is advantageous to include any pertinent information there.


TAB 2

5) The "Library screens and Times found" field is for documenting screening/testing libraries that were used to identify a physical interaction. For example, a cDNA library may be used in a Yeast Two Hybrid screen to identify protein interaction partners with a "Bait" protein. Sometimes (but not always) authors might report the number of times a particular interaction was identified using a particular library. If not, enter the name of the library with double quotes (") like so: 

"cDNA"

if multiple libraries (but no numbers), split on pipes like this: 

"cDNA"    |    "ORFeome"

If a single libary, with a number (for number of times found): 

"AD-TF mini-library" 5

and if multiple libraries, with numbers: 

"AD-TF mini-library" 5   |   "AD-wrmcDNA library" 1

As with the Database field entries, if (for some reason) the name of the library has double quotes (") in the name itself, the double quotes will need to be escaped like this: 

"AD-TF \"Mini\" library" 5

so that the library name eventually reads like this: 

AD-TF "Mini" library


6) Sequence fields: "Sequence Bait", "Sequence Target(s)", and "Non-directional Sequence(s)"

To enter a single sequence object, type in the sequence object name, no quotes: 

CK583862

For multiple sequence objects, split on pipes ("|"): 

CK583862   |   CK583870


The same rules apply for Protein and CDS objects.


7) The Non-directional fields; For each type of interaction object, there is a "Non-directional" field, allowing a curator to enter all interactors of that type for a Non-directional type of interaction. Note that the "Non-directional Genes" field (which could apply to physical, genetic, and predicted interactions) lies in TAB 3.


8) For Directional interactions, there are "Bait" and "Target" fields for physical interactions (TAB 2) and "Effector" and "Affected" fields for genetic interactions (TAB 3).


TAB 3

9) Effector Variation(s), Affected Variation(s), and Non-directional Variation(s) fields are for variations that implicate an affiliated gene as an effector or affected interactor in a directional genetic interaction or non-directional interactors in a non-directional interaction. These fields can be populated without the need to populate the respective gene in the relevant gene field, as the dumping script (or build process) will make the appropriate associations.

TAB 4

10) The RNAi fields: There are two fields for references to RNAi objects: "RNAi" and "Large scale RNAi". The reason for two fields is that one field ("RNAi") is an ontology field reading off of RNAi experiments that live in the RNAi OA and Postgres. As RNAi experiments from papers containing 2,000 or more RNAi experiments (WBPaper00029258 for example) were excluded from the RNAi OA for performance reasons, any RNAi experiments from such papers will not be recognized by the "RNAi" ontology field, and therefore must be entered as free-text in the "Large scale RNAi" field.


11) The Transgene(s) field is for transgenes involved in the interaction, regardless of whether it is related to an "Effector" gene or "Affected" gene or the interaction is Non-directional. The dumping script will automatically associate the transgene with the appropriate interacting gene and dump in .ACE format accordingly.


12) Non-Directional Other, Effector Other, and Affected Other fields: these fields allow for the curation of entities that don't exists as proper WormBase/ACEDB objects, for example transgenes that only express human proteins, or experimental conditions or treatments (e.g. "Ionizing radiation") that are interactors

TAB 5

13) Confidence description: This field will capture free-text descriptions of the confidence the authors suggest they have for this interaction. In the Yeast Two Hybrid experiments, for example, the interaction may be described as "Interactome Core 1", "Interactome Core 2", or "Interactome Noncore" referring to the varying degrees of confidence for those interactions.


14) The P-value and Log-likelihood score fields are mostly to capture confidence values for predicted interactions that have been reported.


15) High_throughput toggle field is intended to capture whether or not the interaction was observed as one of several (50 - 1000s) interactions and thus should be interpreted with caution, or at least acknowledged as from a large scale experiment. The default is OFF and indicates that the experiment is low throughput.


16) The Sentence ID and False Positve fields are exclusively for Textpresso sentence-based curation

Nightly Cron Job to Assign New Interaction IDs

Every night at 4am a cron job script will run to assign new Interaction IDs to any row/PGID in the Interaction OA that does not already have an Interaction ID and that meets a few criteria. The script is located on Tazendra here:

/home/acedb/xiaodong/assigning_interaction_ids/assign_interaction_ids.pl

and the criteria for getting a new Interaction ID are as follows:

1) The curator of the interaction object/PGID is NOT Arun

2) The interaction object/PGID does NOT already have an Interaction ID

3) The interaction object/PGID is NOT flagged as False Positive

Any interactions/PGIDs that meet these three criteria will be assigned a new Interaction ID by the cron job.


