WS244 Models.wrm

From WormBaseWiki
Jump to: navigation, search

Model changes for WS244

  • This cycle we see 5 model changes in 4 classes:

1) ?Clone - extension to incorporate the AddGene data

2) ?Interaction - tag addition and tag name change

3) ?RNAi - connection to ?Clone

4) ?Expression_cluster - Mass_spectrometry tag addition.


Full diff file

cvs diff: Diffing .
Index: models.wrm
===================================================================
RCS file: /nfs/ensembl/cvsroot/wormbase/wspec/models.wrm,v
retrieving revision 1.403
retrieving revision 1.406
diff -r1.403 -r1.406
17c17
< // Last edited on: $Date: 2014-03-14 12:38:51 $
---
> // Last edited on: $Date: 2014-05-10 09:56:35 $
62c62
< 		 Gene  ?Gene XREF Map
---
> 		 Gene ?Gene XREF Map
69c69
<                  Transgene  ?Transgene //sdm added to display gmaps //removed XREF ky 2011 
---
>                  Transgene ?Transgene //sdm added to display gmaps //removed XREF ky 2011 
78c78
< 			Multi_Position  Float #Map_error
---
> 			Multi_Position Float #Map_error
156c156
< 			Point_pe  #Colour // positive, error
---
> 			Point_pe #Colour  // positive, error
158c158
<                 	Point_ne  #Colour // negative, error
---
>                 	Point_ne #Colour  // negative, error
208c208
< 			Pe  #Colour // positive, error
---
> 			Pe #Colour  // positive, error
210c210
<                 	Ne  #Colour // negative, error
---
>                 	Ne #Colour  // negative, error
234c234
<                 Main_name  ?Gene_class XREF Other_name
---
>                 Main_name ?Gene_class XREF Other_name
250,256c250,256
<         Type	Polymorphism    SNP  Text       // Todd [171001 krb]
<                                 Status Text
<                                 SNP_assay ?PCR_product XREF SNP_locus ?Text
<                                 RFLP    Text
<                                 Transposon_insertion  Text
<                                 Detection_method Text
<         Map    UNIQUE ?Map XREF Locus #Map_position
---
>         Type Polymorphism    SNP Text        // Todd [171001 krb]
>                              Status Text
>                              SNP_assay ?PCR_product XREF SNP_locus ?Text
>                              RFLP Text
>                              Transposon_insertion Text
>                              Detection_method Text
>         Map UNIQUE ?Map XREF Locus #Map_position
278,294c278,294
<         Identity  Version UNIQUE Int
<                   Name  CGC_name        UNIQUE ?Gene_name XREF CGC_name_for #Evidence
<                         Sequence_name   UNIQUE ?Gene_name XREF Sequence_name_for // captures main CDS name without isoforms
< 			Molecular_name         ?Gene_name XREF Molecular_name_for  // for linking to full CDS names, wormpep etc.
<                         Other_name             ?Gene_name XREF Other_name_for #Evidence // other unapproved CGC-style gene names
<                         Public_name     UNIQUE ?Gene_name XREF Public_name_for // the one name that should be used
< 		  DB_info Database ?Database ?Database_field ?Text
<                   Species UNIQUE ?Species
<                   History Version_change Int UNIQUE DateType UNIQUE ?Person #Gene_history_action
<                           Merged_into UNIQUE ?Gene XREF Acquires_merge
<                           Acquires_merge ?Gene XREF Merged_into
<                           Split_from UNIQUE ?Gene XREF Split_into
<                           Split_into ?Gene XREF Split_from
< 			  Transposon_in_origin // for genes that are identified as having CDSs/Proteins that are Transposon in origin
< 		  Status UNIQUE Live #Evidence
<                                 Suppressed #Evidence
<                                 Dead #Evidence   
---
>         Identity Version UNIQUE Int
>                  Name  CGC_name UNIQUE ?Gene_name XREF CGC_name_for #Evidence
>                        Sequence_name UNIQUE ?Gene_name XREF Sequence_name_for // captures main CDS name without isoforms
> 		       Molecular_name ?Gene_name XREF Molecular_name_for      // for linking to full CDS names, wormpep etc.
>                        Other_name ?Gene_name XREF Other_name_for #Evidence    // other unapproved CGC-style gene names
>                        Public_name UNIQUE ?Gene_name XREF Public_name_for     // the one name that should be used
> 		 DB_info Database ?Database ?Database_field ?Text
>                  Species UNIQUE ?Species
>                  History Version_change Int UNIQUE DateType UNIQUE ?Person #Gene_history_action
>                          Merged_into UNIQUE ?Gene XREF Acquires_merge
>                          Acquires_merge ?Gene XREF Merged_into
>                          Split_from UNIQUE ?Gene XREF Split_into
>                          Split_into ?Gene XREF Split_from
> 			 Transposon_in_origin // for genes that are identified as having CDSs/Proteins that are Transposon in origin
> 		 Status UNIQUE Live #Evidence
>                                Suppressed #Evidence
>                                Dead #Evidence   
305c305
< 		  RNASeq_FPKM  ?Life_stage  Float  #Evidence
---
> 		  RNASeq_FPKM ?Life_stage Float #Evidence
310c310
< 		  Ortholog_other  ?Protein XREF Ortholog_gene #Evidence // to allow Orthologues links to none ?Gene genes eg remanei (ar2 Nov06)
---
> 		  Ortholog_other ?Protein XREF Ortholog_gene #Evidence // to allow Orthologues links to none ?Gene genes eg remanei (ar2 Nov06)
321,323c321,323
< 	Disease_info 	Experimental_model ?DO_term XREF Gene_by_biology   ?Species   #Evidence	            
< 			Potential_model	   ?DO_term XREF Gene_by_orthology ?Species #Evidence
< 			Disease_relevance  ?Text ?Species #Evidence
---
> 	Disease_info Experimental_model ?DO_term XREF Gene_by_biology ?Species #Evidence	            
> 		     Potential_model ?DO_term XREF Gene_by_orthology ?Species #Evidence
> 		     Disease_relevance ?Text ?Species #Evidence
353c353
<                   Positive Inside_rearr   ?Rearrangement XREF Gene_inside #Evidence
---
>                   Positive Inside_rearr ?Rearrangement XREF Gene_inside #Evidence
355c355
<                   Negative Outside_rearr  ?Rearrangement XREF Gene_outside #Evidence
---
>                   Negative Outside_rearr ?Rearrangement XREF Gene_outside #Evidence
365d364
< 	
415,416c414,415
< ?Gene_name CGC_name_for       ?Gene XREF CGC_name
<            Sequence_name_for  ?Gene XREF Sequence_name
---
> ?Gene_name CGC_name_for ?Gene XREF CGC_name
>            Sequence_name_for ?Gene XREF Sequence_name
418,420c417,419
<            Other_name_for     ?Gene XREF Other_name     // main reason for this class
<            Former_member_of   ?Gene_class XREF Old_member // track old members of a class
<            Public_name_for    ?Gene XREF Public_name    // the main name for a gene
---
>            Other_name_for ?Gene XREF Other_name     // main reason for this class
>            Former_member_of ?Gene_class XREF Old_member // track old members of a class
>            Public_name_for ?Gene XREF Public_name    // the main name for a gene
471,474c470,473
< 		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 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
476,479c475,478
< 			   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
< 			   Rearrangement  ?Rearrangement XREF Interactor #Interactor_info
---
> 			   Molecule_interactor ?Molecule XREF Interaction #Interactor_info     // Molecule that regulates a gene or protein (ported from Gene_regulation Class) Modified Chris WS244
> 			   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
> 			   Rearrangement ?Rearrangement XREF Interactor #Interactor_info
482,518c481,518
< 		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
< 				 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
< 		Deviation_from_expectation Text				  // A text description of the way in which the phenotype deviated from expectation in genetic interactions	
< 		Neutrality_function UNIQUE Multiplicative		  // The multiplicative neutrality function defines expectation as the product of two quantified phenotypes (relative to wild type) 
< 					   Additive		          // The additive neutrality function defines expectation as the sum of two quantified phenotypes (relative to wild type) 
< 					   Minimal		          // The minimal neutrality function defines expectation as the most severe of two quantified phenotypes (relative to wild type) 
< 		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
---
> 		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
> 				 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
> 				 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
> 		Deviation_from_expectation Text                          // A text description of the way in which the phenotype deviated from expectation in genetic interactions	
> 		Neutrality_function UNIQUE Multiplicative                // The multiplicative neutrality function defines expectation as the product of two quantified phenotypes (relative to wild type) 
> 					   Additive                      // The additive neutrality function defines expectation as the sum of two quantified phenotypes (relative to wild type) 
> 					   Minimal                       // The minimal neutrality function defines expectation as the most severe of two quantified phenotypes (relative to wild type) 
> 		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
521,525c521,525
< 				  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
---
> 				  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
527,534c527,534
< 		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
< 		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
---
> 		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
> 		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
537c537
< 		Historical_gene   ?Gene #Evidence
---
> 		Historical_gene ?Gene #Evidence
551,552c551,552
< 		       Intragenic_effector_variation   ?Variation   XREF   Interactor
< 		       Intragenic_affected_variation   ?Variation   XREF   Interactor
---
> 		       Intragenic_effector_variation ?Variation XREF Interactor
> 		       Intragenic_affected_variation ?Variation XREF Interactor
600c600
< 				Source_rearrangement  ?Rearrangement XREF Derived_rearrangement
---
> 				Source_rearrangement ?Rearrangement XREF Derived_rearrangement
602,603c602,603
<                 Map     ?Map XREF Rearrangement #Map_position
< 		Positive Gene_inside  ?Gene  XREF Inside_rearr #Evidence
---
>                 Map ?Map XREF Rearrangement #Map_position
> 		Positive Gene_inside ?Gene XREF Inside_rearr #Evidence
605c605
< 			 Clone_inside  ?Clone XREF Inside_rearr ?Author
---
> 			 Clone_inside ?Clone XREF Inside_rearr ?Author
607c607
< 		Negative Gene_outside  ?Gene  XREF Outside_rearr #Evidence
---
> 		Negative Gene_outside ?Gene XREF Outside_rearr #Evidence
618c618
< 	        Strain   ?Strain XREF Rearrangement
---
> 	        Strain ?Strain XREF Rearrangement
630,645c630,645
< 	 Contains  Gene	 ?Gene XREF Strain
< 	  	   Variation  ?Variation XREF Strain 
< 		   Rearrangement	 ?Rearrangement XREF Strain
<                    Clone ?Clone XREF In_strain		  
< 		   Transgene ?Transgene XREF Strain
< 	 Properties  Inbreeding_state UNIQUE Selfed Text
<                                              Isofemale Text
<                                              Multifemale Text
<                                              Inbred Text 
< 		     Outcrossed Text
< 		     Mutagen Text
< 		     Strain_history Text
< 		     Date_first_frozen UNIQUE DateType
< 		     CGC_received DateType
< 		     Phenotype ?Phenotype XREF Strain #Phenotype_info
< 		     Phenotype_not_observed ?Phenotype XREF Not_in_Strain #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes 
---
> 	 Contains Gene	 ?Gene XREF Strain
> 	  	  Variation ?Variation XREF Strain 
> 		  Rearrangement	 ?Rearrangement XREF Strain
>                   Clone ?Clone XREF In_strain		  
> 		  Transgene ?Transgene XREF Strain
> 	 Properties Inbreeding_state UNIQUE Selfed Text
>                                             Isofemale Text
>                                             Multifemale Text
>                                             Inbred Text 
> 		    Outcrossed Text
> 		    Mutagen Text
> 		    Strain_history Text
> 		    Date_first_frozen UNIQUE DateType
> 		    CGC_received DateType
> 		    Phenotype ?Phenotype XREF Strain #Phenotype_info
> 		    Phenotype_not_observed ?Phenotype XREF Not_in_Strain #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes 
686,689c686,689
< ?Lab_Location	Freezer		Text
< 		LiquidN2        Text
< 		Minus70		Text
<                 Remark		?Text #Evidence
---
> ?Lab_Location	Freezer	Text
> 		LiquidN2 Text
> 		Minus70	Text
>                 Remark ?Text #Evidence
693c693
< // ##                 worm physical map classes                 ##
---
> //                    worm physical map classes
697a698
> //
698a700,701
> // Class extended to incorporate AddGene data for WS244
> //
701a705,709
> 	Species UNIQUE ?Species
>   	Reference ?Paper XREF Clone
> 	Produced_by Person ?Person              // Paul D. WS244
> 		    Author ?Author              // Paul D. WS244
> 	Sequence ?Sequence XREF Clone
705,714c713,721
< 	Position  Map ?Map XREF Clone #Map_position
<         	  pMap UNIQUE  ?Contig XREF Clone  UNIQUE Int UNIQUE Int 
< 						// pMap units are bands
< 		  Clone_left_end ?Sequence	// filled by XREF
< 		  Clone_right_end ?Sequence	// filled by XREF
< 		  Pos_neg_data ?Pos_neg_data
< 	Positive Positive_gene   ?Gene XREF Positive_clone
< 		 Positive_variation  ?Variation XREF Positive_clone ?Author
< 		 Inside_rearr    ?Rearrangement XREF Clone_inside ?Author
< 		 Hybridizes_to   ?Clone XREF Positive_probe ?Grid
---
> 	Position Map ?Map XREF Clone #Map_position
>                  pMap UNIQUE ?Contig XREF Clone UNIQUE Int UNIQUE Int // pMap units are bands
>                  Clone_left_end ?Sequence	// filled by XREF
>                  Clone_right_end ?Sequence	// filled by XREF
>                  Pos_neg_data ?Pos_neg_data
> 	Positive Positive_gene ?Gene XREF Positive_clone
> 		 Positive_variation ?Variation XREF Positive_clone ?Author
> 		 Inside_rearr ?Rearrangement XREF Clone_inside ?Author
> 		 Hybridizes_to ?Clone XREF Positive_probe ?Grid
716,721c723,728
< 		 Positive_probe  ?Clone XREF Hybridizes_to ?Grid
< 		 Pos_probe_weak  ?Clone XREF Hybridizes_weak ?Grid
< 	Negative Negative_gene   ?Gene XREF Negative_clone
< 		 Negative_locus  ?Locus XREF Negative_clone ?Author
< 		 Outside_rearr   ?Rearrangement XREF Clone_outside ?Author
< 		 Negative_probe  ?Clone XREF Does_not_hybridize_to ?Grid
---
> 		 Positive_probe ?Clone XREF Hybridizes_to ?Grid
> 		 Pos_probe_weak ?Clone XREF Hybridizes_weak ?Grid
> 	Negative Negative_gene ?Gene XREF Negative_clone
> 		 Negative_locus ?Locus XREF Negative_clone ?Author
> 		 Outside_rearr ?Rearrangement XREF Clone_outside ?Author
> 		 Negative_probe ?Clone XREF Does_not_hybridize_to ?Grid
724,725c731
< 	Species UNIQUE ?Species
< 	Sequence    ?Sequence XREF Clone
---
> 	Mutation ?Text                                  // Paul D. WS244
727,728c733,739
< 	Length	Seq_length UNIQUE Int 			// bp
< 		Gel_length UNIQUE Float			// Kb
---
> 	Primer1 ?Text                                   // Paul D. WS244
> 	Primer2 ?Text                                   // Paul D. WS244
> 	Resistance_marker ?Text                         // Paul D. WS244
> 	Length	Seq_length UNIQUE Int                   // bp
> 		Gel_length UNIQUE Float                 // Kb
> 		Insert UNIQUE Int                       // bp Paul D. WS244
> 		Backbone UNIQUE Int                     // bp Paul D. WS244
739,740c750,751
<                         Bands   UNIQUE Int UNIQUE Int
<                         Gel ?Motif  #Lane               // Magic tag2 construct
---
>                         Bands UNIQUE Int UNIQUE Int
>                         Gel ?Motif #Lane               // Magic tag2 construct
743c754
< 		In_Situ  UNIQUE Int UNIQUE Int // percent of physical chromosome
---
> 		In_Situ UNIQUE Int UNIQUE Int // percent of physical chromosome
746c757
< 	        Flag    UNIQUE Int
---
> 	        Flag UNIQUE Int
749d759
<   	Reference ?Paper XREF Clone
753a764
> 	Used_in_RNAi ?RNAi XREF Clone           // Chris WS244
765c776,779
<         Derived_from	?Clone
---
> 	Vector_type ?Text
>         Derived_from ?Clone XREF Parent_of
> 	Parent_of ?Clone XREF Derived_from
> 	Ligation ?Text
768c782
<              Band_Lengths  UNIQUE Float REPEAT // in mm: if you prefer to minimise the ace format
---
>              Band_Lengths UNIQUE Float REPEAT // in mm: if you prefer to minimise the ace format
789c803
< 			    Date  UNIQUE DateType
---
> 			    Date UNIQUE DateType
830,831c844,845
< 		Genotype  UNIQUE Text
< 		Results  UNIQUE Text
---
> 		Genotype UNIQUE Text
> 		Results UNIQUE Text
834c848
< 				Date  UNIQUE DateType
---
> 				Date UNIQUE DateType
836,837c850,851
< 		Point_1 UNIQUE Gene_1   UNIQUE ?Gene  XREF 2_point UNIQUE ?Variation XREF In_2_point
< 			       Locus_1	UNIQUE ?Locus XREF 2_point UNIQUE ?Variation XREF In_2_point
---
> 		Point_1 UNIQUE Gene_1 UNIQUE ?Gene XREF 2_point UNIQUE ?Variation XREF In_2_point
> 			       Locus_1 UNIQUE ?Locus XREF 2_point UNIQUE ?Variation XREF In_2_point
841,842c855,856
< 		Point_2 UNIQUE Gene_2   UNIQUE ?Gene  XREF 2_point UNIQUE ?Variation XREF In_2_point
< 			       Locus_2	UNIQUE ?Locus XREF 2_point UNIQUE ?Variation XREF In_2_point
---
> 		Point_2 UNIQUE Gene_2 UNIQUE ?Gene XREF 2_point UNIQUE ?Variation XREF In_2_point
> 			       Locus_2 UNIQUE ?Locus XREF 2_point UNIQUE ?Variation XREF In_2_point
872c886
< 	        Simple_distance	Min      UNIQUE Float 
---
> 	        Simple_distance	Min UNIQUE Float 
874,876c888,890
<                                 Max      UNIQUE Float
<                                 Error    UNIQUE Float
<                                 Linkage  UNIQUE Text
---
>                                 Max UNIQUE Float
>                                 Error UNIQUE Float
>                                 Linkage UNIQUE Text
884,885c898,899
< 		Genotype  UNIQUE Text
< 		Results  UNIQUE Text
---
> 		Genotype UNIQUE Text
> 		Results UNIQUE Text
888,889c902,903
< 			   Date  UNIQUE DateType
< 		Item_1	UNIQUE	Gene_1  UNIQUE ?Gene  XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data
---
> 			   Date UNIQUE DateType
> 		Item_1	UNIQUE	Gene_1 UNIQUE ?Gene XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data
894c908
< 		Item_2	UNIQUE	Gene_2  UNIQUE ?Gene  XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data
---
> 		Item_2	UNIQUE	Gene_2 UNIQUE ?Gene XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data
906c920
< 		Genotype  UNIQUE Text
---
> 		Genotype UNIQUE Text
909,912c923,926
< 			    Date  UNIQUE DateType
< 		Selected A UNIQUE Gene_A          UNIQUE ?Gene UNIQUE ?Variation XREF In_multi_point
< 				  Locus_A         UNIQUE ?Locus UNIQUE ?Variation XREF In_multi_point
< 				  Allele_A        UNIQUE ?Variation
---
> 			    Date UNIQUE DateType
> 		Selected A UNIQUE Gene_A UNIQUE ?Gene UNIQUE ?Variation XREF In_multi_point
> 				  Locus_A UNIQUE ?Locus UNIQUE ?Variation XREF In_multi_point
> 				  Allele_A UNIQUE ?Variation
914,917c928,931
<                                   Transgene_A     UNIQUE ?Transgene XREF Multi_point 	
< 			 B UNIQUE Gene_B          UNIQUE ?Gene UNIQUE ?Variation XREF In_multi_point
< 				  Locus_B         UNIQUE ?Locus UNIQUE ?Variation XREF In_multi_point
< 				  Allele_B        UNIQUE ?Variation
---
>                                   Transgene_A UNIQUE ?Transgene XREF Multi_point 	
> 			 B UNIQUE Gene_B UNIQUE ?Gene UNIQUE ?Variation XREF In_multi_point
> 				  Locus_B UNIQUE ?Locus UNIQUE ?Variation XREF In_multi_point
> 				  Allele_B UNIQUE ?Variation
920c934
< 		Gene  ?Gene  UNIQUE ?Variation XREF In_multi_point     // Connect to ?Gene model
---
> 		Gene ?Gene UNIQUE ?Variation XREF In_multi_point       // Connect to ?Gene model
931,933c945,947
< ?Multi_counts UNIQUE Gene          UNIQUE ?Gene	         XREF Multi_point UNIQUE Int #Multi_counts
< 		     Locus	   UNIQUE ?Locus	 XREF Multi_point UNIQUE Int #Multi_counts
< 		     Allele	   UNIQUE ?Variation	 XREF Multi_point UNIQUE Int #Multi_counts
---
> ?Multi_counts UNIQUE Gene UNIQUE ?Gene XREF Multi_point UNIQUE Int #Multi_counts
> 		     Locus UNIQUE ?Locus XREF Multi_point UNIQUE Int #Multi_counts
> 		     Allele UNIQUE ?Variation XREF Multi_point UNIQUE Int #Multi_counts
935c949
< 		     Transgene	   UNIQUE ?Transgene	 XREF Multi_point UNIQUE Int #Multi_counts  
---
> 		     Transgene UNIQUE ?Transgene XREF Multi_point UNIQUE Int #Multi_counts  
985,989c999,1003
< 	 Attributes_of Cell       ?Cell       XREF GO_term
< 		       Motif      ?Motif      XREF GO_term
< 		       Gene       ?Gene       XREF GO_term // will this replace CDS? [040203 krb]
< 		       CDS        ?CDS        XREF GO_term
< 		       Sequence   ?Sequence   XREF GO_term // Erich, [011210 krb]
---
> 	 Attributes_of Cell ?Cell XREF GO_term
> 		       Motif ?Motif XREF GO_term
> 		       Gene ?Gene XREF GO_term // will this replace CDS? [040203 krb]
> 		       CDS ?CDS XREF GO_term
> 		       Sequence ?Sequence XREF GO_term // Erich, [011210 krb]
991,992c1005,1006
< 		       Phenotype  ?Phenotype  XREF GO_term // Erich, [020128 dl]
< 		       Index Ancestor   ?GO_term XREF Descendent // Lincoln [020709 [krb]
---
> 		       Phenotype ?Phenotype XREF GO_term // Erich, [020128 dl]
> 		       Index Ancestor ?GO_term XREF Descendent // Lincoln [020709 [krb]
1032c1046
<          Ancestor   ?SO_term XREF Descendent
---
>          Ancestor ?SO_term XREF Descendent
1064,1066c1078,1080
< 	 Synonym Broad   ?Text
< 		 Exact   ?Text
< 		 Narrow  ?Text
---
> 	 Synonym Broad ?Text
> 		 Exact ?Text
> 		 Narrow ?Text
1077,1081c1091,1095
< 	 Attribute_of Gene_by_biology    ?Gene       XREF   Experimental_model
< 		      Gene_by_orthology  ?Gene       XREF   Potential_model
< 		      Phenotype  ?Phenotype  XREF   DO_term
< 		      WBProcess  ?WBProcess  XREF   DO_term
< 		      Reference  ?Paper      XREF   DO_term 
---
> 	 Attribute_of Gene_by_biology ?Gene XREF Experimental_model
> 		      Gene_by_orthology ?Gene XREF Potential_model
> 		      Phenotype ?Phenotype XREF DO_term
> 		      WBProcess ?WBProcess XREF DO_term
> 		      Reference ?Paper XREF DO_term 
1113,1118c1127,1132
< ?Neurodata      Send            Text    UNIQUE Int #Neuro_location   // Text=series,Int=count
<                 Send_joint      Text    UNIQUE Int #Neuro_location   // "joint" indicates polyadic synapse
<                 Receive         Text    UNIQUE Int #Neuro_location
<                 Receive_joint   Text    UNIQUE Int #Neuro_location
<                 Gap_junction    Text    UNIQUE Int #Neuro_location
<                 Evidence        #Evidence
---
> ?Neurodata      Send Text UNIQUE Int #Neuro_location   // Text=series,Int=count
>                 Send_joint Text UNIQUE Int #Neuro_location   // "joint" indicates polyadic synapse
>                 Receive Text UNIQUE Int #Neuro_location
>                 Receive_joint Text UNIQUE Int #Neuro_location
>                 Gap_junction Text UNIQUE Int #Neuro_location
>                 Evidence #Evidence
1165,1168c1179,1182
< 			       Genomic_parent   UNIQUE ?Sequence XREF Nongenomic
< 			       AGP_parent       UNIQUE ?Sequence XREF AGP_fragment // added to hold briggsae data [krb 020726]
< 	       S_child Gene_child ?Gene       XREF Sequence UNIQUE Int UNIQUE Int #SMap_info  // maximal extent of Gene objects
< 		       CDS_child  ?CDS        XREF Sequence UNIQUE Int UNIQUE Int #SMap_info  // For ?CDS [031104 krb]
---
> 			       Genomic_parent UNIQUE ?Sequence XREF Nongenomic
> 			       AGP_parent UNIQUE ?Sequence XREF AGP_fragment // added to hold briggsae data [krb 020726]
> 	       S_child Gene_child ?Gene XREF Sequence UNIQUE Int UNIQUE Int #SMap_info  // maximal extent of Gene objects
> 		       CDS_child ?CDS XREF Sequence UNIQUE Int UNIQUE Int #SMap_info  // For ?CDS [031104 krb]
1221c1235
< 		  Interaction  ?Interaction
---
> 		  Interaction ?Interaction
1260,1261c1274,1275
< 		     Match_type  UNIQUE Match_with_function
< 					Match_without_function
---
> 		     Match_type UNIQUE Match_with_function
> 				       Match_without_function
1267,1268c1281,1282