Interaction OA .ACE Dumper

The script for the interaction OA dumper is located on Tazendra at: 

/home/postgres/work/citace_upload/interaction/use_package.pl*


Error Checks During Dump Process

The following is a list of checks that the .ACE dumper script will perform on all interactions being dumped out of the OA to make sure that the data is consistent and doesn't have any nonsensical information:

Fatal Errors (Interactions will not get dumped)

1) If there are fewer than two interactors in an interaction, the dumper script will generate an error message that is printed to the ERROR output file and the object will not get dumped. This is determined by checking that:

a) There is at least one "Bait" entry and one "Target" entry OR

b) There is at least one "Effector" and one "Affected" entry OR

c) There is at least two "Non-directional" entries

If none of these conditions hold true, then an error message will be printed in tab-delimited format like this: 

PGID  <TAB>  Dump_status  <TAB>  Curator ID  <TAB>  Explanation

so, for example: 

12345   nodump    WBPerson1234   There are not two interactors


2) If there is no reference (Paper or Person) then the object will not get dumped and an error message is printed: 

PGID  <TAB>  Dump_status  <TAB>  Curator ID  <TAB>  Explanation

so, for example: 

12345   nodump    WBPerson1234   There is no reference, neither paper nor person


3) If there are incompatible interactor types, the interaction object will not get dumped. This means that the object will not get dumped if the following conditions are not met:

a) If there is a "Non-directional" entry, there are no "Effector", "Affected", "Bait", or "Target" entries AND

b) If there is an "Effector" entry, there is at least one "Affected" entry AND there are no "Non-directional", "Bait", or "Target" entries AND

c) If there is an "Affected" entry, there is at least one "Effector" entry AND there are no "Non-directional", "Bait", or "Target" entries AND

d) If there is a "Bait" entry, there is at least one "Target" entry AND there are no "Non-directional", "Effector", or "Affected" entries AND

e) If there is a "Target" entry, there is at least one "Bait" entry AND there are no "Non-directional", "Effector", or "Affected" entries

If these conditions are not met, the object will not get dumped and an error message will print to the ERROR output file like this: 

PGID  <TAB>  Dump_status  <TAB>  Curator ID  <TAB>  Explanation

so, for example: 

12345   nodump    WBPerson1234   has nondiretional + bait
12345   nodump    WBPerson1234   has nondiretional + target
12345   nodump    WBPerson1234   has nondiretional + effected
12345   nodump    WBPerson1234   has nondiretional + effector
12345   nodump    WBPerson1234   has effector but no effected
12345   nodump    WBPerson1234   has effector + bait
12345   nodump    WBPerson1234   has effector + target
12345   nodump    WBPerson1234   has effected + bait
12345   nodump    WBPerson1234   has effected + target
12345   nodump    WBPerson1234   has bait but no target


4) If there is no Interaction ID, the object will not get dumped and an error message will print to the ERROR output file like this: 

PGID  <TAB>  Dump_status  <TAB>  Curator ID  <TAB>  Explanation

so, for example: 

12345   nodump    WBPerson1234   There is no Interaction ID

The script will determine this by 1) generating a list of all PGIDs from the Interaction OA, 2) Removing all PGIDs where Arun is the curator, and then 3) looking for any PGIDs for which there is no Interaction ID. As there is a cronjob to add Interaction IDs to any PGIDs (Postgres rows) that are missing IDs, this problem should be rare (unless objects have been added that day (before the next cronjob) without Interaction IDs).


5) If there is no Interaction Type, the object will not get dumped and an error message will print to the ERROR output file like this: 

PGID  <TAB>  Dump_status  <TAB>  Curator ID  <TAB>  Explanation

so, for example: 

12345   nodump    WBPerson1234   There is no Interaction Type


6) If there is an Interaction object that exists on multiple Postgres lines/rows (i.e. the same Interaction ID with multiple PGIDs), the object will not get dumped and an error message will print to the ERROR output file like this: 

PGID  <TAB>  Dump_status  <TAB>  Curator ID  <TAB>  Explanation

so, for example: 

12345   nodump    WBPerson1234   WBInteraction000123456 exists across multiple lines

Non-Fatal Errors (Interactions will get dumped, but error message will get printed)