< 		     Link // Enable gene curation of link genes [020805 krb]
< 	  Splices    Confirmed_intron  Int Int #Splice_confirmation
---
> 		     Link       // Enable gene curation of link genes [020805 krb]
> 	  Splices    Confirmed_intron Int Int #Splice_confirmation
1271c1285
< 	  Cluster_information Contains_reads       ?Sequence XREF Contained_in_cluster  // Links cluster contig and
---
> 	  Cluster_information Contains_reads ?Sequence XREF Contained_in_cluster  // Links cluster contig and
1383,1397c1397,1411
< ?Sequence_collection Origin	Evidence #Evidence
< 				Name ?Text // name that the author gave this collection
< 				Species UNIQUE ?Species
< 				Strain UNIQUE ?Strain
< 				Laboratory ?Laboratory
< 				DB_info Database ?Database ?Database_field ?Text
< 		     History    First_WS_release Int // first WormBase release this assembly was used
< 				Latest_WS_release Int // latest release where it was used
< 				Supercedes    UNIQUE ?Sequence_collection XREF Superceded_by
< 				Superceded_by UNIQUE ?Sequence_collection XREF Supercedes
< 		     Remark	?Text
< 		     Status     UNIQUE Live #Evidence
< 				       Suppressed #Evidence
< 				       Dead #Evidence   
< 		     Sequences	?Sequence
---
> ?Sequence_collection Origin Evidence #Evidence
> 			    Name ?Text // name that the author gave this collection
> 			    Species UNIQUE ?Species
> 			    Strain UNIQUE ?Strain
> 			    Laboratory ?Laboratory
> 			    DB_info Database ?Database ?Database_field ?Text
> 		     History First_WS_release Int // first WormBase release this assembly was used
> 			     Latest_WS_release Int // latest release where it was used
> 			     Supercedes UNIQUE ?Sequence_collection XREF Superceded_by
> 			     Superceded_by UNIQUE ?Sequence_collection XREF Supercedes
> 		     Remark ?Text
> 		     Status UNIQUE Live #Evidence
> 				   Suppressed #Evidence
> 				   Dead #Evidence   
> 		     Sequences ?Sequence
1409c1423
< 	SMap S_parent UNIQUE Sequence   UNIQUE ?Sequence   XREF CDS_child
---
> 	SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF CDS_child
1436c1450
< 		Interaction  ?Interaction
---
> 		Interaction ?Interaction
1451c1465
< 		RNASeq_FPKM  ?Life_stage  Float  #Evidence
---
> 		RNASeq_FPKM ?Life_stage Float #Evidence
1488c1502
< 			RNASeq_FPKM  ?Life_stage  Float  #Evidence
---
> 			RNASeq_FPKM ?Life_stage Float #Evidence
1528,1534c1542,1548
<                 Origin  From_laboratory UNIQUE ?Laboratory
<                         Species UNIQUE ?Species
<                 Type    UNIQUE Coding_pseudogene #Evidence //Pseudogene of a once coding loci 
<                                RNA_pseudogene #Evidence    //Pseudogene of a ncRNA loci
<                                Transposon_pseudogene #Evidence //Pseudogene of Transposon origins
< 	        Attributes   Transcribed #Evidence
< 			     Fragment #Evidence 
---
>                 Origin From_laboratory UNIQUE ?Laboratory
>                        Species UNIQUE ?Species
>                 Type UNIQUE Coding_pseudogene #Evidence //Pseudogene of a once coding loci 
>                             RNA_pseudogene #Evidence    //Pseudogene of a ncRNA loci
>                             Transposon_pseudogene #Evidence //Pseudogene of Transposon origins
> 	        Attributes Transcribed #Evidence
> 			   Fragment #Evidence 
1536c1550
<                 Visible Gene         UNIQUE ?Gene XREF Corresponding_pseudogene         // when Pseudogene is live
---
>                 Visible Gene UNIQUE ?Gene XREF Corresponding_pseudogene         // when Pseudogene is live
1542c1556
< 			Corresponding_transposon    UNIQUE ?Transposon XREF Corresponding_pseudogene
---
> 			Corresponding_transposon UNIQUE ?Transposon XREF Corresponding_pseudogene
1551c1565
< 			RNASeq_FPKM  ?Life_stage  Float  #Evidence
---
> 			RNASeq_FPKM ?Life_stage Float #Evidence
1599c1613
< 		   Associated_motif   ?Motif   XREF Associated_transposon_family // to connect Transposon famillies to Repeat motifs ar2
---
> 		   Associated_motif ?Motif XREF Associated_transposon_family // to connect Transposon famillies to Repeat motifs ar2
1634,1639c1648,1653
<                 Group_type  UNIQUE COG	   COG_type #Homology_type
< 					   COG_code #COG_codes
< 				   eggNOG  eggNOG_type #Homology_type
< 					   eggNOG_code #COG_codes
< 				   InParanoid_group
< 				   OrthoMCL_group     //erich Nov06
---
>                 Group_type UNIQUE COG    COG_type #Homology_type
> 					 COG_code #COG_codes
> 				  eggNOG eggNOG_type #Homology_type
> 					 eggNOG_code #COG_codes
> 				  InParanoid_group
> 				  OrthoMCL_group     //erich Nov06
1716,1717c1730,1731
< 		    Strain  UNIQUE ?Strain//added by pad, as we are moving towards multi strain readyness.
< 	 History    Merged_into	   UNIQUE    ?Feature XREF Acquires_merge #Evidence
---
> 		    Strain UNIQUE ?Strain//added by pad, as we are moving towards multi strain readyness.
> 	 History    Merged_into	UNIQUE ?Feature XREF Acquires_merge #Evidence
1719c1733
< 		    Deprecated	   Text	     #Evidence 
---
> 		    Deprecated Text #Evidence 
1723,1725c1737,1739
< 		    Defined_by_paper    ?Paper XREF Feature #Evidence
< 		    Defined_by_person   ?Person
< 		    Defined_by_author   ?Author
---
> 		    Defined_by_paper ?Paper XREF Feature #Evidence
> 		    Defined_by_person ?Person
> 		    Defined_by_author ?Author
1728,1730c1742,1744
< 	 Associations Associated_with_gene	 ?Gene	     XREF Associated_feature #Evidence // richard
<                       Associated_with_CDS	 ?CDS	     XREF Associated_feature #Evidence  // richard
<                       Associated_with_transcript ?Transcript XREF Associated_feature #Evidence  // richard
---
> 	 Associations Associated_with_gene ?Gene XREF Associated_feature #Evidence // richard
>                       Associated_with_CDS ?CDS XREF Associated_feature #Evidence // richard
>                       Associated_with_transcript ?Transcript XREF Associated_feature #Evidence // richard
1733,1735c1747,1749
< 		      Associated_with_variation  ?Variation  XREF Feature #Evidence  
< 		      Associated_with_Position_Matrix	      ?Position_Matrix XREF Associated_feature #Evidence
< 		      Associated_with_operon      ?Operon XREF Associated_feature #Evidence
---
> 		      Associated_with_variation ?Variation XREF Feature #Evidence
> 		      Associated_with_Position_Matrix ?Position_Matrix XREF Associated_feature #Evidence
> 		      Associated_with_operon ?Operon XREF Associated_feature #Evidence
1737,1738c1751,1752
< 		      Associated_with_expression_pattern	 ?Expr_pattern XREF Associated_feature #Evidence 
< 		      Associated_with_Feature ?Feature XREF Associated_with_Feature #Evidence 
---
> 		      Associated_with_expression_pattern ?Expr_pattern XREF Associated_feature #Evidence 
> 		      Associated_with_Feature ?Feature XREF Associated_with_Feature #Evidence
1741c1755
< 	 Annotation UNIQUE ?LongText		// added for data attribution [030220 dl]
---
> 	 Annotation UNIQUE ?LongText // added for data attribution [030220 dl]
1753c1767
< 	      Strain  UNIQUE ?Strain
---
> 	      Strain UNIQUE ?Strain
1756,1758c1770,1772
< 	      Splices	Confirmed_intron  Int Int #Splice_confirmation
< 			Predicted_5 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
< 			Predicted_3 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
---
> 	      Splices Confirmed_intron Int Int #Splice_confirmation
> 		      Predicted_5 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
> 		      Predicted_3 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
1771c1785
< 			Position_matrix  ?Position_Matrix XREF Transcription_factor #Evidence
---
> 			Position_matrix ?Position_Matrix XREF Transcription_factor #Evidence
1785,1788c1799,1802
< ?Position_Matrix  Description  ?Text #Evidence
< 		  Brief_id  UNIQUE ?Text			// Addition Xiaodong 
<                   Type  UNIQUE Frequency
<                                Weight
---
> ?Position_Matrix  Description ?Text #Evidence
> 		  Brief_id UNIQUE ?Text			// Addition Xiaodong 
>                   Type UNIQUE Frequency
>                               Weight
1790,1792c1804,1806
<                   Site_values      Text UNIQUE Float REPEAT
<                   Threshold        Float
<                   Consensus	   Text	#Evidence
---
>                   Site_values Text UNIQUE Float REPEAT
>                   Threshold Float
>                   Consensus Text #Evidence
1797,1798c1811,1812
< 		  Transcription_factor  UNIQUE ?Transcription_factor XREF Position_matrix #Evidence //gw3
<                   Remark ?Text  #Evidence
---
> 		  Transcription_factor UNIQUE ?Transcription_factor XREF Position_matrix #Evidence //gw3
>                   Remark ?Text #Evidence
1828,1829c1842,1843
<                 NCBI_id   UNIQUE        Int
<                 Translation  UNIQUE Text
---
>                 NCBI_id UNIQUE Int
>                 Translation UNIQUE Text
1831c1845
< 		Stop  UNIQUE Text 
---
> 		Stop UNIQUE Text 
1848,1849c1862,1863
<                   Gene_name  ?Text
<                   Description   UNIQUE ?Text
---
>                   Gene_name ?Text
>                   Description UNIQUE ?Text
1863,1864c1877,1878
<           Homol DNA_homol ?Sequence XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int  #Homol_info
<                 Pep_homol ?Protein XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int  #Homol_info
---
>           Homol DNA_homol ?Sequence XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
>                 Pep_homol ?Protein XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
1866c1880
<                 Motif_homol ?Motif XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int  #Homol_info
---
>                 Motif_homol ?Motif XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
1879c1893
< ?Motif	Match_sequence  UNIQUE Text	// Text is the DNA or protein sequence
---
> ?Motif	Match_sequence UNIQUE Text	// Text is the DNA or protein sequence
1882,1887c1896,1901
< 	Restriction     Isoschizomer ?Motif XREF Isoschizomer
< 		        Offset UNIQUE Int   
< 			Cleavage UNIQUE Text  // will show the cleavage points ex: G_ACGT'C
< 		        Overhang UNIQUE Int
< 		        Company UNIQUE Text
<                         Redundant
---
> 	Restriction Isoschizomer ?Motif XREF Isoschizomer
> 		    Offset UNIQUE Int   
> 		    Cleavage UNIQUE Text  // will show the cleavage points ex: G_ACGT'C
> 		    Overhang UNIQUE Int
> 		    Company UNIQUE Text
>                     Redundant
1896,1899c1910,1913
< 	Homol	DNA_homol ?Sequence XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
< 		Pep_homol ?Protein XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
< 		Motif_homol ?Motif XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
< 		Homol_homol ?Homol_data XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
---
> 	Homol DNA_homol ?Sequence XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
> 	      Pep_homol ?Protein XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
> 	      Motif_homol ?Motif XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
> 	      Homol_homol ?Homol_data XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
1932,1936c1946,1950
< ?Database  Name        UNIQUE ?Text            // name of the database
<            Description UNIQUE Text             // description of database contacts
<            URL         UNIQUE Text             // Link to database home page
<            Email              Text             // Contact email 
<            URL_constructor UNIQUE Text         // rule to build URL to specific database entry page 
---
> ?Database  Name UNIQUE ?Text           // name of the database
>            Description UNIQUE Text     // description of database contacts
>            URL UNIQUE Text             // Link to database home page
>            Email Text                  // Contact email 
>            URL_constructor UNIQUE Text // rule to build URL to specific database entry page 
2021,2063c2035,2077
< ?Expr_pattern	Expression_of	Gene ?Gene XREF Expr_pattern #Evidence
< 				Reflects_endogenous_expression_of ?Gene
< 				CDS        ?CDS XREF Expr_pattern // for coding genes
< 				Sequence   ?Sequence XREF Expr_pattern // for clones???
< 				Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb]
< 				Clone ?Clone XREF Expr_pattern
< 				Protein ?Protein XREF Expr_pattern
<                                 Protein_description Text   // stores information for Expr_patterns with unknown antigens [031105 krb]
< 		Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
< 		Expressed_in	Cell         ?Cell         XREF Expr_pattern #Qualifier
< 				Cell_group   ?Cell_group   XREF Expr_pattern #Qualifier
< 				Life_stage   ?Life_stage   XREF Expr_pattern #Qualifier
< 				Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
< 				GO_term      ?GO_term      XREF Expr_pattern #GR_condition
<                 Subcellular_localization ?Text
< 		Type	Reporter_gene ?Text
< 			In_situ Text
< 			Antibody ?Text
< 			Northern Text // Wen [krb 030425]
<                         Western Text  // Wen 
<                         RT_PCR Text   // Wen
< 			Localizome ?Text //added by Wen
< 			Microarray ?Microarray_experiment
< 			Tiling_array ?Analysis
< 			EPIC	  ?Text 
< 		Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
< 		Pattern ?Text
< 		Picture ?Picture XREF Expr_pattern
< 		MovieURL Text //Added by wen for link to movie URLs. 
< 		Movie    ?Movie    XREF Expr_pattern  //Added by Wen to curate Expr_pattern video
<                 Remark ?Text #Evidence
< 		DB_info ?Database ?Database_field Text
<                 Experiment	Laboratory ?Laboratory
< 				Author ?Author 
< 				Date UNIQUE DateType
< 				Strain UNIQUE ?Strain
< 		Reference ?Paper XREF Expr_pattern
<                 Transgene ?Transgene XREF Expr_pattern
< 		Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
< 		Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
<                                                           // added [031120 krb]
< 		Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
< 		Historical_gene   ?Gene #Evidence
---
> ?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence
> 			    Reflects_endogenous_expression_of ?Gene
> 			    CDS ?CDS XREF Expr_pattern               // for coding genes
> 			    Sequence ?Sequence XREF Expr_pattern     // for clones???
> 			    Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb]
> 			    Clone ?Clone XREF Expr_pattern
> 			    Protein ?Protein XREF Expr_pattern
>                             Protein_description Text   // information for Expr_patterns with unknown antigens [031105 krb]
> 	      Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
> 	      Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier
> 			   Cell_group ?Cell_group XREF Expr_pattern #Qualifier
> 			   Life_stage ?Life_stage XREF Expr_pattern #Qualifier
> 			   Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
> 			   GO_term ?GO_term XREF Expr_pattern #GR_condition
>               Subcellular_localization ?Text
> 	      Type Reporter_gene ?Text
> 		   In_situ Text
> 		   Antibody ?Text
> 		   Northern Text // Wen [krb 030425]
>                    Western Text  // Wen 
>                    RT_PCR Text   // Wen
> 		   Localizome ?Text //added by Wen
> 		   Microarray ?Microarray_experiment
> 		   Tiling_array ?Analysis
> 		   EPIC ?Text 
> 	      Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
> 	      Pattern ?Text
> 	      Picture ?Picture XREF Expr_pattern
> 	      MovieURL Text //Added by wen for link to movie URLs. 
> 	      Movie ?Movie XREF Expr_pattern  //Added by Wen to curate Expr_pattern video
>               Remark ?Text #Evidence
> 	      DB_info ?Database ?Database_field Text
>               Experiment Laboratory ?Laboratory
> 			 Author ?Author 
> 			 Date UNIQUE DateType
> 			 Strain UNIQUE ?Strain
> 	      Reference ?Paper XREF Expr_pattern
>               Transgene ?Transgene XREF Expr_pattern
> 	      Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
> 	      Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
>                                                         // added [031120 krb]
> 	      Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
> 	      Historical_gene ?Gene #Evidence
2068c2082
< #Qualifier Certain   Text
---
> #Qualifier Certain Text
2070c2084
<            Partial   Text    //For expression of unidentified cell in a cell group
---
>            Partial Text      //For expression of unidentified cell in a cell group
2118c2132
< 		    No_original_reference    Text //proposed by Wen
---
> 		    No_original_reference Text //proposed by Wen
2133c2147
< 	  Historical_gene   ?Gene #Evidence 			
---
> 	  Historical_gene ?Gene #Evidence 			
2182,2184c2196,2198
< 	Fate	 Cell_type  ?Text        // e.g. muscle, neuron,hypodermis, gland
< 		 Program ?Text           //division, differentiation, death, and differs between sexes
< 		 Syncitial_cell ?Cell_group XREF Nucleus //see Cell_group,
---
> 	Fate Cell_type ?Text             // e.g. muscle, neuron,hypodermis, gland
> 	     Program ?Text               //division, differentiation, death, and differs between sexes
> 	     Syncitial_cell ?Cell_group XREF Nucleus //see Cell_group,
2187,2190c2201,2204
<         Remark        ?Text #Evidence
<         Lineage Parent  UNIQUE  ?Cell XREF Daughter
<                 Daughter      ?Cell XREF Parent
<                 Lineage_name    Text
---
>         Remark ?Text #Evidence
>         Lineage Parent UNIQUE ?Cell XREF Daughter
>                 Daughter ?Cell XREF Parent
>                 Lineage_name Text
2239,2243c2253,2257
< ?Anatomy_name Primary   Name_for_cell            ?Cell XREF Main_name
<                         Name_for_cell_group      ?Cell_group XREF Main_name
<                         Name_for_anatomy_term    ?Anatomy_term XREF Term
<               Secondary Synonym_for_cell         ?Cell XREF Other_name
<                         Synonym_for_cell_group   ?Cell_group XREF Other_name
---
> ?Anatomy_name Primary   Name_for_cell ?Cell XREF Main_name
>                         Name_for_cell_group ?Cell_group XREF Main_name
>                         Name_for_anatomy_term ?Anatomy_term XREF Term
>               Secondary Synonym_for_cell ?Cell XREF Other_name
>                         Synonym_for_cell_group ?Cell_group XREF Other_name
2264c2278
<                        Fate    Cell_type  ?Text        // e.g. muscle, neuron,hypodermis, gland
---
>                        Fate    Cell_type ?Text         // e.g. muscle, neuron,hypodermis, gland
2267,2269c2281,2283
<                        Lineage Parent_term  UNIQUE  ?Anatomy_term XREF Daughter_term
<                                Daughter_term      ?Anatomy_term XREF Parent_term
<                                Lineage_name    Text
---
>                        Lineage Parent_term UNIQUE ?Anatomy_term XREF Daughter_term
>                                Daughter_term ?Anatomy_term XREF Parent_term
>                                Lineage_name Text
2287,2309c2301,2323
<                 URL     Text // for storing static URLs, such as WormAtlas, WormBook
<                 Child   PART_OF_c	?Anatomy_term   XREF    PART_OF_p
<                         IS_A_c		?Anatomy_term   XREF    IS_A_p
<                         DESCENDENT_OF_c	?Anatomy_term   XREF	DESCENDENT_OF_p
<                         DESC_IN_HERM_c	?Anatomy_term   XREF	DESC_IN_HERM_p
<                         DESC_IN_MALE_c	?Anatomy_term   XREF	DESC_IN_MALE_p
<                         DEVELOPS_FROM_c	?Anatomy_term   XREF	DEVELOPS_FROM_p
< 			CELL_c		?Anatomy_term	XREF	CELL_p
< 			XUNION_OF_c	?Anatomy_term	XREF	XUNION_OF_p
<                 Parent  PART_OF_p	?Anatomy_term   XREF	PART_OF_c
<                         IS_A_p		?Anatomy_term	XREF	IS_A_c
<                         DESCENDENT_OF_p	?Anatomy_term   XREF	DESCENDENT_OF_c
<                         DESC_IN_HERM_p	?Anatomy_term   XREF	DESC_IN_HERM_c
<                         DESC_IN_MALE_p	?Anatomy_term   XREF	DESC_IN_MALE_c
<                         DEVELOPS_FROM_p	?Anatomy_term   XREF	DEVELOPS_FROM_c
< 			CELL_p		?Anatomy_term	XREF	CELL_c
< 			XUNION_OF_p	?Anatomy_term	XREF	XUNION_OF_c
<                 Attribute_of    Expr_pattern    ?Expr_pattern   XREF    Anatomy_term
< 				Expression_cluster ?Expression_cluster XREF Anatomy_term #Evidence 
<                                 GO_term ?GO_term XREF Anatomy_term ?AO_code #Evidence
<                                 Reference       ?Paper  XREF Anatomy_term
< 				Function Anatomy_function ?Anatomy_function XREF Involved
< 					 Anatomy_function_not ?Anatomy_function XREF Not_involved
---
>                 URL Text // for storing static URLs, such as WormAtlas, WormBook
>                 Child PART_OF_c	?Anatomy_term XREF PART_OF_p
>                       IS_A_c		?Anatomy_term XREF IS_A_p
>                       DESCENDENT_OF_c	?Anatomy_term XREF DESCENDENT_OF_p
>                       DESC_IN_HERM_c	?Anatomy_term XREF DESC_IN_HERM_p
>                       DESC_IN_MALE_c	?Anatomy_term XREF DESC_IN_MALE_p
>                       DEVELOPS_FROM_c	?Anatomy_term XREF DEVELOPS_FROM_p
> 		      CELL_c		?Anatomy_term XREF CELL_p
> 		      XUNION_OF_c	?Anatomy_term XREF XUNION_OF_p
>                 Parent PART_OF_p	?Anatomy_term XREF PART_OF_c
>                        IS_A_p		?Anatomy_term XREF IS_A_c
>                        DESCENDENT_OF_p	?Anatomy_term XREF DESCENDENT_OF_c
>                        DESC_IN_HERM_p	?Anatomy_term XREF DESC_IN_HERM_c
>                        DESC_IN_MALE_p	?Anatomy_term XREF DESC_IN_MALE_c
>                        DEVELOPS_FROM_p	?Anatomy_term XREF DEVELOPS_FROM_c
> 		       CELL_p		?Anatomy_term XREF CELL_c
> 		       XUNION_OF_p	?Anatomy_term XREF XUNION_OF_c
>                 Attribute_of Expr_pattern ?Expr_pattern XREF Anatomy_term
> 			     Expression_cluster ?Expression_cluster XREF Anatomy_term #Evidence 
>                              GO_term ?GO_term XREF Anatomy_term ?AO_code #Evidence
>                              Reference ?Paper XREF Anatomy_term
> 			     Function Anatomy_function ?Anatomy_function XREF Involved
> 				      Anatomy_function_not ?Anatomy_function XREF Not_involved
2314,2316c2328,2330
<                 Index   Ancestor ?Anatomy_term XREF Descendent  //store ancestors of relationship IS_A and PART_OF
<                         Descendent ?Anatomy_term XREF Ancestor  //store descendents of relationship IS_A and PART_OF
<                 Remark  ?Text #Evidence
---
>                 Index Ancestor ?Anatomy_term XREF Descendent  //store ancestors of relationship IS_A and PART_OF
>                       Descendent ?Anatomy_term XREF Ancestor  //store descendents of relationship IS_A and PART_OF
>                 Remark ?Text #Evidence
2377c2391
<                      Normalization    UNIQUE Float	// Normalization factor for display (defaults to 1.0)
---
>                      Normalization UNIQUE Float	// Normalization factor for display (defaults to 1.0)
2386,2404c2400,2418
< ?TreeNode       Label UNIQUE ?Text		// Tree vertex label, e.g. sequence name or taxon   
<                 Id    UNIQUE Int		// Node numbering...