1) If there is a Variation, Expression pattern, Transgene, or Antibody that cannot be matched to a gene interactor, the object will be identified as "Unaffiliated" in the .ACE file and an error message will print to the ERROR output file like this: 

PGID  <TAB>  Dump_status  <TAB>  Curator ID  <TAB>  Interaction ID  <TAB>  Unaffiliated Object  <TAB>  Object Name

so, for example: 

12345   lineonly    WBPerson1234   WBInteraction000123456   Unaffiliated_variation     WBVar00600763
12345   lineonly    WBPerson1234   WBInteraction000123456   Unaffiliated_transgene     kyEx456
12345   lineonly    WBPerson1234   WBInteraction000123456   Unaffiliated_antibody      [cgc2826]:hlh-2
12345   lineonly    WBPerson1234   WBInteraction000123456   Unaffiliated_expr_pattern  Expr1234


2) If there is an inconsistency between the directionality of the Interaction Type and the Interactors, the interaction object will get dumped to the .ACE file, but an error message will print to the ERROR output file like this: 

PGID  <TAB>  Dump_status  <TAB>  Curator ID  <TAB>  Explanation

so, for example: 

12345   flagonly   WBPerson1234   has diretional type Enhancement + nondirectional data
12345   flagonly   WBPerson1234   has diretional type Epistasis + nondirectional data
12345   flagonly   WBPerson1234   has diretional type Suppression + nondirectional data
12345   flagonly   WBPerson1234   has nondiretional type Mutual_enhancement + effected data
12345   flagonly   WBPerson1234   has nondiretional type Mutual_enhancement + effector data
12345   flagonly   WBPerson1234   has nondiretional type Mutual_suppression + effector data
12345   flagonly   WBPerson1234   has nondiretional type No_interaction + effected data
12345   flagonly   WBPerson1234   has nondiretional type Synthetic + effector data


3) If no curator is listed for the interaction, the interaction object will get dumped, but an error message will print to the ERROR output file like this: 

PGID  <TAB>  Dump_status  <TAB>  Curator ID  <TAB>  Explanation

so, for example: 

12345   flagonly   no curator   has no curator


Handling Dead Genes During Dump Process

The dumper script will now (as of May, 2013) run an automatic check for dead genes in any gene field. Any genes that are considered dead that are referenced in an Interaction object in the OA will be handled in the following manner:

1) If there is a replacement for the gene (i.e. the gene has merged into another gene), the dead gene will be dumped into a "Historical_gene" field in the .ACE file, the replacement gene will fill the original gene field. A comment will be added to the Historical_gene field via a 'Text' tag (updated as of 3-18-2015). The original gene field (now with the updated gene reference) will be printed with an "Inferred_automatically" tag after the gene. So, for example, if WBGene00001234 is now a dead gene that has been merged into WBGene00002345: 

Gene  "WBGene00001234"

becomes 

Gene  "WBGene00002345"  Inferred_automatically
Historical_gene  "WBGene00001234"  "Note: This object originally referred to WBGene00001234.
WBGene00001234 is now considered dead and has been merged into WBGene00002345. WBGene00002345 has 
replaced WBGene00001234 accordingly."

Also, since Antibodies, Transgenes, Expression patterns, Variations are mapped to an interactor where possible (or else they are dumped as "Unaffiliated"), this mapping will now occur to only the newest genes that the interactor refers to.

2) If there is no replacement for the gene (Dead or Suppressed), we would dump the following: 

Gene  "WBGene00001234"
Historical_gene  "WBGene00001234"  "Note: This object originally referred to a gene
 (WBGene00001234) that is now considered dead. Please interpret with discretion."

OR 

Gene  "WBGene00001234"
Historical_gene  "WBGene00001234"  "Note: This object originally referred to a gene
 (WBGene00001234) that has been suppressed. Please interpret with discretion."

and lastly,

3) If the gene has undergone a split, such genes will be dumped as: 

Gene  "WBGene00001234"
Historical_gene  "WBGene00001234"  "Note: This object originally referred to a gene 
(WBGene00001234) that is now considered split. Please interpret with discretion."

and also printed out in the error output file of the dumping script for a curator to go back and manually change according to best judgement.


Gene Examples:
A split gene: WBGene00012507
A merged gene: WBGene00007524
A dead gene: WBGene00007814
A suppressed gene: WBGene00015490

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