<                 Description  ?Text
< 		Type UNIQUE  Root		// Root ?TreeNode should be so designated!
<                              Interior
< 		             Leaf
<                 Distance UNIQUE	Float		// "Evolutionary distance" or branch length
<                 Bootstrap UNIQUE	Float		// Node subtree "bootstrap" values
<                 Tree   UNIQUE   ?Tree
< 		Parent UNIQUE   ?TreeNode XREF  Child
< 		Child           ?TreeNode XREF  Parent
<                 Display  Hide			// Hide the subtree (children) of this node
<                          Colour   UNIQUE #Colour // Fixes the colour of the subtree; 
<                                                  // overridden by child node settings
<                          Hide_Bootstraps         // Hide all bootstraps in subtree...
<                          Show_Bootstrap          // ... except those with the "Show_Bootstrap" tag set
<                 Contains Taxon                //    UNIQUE ?Taxon    XREF Tree_Node
<                          Cell     UNIQUE ?Cell     XREF Tree_Node
<                          Cell_group UNIQUE ?Cell_group  XREF Tree_Node 
---
> ?TreeNode       Label UNIQUE ?Text              // Tree vertex label, e.g. sequence name or taxon   
>                 Id UNIQUE Int                   // Node numbering...
>                 Description ?Text
> 		Type UNIQUE Root                // Root ?TreeNode should be so designated!
>                             Interior
> 		            Leaf
>                 Distance UNIQUE	Float           // "Evolutionary distance" or branch length
>                 Bootstrap UNIQUE Float          // Node subtree "bootstrap" values
>                 Tree UNIQUE ?Tree
> 		Parent UNIQUE ?TreeNode XREF Child
> 		Child ?TreeNode XREF Parent
>                 Display Hide			 // Hide the subtree (children) of this node
>                         Colour UNIQUE #Colour   // Fixes the colour of the subtree; 
>                                                 // overridden by child node settings
>                         Hide_Bootstraps         // Hide all bootstraps in subtree...
>                         Show_Bootstrap          // ... except those with the "Show_Bootstrap" tag set
>                 Contains Taxon                   // UNIQUE ?Taxon XREF Tree_Node
>                          Cell UNIQUE ?Cell XREF Tree_Node
>                          Cell_group UNIQUE ?Cell_group XREF Tree_Node 
2426,2433c2440,2447
< 		Summary UNIQUE ?Text								// concise genomic description of the transgene
<                 Synonym ?Text									// for alternative names
<                 Promoter  Driven_by_gene ?Gene XREF Drives_transgene #Evidence			// eventually change this tag to promoter_gene
<                           Driven_by_construct  ?Text						// eventually change this tag to promoter_artificial
<                 Reporter  Reporter_product ?Text						// removed multiple tags for Reporter_product
<                           Gene ?Gene XREF Transgene_product #Evidence 
< 			  3_UTR  ?Gene #Evidence
<                 Reporter_type  ?Text								// added for Transcriptional fusion or Translational fusion
---
> 		Summary UNIQUE ?Text                                                            // concise genomic description of the transgene
>                 Synonym ?Text                                                                   // for alternative names
>                 Promoter  Driven_by_gene ?Gene XREF Drives_transgene #Evidence                  // eventually change this tag to promoter_gene
>                           Driven_by_construct ?Text                                             // eventually change this tag to promoter_artificial
>                 Reporter  Reporter_product ?Text                                                // removed multiple tags for Reporter_product
>                           Gene ?Gene XREF Transgene_product #Evidence
> 			  3_UTR ?Gene #Evidence
>                 Reporter_type ?Text                                                             // Transcriptional fusion or Translational fusion
2435c2449
< 			      Fragment ?Text							// new tag to collect the following as subtags, Fragment may be deleted later
---
> 			      Fragment ?Text                                                    // new tag to collect the following as subtags, Fragment may be deleted later
2437,2454c2451,2468
<                               Integration_method UNIQUE ?Text					// changed from Integrated_by
<                               Laboratory ?Laboratory #Lab_Location				// changed from Location
<                               Author ?Author							// may eventually be deleted
< 			      Person ?Person							// new tag ky 2011
<                 Genetic_information  Extrachromosomal						// new subtag and tags
<                                      Integrated							// new subtag and collects the mapping tags
< 				     Map ?Map  #Map_position  
<                                      Map_evidence #Evidence 
<                                      Mapping_data  2_point ?2_point_data			// if no data can be removed
<                                                    Multi_point ?Multi_pt_data			// if no data can be removed
<                          	     Phenotype ?Phenotype XREF Transgene #Phenotype_info
<                          	     Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info   
<                 Used_for   Expr_pattern ?Expr_pattern XREF Transgene  
<                            Marker_for   ?Text #Evidence 
<                            Interactor ?Interaction 
<                 Associated_with   Marked_rearrangement ?Rearrangement XREF By_transgene		//new tag to collect the following as subtags
<                           	  Clone ?Clone XREF Transgene Text 
<                           	  Strain ?Strain XREF Transgene 
---
>                               Integration_method UNIQUE ?Text                                   // changed from Integrated_by
>                               Laboratory ?Laboratory #Lab_Location                              // changed from Location
>                               Author ?Author                                                    // may eventually be deleted
> 			      Person ?Person                                                    // new tag ky 2011
>                 Genetic_information Extrachromosomal                                            // new subtag and tags
>                                     Integrated                                                  // new subtag and collects the mapping tags
> 				    Map ?Map #Map_position  
>                                     Map_evidence #Evidence 
>                                     Mapping_data  2_point ?2_point_data                         // if no data can be removed
>                                                   Multi_point ?Multi_pt_data                    // if no data can be removed
>                          	    Phenotype ?Phenotype XREF Transgene #Phenotype_info
>                          	    Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info   
>                 Used_for Expr_pattern ?Expr_pattern XREF Transgene  
>                          Marker_for ?Text #Evidence 
>                          Interactor ?Interaction 
>                 Associated_with Marked_rearrangement ?Rearrangement XREF By_transgene           // new tag to collect the following as subtags
>                           	Clone ?Clone XREF Transgene Text 
>                           	Strain ?Strain XREF Transgene 
2457,2458c2471,2472
<                 Historical_gene   ?Gene #Evidence
<                 Remark ?Text #Evidence								//contains a lot of construction notes
---
>                 Historical_gene ?Gene #Evidence
>                 Remark ?Text #Evidence                                                          // contains a lot of construction notes
2475,2480c2489,2495
<         Sequence_info   DNA_text Text UNIQUE Text //stores actual probe sequence for automated mapping
< 						  // 1st Text is DNA, 2nd is probe name
<                         Sequence ?Sequence XREF RNAi  //links to a real Sequence object used in the experiment 
< 						      // such as yk clone; not UNIQUE anymore
<                         PCR_product ?PCR_product XREF RNAi // links to a PCR_product object used in 
< 							   // the experiment; not UNIQUE anymore
---
>         Sequence_info DNA_text Text UNIQUE Text          //stores actual probe sequence for automated mapping
> 						         // 1st Text is DNA, 2nd is probe name
>                       Sequence ?Sequence XREF RNAi       //links to a real Sequence object used in the experiment 
> 						         // such as yk clone; not UNIQUE anymore
>                       Clone ?Clone XREF Used_in_RNAi     // Chris WS244
>                       PCR_product ?PCR_product XREF RNAi // links to a PCR_product object used in 
> 							 // the experiment; not UNIQUE anymore
2482,2497c2497,2512
< 			// which maps to a single place in the genome
<         Experiment      Laboratory ?Laboratory
<                         Date UNIQUE DateType
<                         Strain UNIQUE ?Strain
<                         Genotype UNIQUE ?Text   //used when no Strain object exists
<                         Treatment UNIQUE ?Text
<                         Life_stage UNIQUE ?Life_stage
<                         Temperature UNIQUE Int
<                         Delivered_by UNIQUE Bacterial_feeding      //RL [010327]
<                                             Injection              //RL [010327]
<                                             Soaking                //RL [010327]
<                                             Transgene_expression   //RL [010327]
<         Inhibits        Predicted_gene ?CDS XREF RNAi_result #Evidence // "gene" parent (unreliable)
<                         Gene ?Gene   XREF RNAi_result #Evidence           //RL [010327]
<                         Transcript ?Transcript XREF RNAi_result #Evidence // [021126 krb]
<                         Pseudogene ?Pseudogene XREF RNAi_result #Evidence // [030801 krb]
---
> 			 // which maps to a single place in the genome
>         Experiment Laboratory ?Laboratory
>                    Date UNIQUE DateType
>                    Strain UNIQUE ?Strain
>                    Genotype UNIQUE ?Text   //used when no Strain object exists
>                    Treatment UNIQUE ?Text
>                    Life_stage UNIQUE ?Life_stage
>                    Temperature UNIQUE Int
>                    Delivered_by UNIQUE Bacterial_feeding      //RL [010327]
>                                        Injection              //RL [010327]
>                                        Soaking                //RL [010327]
>                                        Transgene_expression   //RL [010327]
>         Inhibits Predicted_gene ?CDS XREF RNAi_result #Evidence // "gene" parent (unreliable)
>                  Gene ?Gene XREF RNAi_result #Evidence           //RL [010327]
>                  Transcript ?Transcript XREF RNAi_result #Evidence // [021126 krb]
>                  Pseudogene ?Pseudogene XREF RNAi_result #Evidence // [030801 krb]
2517,2561c2532,2576
< #Phenotype_info		Paper_evidence ?Paper
< 			Person_evidence	?Person
< 			Curator_confirmed	?Person
< 		    	Remark  ?Text   #Evidence // specific remarks about the phenotype
< 			Quantity_description ?Text #Evidence //Remark to describe what quantity describes, below
< 			Quantity        UNIQUE  Int UNIQUE      Int     #Evidence
< 			Not      	#Evidence //This is being phased out but is needed for the next phase [06/08/10].
< 			Anatomy_term	?Anatomy_term #Evidence 
<                 	Penetrance      	Incomplete      Text    #Evidence
<                                 		Low             Text    #Evidence
<                                 		High            Text    #Evidence
<                                 		Complete        Text	#Evidence
< 						Range UNIQUE Int UNIQUE Int #Evidence // Range of penetrance
<                 	Recessive               #Evidence
<                 	Semi_dominant           #Evidence
<                 	Dominant                #Evidence
<                 	Haplo_insufficient      #Evidence
< 			Caused_by ?Gene #Evidence
< 			Caused_by_other ?Text #Evidence
< 			Rescued_by_transgene ?Transgene
<                 	Loss_of_function  UNIQUE  	Hypomorph                               #Evidence
<                                  			Amorph                                  #Evidence
<                                                 	Uncharacterised_loss_of_function        #Evidence
<                 	Gain_of_function  UNIQUE  	Dominant_negative       #Evidence
<                                                 	Hypermorph              #Evidence
<                                                 	Neomorph                #Evidence
<                                                 	Uncharacterised_gain_of_function        #Evidence
<                 	Other_allele_type UNIQUE  Wild_type	#Evidence
<                                                	  Isoallele     #Evidence  
< 						  Mixed      	#Evidence       
< 			Affected_by	Molecule    ?Molecule    #Evidence // ?Molecule model Karen Yook
<                 	Temperature_sensitive   Heat_sensitive  Text            #Evidence
<                                         	Cold_sensitive  Text            #Evidence
<                 	Maternal        UNIQUE  Strictly_maternal       #Evidence
<                                         	With_maternal_effect    #Evidence
<                 	Paternal        #Evidence
< 			Phenotype_assay Life_stage  ?Life_stage	 #Evidence
< 					Strain	    ?Strain	 #Evidence
< 					Treatment   ?Text	 #Evidence
< 					Temperature ?Text	 #Evidence
< 					Genotype    ?Text	 #Evidence
< 			Ease_of_scoring UNIQUE ES0_Impossible_to_score #Evidence
< 					       ES1_Very_hard_to_score #Evidence
< 					       ES2_Difficult_to_score #Evidence
< 					       ES3_Easy_to_score #Evidence
---
> #Phenotype_info	Paper_evidence ?Paper
> 		Person_evidence	?Person
> 		Curator_confirmed	?Person
> 		Remark ?Text #Evidence // specific remarks about the phenotype
> 		Quantity_description ?Text #Evidence //Remark to describe what quantity describes, below
> 		Quantity UNIQUE Int UNIQUE Int #Evidence
> 		Not #Evidence //This is being phased out but is needed for the next phase [06/08/10].
> 		Anatomy_term ?Anatomy_term #Evidence 
>                 Penetrance Incomplete Text #Evidence
>                            Low Text #Evidence
>                            High Text #Evidence
>                            Complete Text #Evidence
> 			   Range UNIQUE Int UNIQUE Int #Evidence // Range of penetrance
>                 Recessive #Evidence
>                 Semi_dominant #Evidence
>                 Dominant #Evidence
>                 Haplo_insufficient #Evidence
> 		Caused_by ?Gene #Evidence
> 		Caused_by_other ?Text #Evidence
> 		Rescued_by_transgene ?Transgene
>                 Loss_of_function UNIQUE Hypomorph #Evidence
>                                         Amorph #Evidence
>                                         Uncharacterised_loss_of_function #Evidence
>                 Gain_of_function UNIQUE Dominant_negative #Evidence
>                                         Hypermorph #Evidence
>                                         Neomorph #Evidence
>                                         Uncharacterised_gain_of_function #Evidence
>                 Other_allele_type UNIQUE Wild_type #Evidence
>                                          Isoallele #Evidence  
> 					 Mixed #Evidence       
> 		Affected_by Molecule ?Molecule #Evidence // ?Molecule model Karen Yook
>                 Temperature_sensitive Heat_sensitive Text #Evidence
>                                       Cold_sensitive Text #Evidence
>                 Maternal UNIQUE Strictly_maternal #Evidence
>                                 With_maternal_effect #Evidence
>                 Paternal #Evidence
> 		Phenotype_assay Life_stage ?Life_stage #Evidence
> 				Strain ?Strain #Evidence
> 				Treatment ?Text	#Evidence
> 				Temperature ?Text #Evidence
> 				Genotype ?Text #Evidence
> 		Ease_of_scoring UNIQUE ES0_Impossible_to_score #Evidence
> 				       ES1_Very_hard_to_score #Evidence
> 				       ES2_Difficult_to_score #Evidence
> 				       ES3_Easy_to_score #Evidence
2584c2599
< 	     Interaction  ?Interaction
---
> 	     Interaction ?Interaction
2594,2597c2609,2612
< ?Phenotype Description UNIQUE ?Text	#Evidence
< 	   Name        Primary_name	UNIQUE	?Phenotype_name	XREF Primary_name_for	#Evidence
<                        Synonym		?Phenotype_name	XREF Synonym_for	#Evidence
<                        Short_name 	?Phenotype_name XREF Short_name_for	#Evidence
---
> ?Phenotype Description UNIQUE ?Text #Evidence
> 	   Name Primary_name UNIQUE ?Phenotype_name XREF Primary_name_for #Evidence
>                 Synonym	?Phenotype_name	XREF Synonym_for #Evidence
>                 Short_name ?Phenotype_name XREF Short_name_for #Evidence
2603,2617c2618,2632
<            Attribute_of       RNAi 	?RNAi XREF Phenotype
< 			      Variation	?Variation XREF Phenotype
<                               Transgene	?Transgene XREF Phenotype	// Added by Carol
< 			      Anatomy_function ?Anatomy_function XREF Phenotype
< 			      Interaction ?Interaction XREF Interaction_phenotype
< 			      Rearrangement ?Rearrangement XREF Phenotype
< 			      Strain ?Strain XREF Phenotype
< 			      Not_in_RNAi ?RNAi XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
< 			      Not_in_Variation ?Variation XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
< 			      Not_in_Strain ?Strain XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
< 			      Not_in_Transgene ?Transgene XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
< 			      Not_in_Rearrangement ?Rearrangement XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
< 	   Associated_with    GO_term   ?GO_term   XREF Phenotype   ?GO_code  #Evidence	// Tag Associated_with changed by Carol
< 			      WBProcess ?WBProcess XREF Phenotype
< 			      DO_term ?DO_term #Evidence
---
>            Attribute_of RNAi ?RNAi XREF Phenotype
> 			Variation ?Variation XREF Phenotype
>                         Transgene ?Transgene XREF Phenotype	// Added by Carol
> 			Anatomy_function ?Anatomy_function XREF Phenotype
> 			Interaction ?Interaction XREF Interaction_phenotype
> 			Rearrangement ?Rearrangement XREF Phenotype
> 			Strain ?Strain XREF Phenotype
> 			Not_in_RNAi ?RNAi XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
> 			Not_in_Variation ?Variation XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
> 			Not_in_Strain ?Strain XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
> 			Not_in_Transgene ?Transgene XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
> 			Not_in_Rearrangement ?Rearrangement XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
> 	   Associated_with GO_term ?GO_term XREF Phenotype ?GO_code #Evidence	// Tag Associated_with changed by Carol
> 			   WBProcess ?WBProcess XREF Phenotype
> 			   DO_term ?DO_term #Evidence
2640c2655
< 	Description UNIQUE ?Text     #Evidence
---
> 	Description UNIQUE ?Text #Evidence
2642,2646c2657,2661
< 	History    Merged_into      UNIQUE ?Operon XREF Acquires_merge #Evidence
< 		   Acquires_merge   ?Operon XREF Merged_into #Evidence
< 		   Split_from       UNIQUE ?Operon XREF Split_into #Evidence
< 		   Split_into       ?Operon XREF Split_from #Evidence
< 		   Deprecated	    Text   #Evidence //pad - for operons no longer believed.
---
> 	History Merged_into UNIQUE ?Operon XREF Acquires_merge #Evidence
> 		Acquires_merge ?Operon XREF Merged_into #Evidence
> 		Split_from UNIQUE ?Operon XREF Split_into #Evidence
> 		Split_into ?Operon XREF Split_from #Evidence
> 		Deprecated Text #Evidence //pad - for operons no longer believed.
2671c2686
< //	##		Classes for microarray data      ##
---
> //	  		Classes for microarray data
2681,2686c2696,2701
< ?Microarray     Chip_type UNIQUE ?Text  //SMD, Affymetrix, etc.
<                 Chip_info  ?Text        //Describes batch number of the chip, etc.
<                 Reference  ?Paper       //Describes design of the chip
< 		URL Text                //to link to manufacturers site.
<                 Remark     ?Text        #Evidence
<                 Microarray_experiment   ?Microarray_experiment XREF Microarray
---
> ?Microarray Chip_type UNIQUE ?Text  //SMD, Affymetrix, etc.
>             Chip_info ?Text         //Describes batch number of the chip, etc.
>             Reference ?Paper        //Describes design of the chip
> 	    URL Text                //to link to manufacturers site.
>             Remark ?Text #Evidence
>             Microarray_experiment ?Microarray_experiment XREF Microarray
2697,2707c2712,2722
< 			Sequence_info UNIQUE PCR_product     UNIQUE ?PCR_product     XREF Microarray_results
<                                              Oligo_set       UNIQUE ?Oligo_set       XREF Microarray_results
<                         Gene          ?Gene 	  XREF Microarray_results #Evidence   // should be mapped during the build
<                         CDS	      ?CDS 	  XREF Microarray_results #Evidence   // should be mapped during the build
<                         Transcript    ?Transcript XREF Microarray_results #Evidence   // should be mapped during the build
< 			Pseudogene    ?Pseudogene XREF Microarray_results #Evidence   // should be mapped during the build
< 			Microarray    ?Microarray
<                         Results       ?Microarray_experiment UNIQUE #Microarray_data
<                         Range         Min UNIQUE Float UNIQUE ?Microarray_experiment  // mix observed ratio or frequency in all experiments and corresponding experiment
<                                       Max UNIQUE Float UNIQUE ?Microarray_experiment  // max observed ratio or frequency in all experiments and corresponding experiment 
<                         Remark        ?Text   #Evidence
---
> 			Sequence_info UNIQUE PCR_product UNIQUE ?PCR_product XREF Microarray_results
>                                              Oligo_set UNIQUE ?Oligo_set XREF Microarray_results
>                         Gene ?Gene XREF Microarray_results #Evidence               // should be mapped during the build
>                         CDS ?CDS XREF Microarray_results #Evidence                 // should be mapped during the build
>                         Transcript ?Transcript XREF Microarray_results #Evidence   // should be mapped during the build
> 			Pseudogene ?Pseudogene XREF Microarray_results #Evidence   // should be mapped during the build
> 			Microarray ?Microarray
>                         Results ?Microarray_experiment UNIQUE #Microarray_data
>                         Range Min UNIQUE Float UNIQUE ?Microarray_experiment  // mix observed ratio or frequency in all experiments and corresponding experiment
>                               Max UNIQUE Float UNIQUE ?Microarray_experiment  // max observed ratio or frequency in all experiments and corresponding experiment 
>                         Remark ?Text #Evidence
2717,2728c2732,2743
< #Microarray_data        Result          A_vs_B_log_ratio        UNIQUE Float                 // relative abundance               
<                                         A_vs_B_SD               UNIQUE Float                 // standard deviation over a set of experiments
<                                         Frequency               UNIQUE Float                 // absolute abundance in ppm - [14-Mar-06 ar2] Igor wants a float (absolute?)
<                                         Number_of_experiments   UNIQUE Int
<                                         Range_within_paper      UNIQUE Float UNIQUE Float    // min and max observed ratio or frequency in all experiments from a paper
<                         Confidence      Confidence_level        UNIQUE Float                 // Igor [031020
< 					P_value  UNIQUE Float
<                                         Presence UNIQUE PA                                   // present always
<                                                         PS                                   // present sometimes - marginal call
<                                                         NP                                   // never present
< 			Expression_cluster ?Expression_cluster XREF Microarray_results       // one way XREF used to populate Cluster Class (prev ?Cluster)
<                         Remark          Text #Evidence
---
> #Microarray_data Result A_vs_B_log_ratio UNIQUE Float                 // relative abundance               
>                         A_vs_B_SD UNIQUE Float                        // standard deviation over a set of experiments
>                         Frequency UNIQUE Float                        // absolute abundance in ppm - [14-Mar-06 ar2] Igor wants a float (absolute?)
>                         Number_of_experiments UNIQUE Int
>                         Range_within_paper UNIQUE Float UNIQUE Float  // min and max observed ratio or frequency in all experiments from a paper
>                  Confidence Confidence_level UNIQUE Float             // Igor [031020
> 			    P_value UNIQUE Float
>                             Presence UNIQUE PA                        // present always
>                                             PS                        // present sometimes - marginal call
>                                             NP                        // never present
> 		 Expression_cluster ?Expression_cluster XREF Microarray_results       // one way XREF used to populate Cluster Class (prev ?Cluster)
>                  Remark Text #Evidence
2741,2745c2756,2760
<                         Sample  Sample_A     UNIQUE      ?Condition     //for PCR product-base (SMD-type) chips
<                                 Sample_B     UNIQUE      ?Condition     //for PCR product-base (SMD-type) chips
<                                 Microarray_sample UNIQUE ?Condition     //for oligo-based (Affymetrix-type) chips
<                         Reference  ?Paper XREF Microarray_experiment
<                         Remark     Text        #Evidence
---
>                         Sample Sample_A UNIQUE ?Condition     //for PCR product-base (SMD-type) chips
>                                Sample_B UNIQUE ?Condition     //for PCR product-base (SMD-type) chips
>                                Microarray_sample UNIQUE ?Condition     //for oligo-based (Affymetrix-type) chips
>                         Reference ?Paper XREF Microarray_experiment
>                         Remark Text #Evidence
2763c2778
< 		Overlaps_CDS 	    ?CDS 	XREF Corresponding_oligo_set #Evidence
---
> 		Overlaps_CDS ?CDS XREF Corresponding_oligo_set #Evidence
2766c2781
< 		Remark Text    #Evidence
---
> 		Remark Text #Evidence
2781c2796
< ?Expression_cluster  Description  ?Text				             // refers to Biological meaning of this cluster group
---
> ?Expression_cluster  Description ?Text                                       // refers to Biological meaning of this cluster group
2783,2786c2798,2801
< 		     Algorithm    Text				             // refers to the algorithm that was used to get this clustering result.
< 		     Reference    ?Paper XREF Expression_cluster
< 		     Based_on_WB_Release     Int //Wen - to identify clusters not mapped if authors did not provide probe information.
< 		     Microarray_results ?Microarray_results  Text #Evidence  //refers to all experimental results included in the cluster.
---
> 		     Algorithm Text                                          // refers to the algorithm that was used to get this clustering result.
> 		     Reference ?Paper XREF Expression_cluster
> 		     Based_on_WB_Release Int                                 // Wen - if authors did not provide probe information.
> 		     Microarray_results ?Microarray_results Text #Evidence   // refers to all experimental results included in the cluster.
2788,2789c2803,2805
< 		     Gene ?Gene XREF Expression_cluster Text #Evidence       //Igor: populated during build based on Microarray_results mapping
< 		     Attribute_of Microarray_experiment ?Microarray_experiment  XREF Expression_cluster //Wen
---
> 		     Gene ?Gene XREF Expression_cluster Text #Evidence       // Igor - populated during build based on Microarray_results mapping
> 		     Attribute_of Microarray_experiment ?Microarray_experiment XREF Expression_cluster // Wen
> 				  Mass_spectrometry ?Mass_spec_experiment XREF Expression_cluster      // Wen WS244
2793,2798c2809,2814
< 				  Expr_pattern ?Expr_pattern XREF Expression_cluster #Evidence          //Wen originally for Localizome
<                      Regulation   Regulated_by_gene ?Gene		     //Wen WS228
<                                   Regulated_by_treatment Text                //Wen WS228
<                                   Regulated_by_molecule ?Molecule            //Wen WS228
<                      Associated_with  Life_stage ?Life_stage                 //Wen WS228
<                                       GO_term ?GO_term                       //Wen WS228
---
> 				  Expr_pattern ?Expr_pattern XREF Expression_cluster #Evidence          // Wen originally for Localizome
>                      Regulation   Regulated_by_gene ?Gene                    // Wen WS228
>                                   Regulated_by_treatment Text                // Wen WS228
>                                   Regulated_by_molecule ?Molecule            // Wen WS228
>                      Associated_with  Life_stage ?Life_stage                 // Wen WS228
>                                       GO_term ?GO_term                       // Wen WS228
2805c2821
< //      SAGE_tag model
---
> //      SAGE_tag class
2810,2819c2826,2835
<                 Tag_sequence            UNIQUE Text     //tag sequence including the restriction site
<                 Anchoring_enzyme        UNIQUE ?Motif   //NlaIII most commonly
<                 Tag_length              UNIQUE Int      //14 most commonly
<                 Most_three_prime        // added for tags which are the most 3' in a transcript
<                 Unambiguously_mapped    //boolean; describes whether tag is unambiguously mapped to one SAGE transcript or to splice isoforms of the same gene at the same genomic location
<                 Corresponds_to  Predicted_CDS   ?CDS XREF SAGE_tag #SAGE_mapping_info
<                                 Gene            ?Gene XREF SAGE_tag #SAGE_mapping_info
<                                 Transcript      ?Transcript XREF SAGE_tag #SAGE_mapping_info
<                                 Pseudogene      ?Pseudogene XREF SAGE_tag #SAGE_mapping_info
<                 Results ?SAGE_experiment UNIQUE #SAGE_data //contains SAGE data for all experiments using the tag
---
>                 Tag_sequence UNIQUE Text         // tag sequence including the restriction site
>                 Anchoring_enzyme UNIQUE ?Motif   // NlaIII most commonly
>                 Tag_length UNIQUE Int            // 14 most commonly
>                 Most_three_prime                 // added for tags which are the most 3' in a transcript
>                 Unambiguously_mapped             // boolean; describes whether tag is unambiguously mapped to one SAGE transcript or to splice isoforms of the same gene at the same genomic location
>                 Corresponds_to  Predicted_CDS ?CDS XREF SAGE_tag #SAGE_mapping_info
>                                 Gene ?Gene XREF SAGE_tag #SAGE_mapping_info
>                                 Transcript ?Transcript XREF SAGE_tag #SAGE_mapping_info
>                                 Pseudogene ?Pseudogene XREF SAGE_tag #SAGE_mapping_info
>                 Results ?SAGE_experiment UNIQUE #SAGE_data              //contains SAGE data for all experiments using the tag
2821c2837
<                 Method UNIQUE ?Method  //for GFF dumping
---
>                 Method UNIQUE ?Method
2823,2826c2839,2842
< #SAGE_mapping_info Transcript_source      UNIQUE ?Text            //Coding RNA, Mitochondrial, Other...
<                    Position               UNIQUE Int              //the number of the SAGE anchoring enzyme restriction site from the 3' end of the cDNA molecule
<                    Strand                 UNIQUE Sense            //sense/antisense
<                                                  Antisense
---
> #SAGE_mapping_info Transcript_source UNIQUE ?Text   //Coding RNA, Mitochondrial, Other...
>                    Position UNIQUE Int              //the number of the SAGE anchoring enzyme restriction site from the 3' end of the cDNA molecule
>                    Strand UNIQUE Sense              //sense/antisense
>                                  Antisense
2830,2839c2846,2855
< #SAGE_data      Result          Frequency               UNIQUE Int      //tag count
<                                 Total_tag_count         UNIQUE Int      //sum of all tag counts in the experiment
<                                 Relative_abundance      UNIQUE Float    //Frequency/Total_tag_count
<                                 Significance            UNIQUE Float
<                                 Confidence_level        UNIQUE Float
<                                 Standard_deviation      UNIQUE Float
<                                 Number_of_experiments   UNIQUE Int
< 		Expression_cluster ?Expression_cluster XREF SAGE_tag    //Replaces ?Cluster connection
<                 Sequence_quality  UNIQUE Float            //most commonly cumulative phred scores associated with the tag 
< 						// sequences; not in ?SAGE_tag since it will vary from experiment to experiment
---
> #SAGE_data Result Frequency UNIQUE Int              // tag count
>                   Total_tag_count UNIQUE Int        // sum of all tag counts in the experiment
>                   Relative_abundance UNIQUE Float   // Frequency/Total_tag_count
>                   Significance UNIQUE Float
>                   Confidence_level UNIQUE Float
>                   Standard_deviation UNIQUE Float
>                   Number_of_experiments UNIQUE Int
> 	   Expression_cluster ?Expression_cluster XREF SAGE_tag    //Replaces ?Cluster connection
>            Sequence_quality UNIQUE Float            //most commonly cumulative phred scores associated with the tag 
> 						    // sequences; not in ?SAGE_tag since it will vary from experiment to experiment
2849c2865
< ?SAGE_experiment Sample  UNIQUE  ?Condition XREF SAGE_experiment
---
> ?SAGE_experiment Sample UNIQUE ?Condition XREF SAGE_experiment
2851c2867
<                  Reference  ?Paper XREF SAGE_experiment
---
>                  Reference ?Paper XREF SAGE_experiment
2872,2896c2888,2912
< ?3d_data Evidence              #Evidence
<          DB_info  Database ?Database ?Database_field ?Text
<          CDS      ?CDS XREF 3d_data
< 	 Protein  ?Protein XREF 3d_data
< 	 Gene	  ?Gene XREF 3d_data
<          Status                Selected
<                                Cloned
<                                Expressed
<                                Soluble
<                                Purified
<                                Crystallized
<                                Diffraction_quality_crystals    //Diffraction-quality Crystals
<                                Diffraction
<                                NMR_assigned                    //NMR assigned
<                                HSQC
<                                Crystal_structure               //Crystal Structure
<                                NMR_structure                   //NMR Structure
<                                In_PDB                          //In PDB
<                                Work_stopped                    //Work Stopped
<                                Test_target                     //Test Target
<                                Other
<          Origin                Location UNIQUE NESGC           //3d data sources can be added as new sub-tags to the model in the future
<                                First_imported UNIQUE DateType
<                                Last_updated UNIQUE DateType
<          Remark                ?Text #Evidence
---
> ?3d_data Evidence #Evidence
>          DB_info Database ?Database ?Database_field ?Text
>          CDS ?CDS XREF 3d_data
> 	 Protein ?Protein XREF 3d_data
> 	 Gene ?Gene XREF 3d_data
>          Status Selected
>                 Cloned
>                 Expressed
>                 Soluble
>                 Purified
>                 Crystallized
>                 Diffraction_quality_crystals    //Diffraction-quality Crystals
>                 Diffraction
>                 NMR_assigned                    //NMR assigned
>                 HSQC
>                 Crystal_structure               //Crystal Structure
>                 NMR_structure                   //NMR Structure
>                 In_PDB                          //In PDB
>                 Work_stopped                    //Work Stopped
>                 Test_target                     //Test Target
>                 Other
>          Origin Location UNIQUE NESGC           //3d data sources can be added as new sub-tags to the model in the future
>                 First_imported UNIQUE DateType
>                 Last_updated UNIQUE DateType
>          Remark ?Text #Evidence
2911c2927
< ?Person PostgreSQL_id UNIQUE Text     // for linking to internal RDB // Text instead of Int so it says WBperson####
---
> ?Person PostgreSQL_id UNIQUE Text         // for linking to internal RDB // Text instead of Int so it says WBperson####
2913,2919c2929,2935
<         Name    First_name    UNIQUE  Text    // prefered first name
<                 Middle_name   Text            // middle name(s)
<                 Last_name     UNIQUE  ?Person_name XREF Last_name_of    // prefered last name
<                 Standard_name UNIQUE  ?Person_name XREF Standard_name_of   // name to be used for displays
<                                               // default is "First_name Last_name"
< 		Full_name     UNIQUE  ?Person_name XREF Full_name_of // field for storing long name [030321 krb]
<                 Also_known_as   ?Person_name XREF Other_name_of // new XREF added [030310 krb]
---
>         Name    First_name UNIQUE Text    // prefered first name
>                 Middle_name Text          // middle name(s)
>                 Last_name UNIQUE ?Person_name XREF Last_name_of    // prefered last name
>                 Standard_name UNIQUE ?Person_name XREF Standard_name_of   // name to be used for displays
>                                           // default is "First_name Last_name"
> 		Full_name UNIQUE ?Person_name XREF Full_name_of // field for storing long name [030321 krb]
>                 Also_known_as ?Person_name XREF Other_name_of // new XREF added [030310 krb]
2935c2951
<  	Lineage Supervised    ?Person XREF Supervised_by #Role
---
>  	Lineage Supervised ?Person XREF Supervised_by #Role
2937c2953
<                 Worked_with   ?Person XREF Worked_with #Role
---
>                 Worked_with ?Person XREF Worked_with #Role
2946c2962
< #Address  Street_address Text        // multiple lines including town, state, zip/postcode, whatever
---
> #Address  Street_address Text           // multiple lines including town, state, zip/postcode, whatever
2949,2955c2965,2971
<           Email Text                 // multiple emails allowed
<           Main_phone    Text         // phone number for the institution, I presume
<           Lab_phone     Text
<           Office_phone  Text
<           Other_phone   Text UNIQUE Text  // second text can be used to indicate type
<           Fax           Text 
<           Web_page      Text    // web page is part of the address info I think
---
>           Email Text                    // multiple emails allowed
>           Main_phone Text               // phone number for the institution, I presume
>           Lab_phone Text
>           Office_phone Text
>           Other_phone Text UNIQUE Text  // second text can be used to indicate type
>           Fax Text 
>           Web_page Text                 // web page is part of the address info I think
2967,2977c2983,2993
< #Role   Assistant_professor    DateType    UNIQUE    DateType
< 	Phd		DateType UNIQUE DateType
<         Postdoc		DateType UNIQUE DateType
<         Masters		DateType UNIQUE DateType
<         Undergrad	DateType UNIQUE DateType
<         Highschool	DateType UNIQUE DateType
<         Sabbatical	DateType UNIQUE DateType
<         Lab_visitor	DateType UNIQUE DateType
<         Collaborated	DateType UNIQUE DateType
<         Research_staff  DateType UNIQUE DateType
<         Unknown		DateType UNIQUE DateType
---
> #Role Assistant_professor DateType UNIQUE DateType
>       Phd DateType UNIQUE DateType
>       Postdoc DateType UNIQUE DateType
>       Masters DateType UNIQUE DateType
>       Undergrad DateType UNIQUE DateType
>       Highschool DateType UNIQUE DateType
>       Sabbatical DateType UNIQUE DateType
>       Lab_visitor DateType UNIQUE DateType
>       Collaborated DateType UNIQUE DateType
>       Research_staff DateType UNIQUE DateType
>       Unknown DateType UNIQUE DateType
2988c3004
< ?Person_name Name Full_name_of     ?Person XREF Full_name
---
> ?Person_name Name Full_name_of ?Person XREF Full_name
2990,2991c3006,3007
< 		  Last_name_of     ?Person XREF Last_name
< 		  Other_name_of    ?Person XREF Also_known_as // added [030310 krb]
---
> 		  Last_name_of ?Person XREF Last_name
> 		  Other_name_of ?Person XREF Also_known_as // added [030310 krb]
3007c3023
<                 Fax   Text
---
>                 Fax Text
3029,3039c3045,3055
<        Erratum_in      ?Paper XREF Erratum_for
<        Erratum_for     ?Paper XREF Erratum_in
<        Reference       Title UNIQUE ?Text
<                        Journal UNIQUE ?Text     //we are cleaning up Journal names and considering retiring the class
<                        Publisher UNIQUE Text
<                        Editor ?Text            //used for books put in as objects
<                        Page  UNIQUE  Text 
<                        Volume UNIQUE Text
<                        Publication_date UNIQUE ?Text         //YYYY-MM-DD or YYYY-MM, replaces DateType which led to erroneous pub dates
<                        Contained_in ?Paper XREF Contains       // old form
<                        Contains ?Paper XREF Contained_in
---
>        Erratum_in ?Paper XREF Erratum_for
>        Erratum_for ?Paper XREF Erratum_in
>        Reference Title UNIQUE ?Text
>                  Journal UNIQUE ?Text     //we are cleaning up Journal names and considering retiring the class
>                  Publisher UNIQUE Text
>                  Editor ?Text            //used for books put in as objects
>                  Page UNIQUE Text 
>                  Volume UNIQUE Text
>                  Publication_date UNIQUE ?Text         //YYYY-MM-DD or YYYY-MM, replaces DateType which led to erroneous pub dates
>                  Contained_in ?Paper XREF Contains       // old form
>                  Contains ?Paper XREF Contained_in
3048,3071c3064,3087
<        Type    Journal_article        #Evidence
<                Review        #Evidence
<                Comment        #Evidence
<                News        #Evidence
<                Letter        #Evidence
<                Editorial        #Evidence
<                Congresses        #Evidence
<                Historical_article        #Evidence
<                Biography        #Evidence
<                Interview        #Evidence
<                Lectures        #Evidence
<                Interactive_tutorial        #Evidence
<                Retracted_publication        #Evidence
<                Technical_report        #Evidence
<                Directory        #Evidence
<                Monograph        #Evidence
<                Published_erratum        #Evidence
<                Meeting_abstract        #Evidence
<                Gazette_article        #Evidence
<                Book_chapter        #Evidence
<                Book        #Evidence
<                Email        #Evidence
<                WormBook        #Evidence
<                Other        #Evidence
---
>        Type    Journal_article #Evidence
>                Review #Evidence
>                Comment #Evidence
>                News #Evidence
>                Letter #Evidence
>                Editorial #Evidence
>                Congresses #Evidence
>                Historical_article #Evidence
>                Biography #Evidence
>                Interview #Evidence
>                Lectures #Evidence
>                Interactive_tutorial #Evidence
>                Retracted_publication #Evidence
>                Technical_report #Evidence
>                Directory #Evidence
>                Monograph #Evidence
>                Published_erratum #Evidence
>                Meeting_abstract #Evidence
>                Gazette_article #Evidence
>                Book_chapter #Evidence
>                Book #Evidence
>                Email #Evidence
>                WormBook #Evidence
>                Other #Evidence
3106c3122
<        Remark  ?Text   #Evidence
---
>        Remark ?Text #Evidence
3148,3151c3164,3167
< #GR_condition          Life_stage               ?Life_stage      
<                        Cell                     ?Cell
<                        Cell_group               ?Cell_group
< 		       Anatomy_term		?Anatomy_term //Added by wen 02132006
---
> #GR_condition          Life_stage ?Life_stage      
>                        Cell ?Cell
>                        Cell_group ?Cell_group
> 		       Anatomy_term ?Anatomy_term //Added by wen 02132006
3161,3163c3177,3179
< 	   Name Public_name	UNIQUE ?Variation_name XREF Public_name_for
< 		Other_name	?Variation_name XREF Other_name_for #Evidence
<                 Rearrangement	?Rearrangement  XREF Variation // some alleles are really rearrangements		
---
> 	   Name Public_name UNIQUE ?Variation_name XREF Public_name_for
> 		Other_name ?Variation_name XREF Other_name_for #Evidence
>                 Rearrangement ?Rearrangement XREF Variation // some alleles are really rearrangements		
3171,3172c3187,3188
< 					     Insertion    UNIQUE Text      #Evidence
< 					     Deletion     UNIQUE Text      #Evidence  
---
> 					     Insertion UNIQUE Text #Evidence
> 					     Deletion UNIQUE Text #Evidence  
3191,3192c3207,3208
< 		  Author  ?Author // use Person when known, else use Author
<                   Person  ?Person //
---
> 		  Author ?Author // use Person when known, else use Author
>                   Person ?Person //
3210,3215c3226,3231
< 	   Affects Gene	         ?Gene	     XREF Allele #Molecular_change      //#Molecular_change mh6 define precise changes [060217 ar2]
< 		   Predicted_CDS ?CDS	     XREF Variation #Molecular_change
< 		   Transcript    ?Transcript XREF Variation #Molecular_change
< 		   Pseudogene    ?Pseudogene XREF Variation #Molecular_change
< 		   Feature       ?Feature    XREF Associated_with_variation
< 		   Interactor	 ?Interaction
---
> 	   Affects Gene	?Gene XREF Allele #Molecular_change      //#Molecular_change mh6 define precise changes [060217 ar2]
> 		   Predicted_CDS ?CDS XREF Variation #Molecular_change
> 		   Transcript ?Transcript XREF Variation #Molecular_change
> 		   Pseudogene ?Pseudogene XREF Variation #Molecular_change
> 		   Feature ?Feature XREF Associated_with_variation
> 		   Interactor ?Interaction
3217c3233
<            Isolation Date    DateType
---
>            Isolation Date DateType
3223c3239
< 		     Derivative	  ?Variation XREF Derived_from
---
> 		     Derivative	?Variation XREF Derived_from
3233c3249
< 		    Map ?Map   XREF Variation #Map_position
---
> 		    Map ?Map XREF Variation #Map_position
3235,3237c3251,3253
<                     Mapping_data 2_point         ?2_point_data
<                                  Multi_point     ?Multi_pt_data
<                                  Pos_neg_data    ?Pos_neg_data
---
>                     Mapping_data 2_point ?2_point_data
>                                  Multi_point ?Multi_pt_data
>                                  Pos_neg_data ?Pos_neg_data
3239,3240c3255,3256
<                                  In_2_point      ?2_point_data
<                                  In_multi_point  ?Multi_pt_data
---
>                                  In_2_point ?2_point_data
>                                  In_multi_point ?Multi_pt_data
3249,3250c3265,3266
<                                        Opal_UGA  Text #Evidence
<                        Missense Text  #Evidence				// text fields stored details of codon change
---
>                                        Opal_UGA Text #Evidence
>                        Missense Text #Evidence				// text fields stored details of codon change
3257c3273
<            Remark  ?Text #Evidence
---
>            Remark ?Text #Evidence
3259c3275
<            Supporting_data Movie   ?Movie   XREF Variation #Evidence  //Carol [060421 ar2] 
---
>            Supporting_data Movie ?Movie XREF Variation #Evidence  //Carol [060421 ar2] 
3262,3263c3278,3279
< ?Variation_name Other_name_for     ?Variation XREF Other_name // main reason for this class
<                 Public_name_for    ?Variation XREF Public_name // the main name for a gene
---
> ?Variation_name Other_name_for ?Variation XREF Other_name // main reason for this class
>                 Public_name_for ?Variation XREF Public_name // the main name for a gene
3267,3268c3283,3284
< #Molecular_change   Missense Int    Text #Evidence
<                     Silent   Text   #Evidence
---
> #Molecular_change   Missense Int Text #Evidence
>                     Silent Text #Evidence
3271c3287
<                                     Opal_UGA  Text #Evidence
---
>                                     Opal_UGA Text #Evidence
3275c3291
<                     Splice_site UNIQUE  Donor    Text #Evidence
---
>                     Splice_site UNIQUE  Donor Text #Evidence
3343,3344c3359,3360
<                       Ionisation_source     UNIQUE MALDI
<                                                    ESI
---
>                       Ionisation_source UNIQUE MALDI
>                                                ESI
3354a3371
>                       Expression_cluster ?Expression_cluster XREF Mass_spectrometry       // Wen WS244
3372,3373c3389,3390
< #Mass_spec_data  XCorr   UNIQUE Float   // SEQUEST score
<                  DeltaCN UNIQUE Float   // SEQUEST score
---
> #Mass_spec_data  XCorr UNIQUE Float      // SEQUEST score
>                  DeltaCN UNIQUE Float    // SEQUEST score
3375,3376c3392,3393
<                  Sp_rank UNIQUE Int  // SEQUEST score
<                  Sp_score UNIQUE Float  // SEQUEST score
---
>                  Sp_rank UNIQUE Int      // SEQUEST score
>                  Sp_score UNIQUE Float   // SEQUEST score
3380c3397
<                  Matches Protein ?Protein  XREF  Contains_peptide    // matched protein
---
>                  Matches Protein ?Protein XREF Contains_peptide    // matched protein
3393c3410
< 		   Subproject	  ?Analysis XREF Project
---
> 		   Subproject ?Analysis XREF Project
3411,3430c3428,3447
< ?Condition Life_stage      ?Life_stage
< 	   Sex		   UNIQUE Hermaphrodite
< 				  Male
< 				  Female	//not all worms are elegans!
< 				  Unknown
< 	   Food		   Text
< 	   Exposure_time   Text
< 	   Species	   UNIQUE ?Species
< 	   Strain	   ?Strain // added for Microarry_result [030127 krb]
< 	   Preparation	   ?Text // added for Microarray_result [030127 krb]
<            Temperature     Float // Int -> Float WS236
<            Genotype        ?Text
<            Other           ?Text
<            Relationship    Contains        ?Condition XREF Contained_in
<                            Contained_in    ?Condition XREF Contains
<                            Precedes        ?Condition XREF Follows
<                            Follows         ?Condition XREF Precedes
<            Reference       ?Paper  //Defines the condition.
< 	   Tissue	   ?Anatomy_term   // added for Experiment (Microarray_results)
<            Treatment       ?Text // added for Experiment (Microarray_results)
---
> ?Condition Life_stage ?Life_stage
> 	   Sex UNIQUE Hermaphrodite
> 		      Male
> 		      Female	//not all worms are elegans!
> 		      Unknown
> 	   Food	Text
> 	   Exposure_time Text
> 	   Species UNIQUE ?Species
> 	   Strain ?Strain // added for Microarry_result [030127 krb]
> 	   Preparation ?Text // added for Microarray_result [030127 krb]
>            Temperature Float // Int -> Float WS236
>            Genotype ?Text
>            Other ?Text
>            Relationship Contains ?Condition XREF Contained_in
>                         Contained_in ?Condition XREF Contains
>                         Precedes ?Condition XREF Follows
>                         Follows ?Condition XREF Precedes
>            Reference ?Paper  //Defines the condition.
> 	   Tissue ?Anatomy_term   // added for Experiment (Microarray_results)
>            Treatment ?Text // added for Experiment (Microarray_results)
3432,3433c3449,3450
< 	   Analysis	   ?Analysis XREF Sample 
<            Remark          ?Text #Evidence
---
> 	   Analysis ?Analysis XREF Sample 
>            Remark ?Text #Evidence
3446c3463
<            Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule //Wen WS228
---
>            Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule    // Wen WS228
3448,3454c3465,3471
<            Affects_phenotype_of     Variation ?Variation ?Phenotype #Evidence
<                                     Strain    ?Strain    ?Phenotype #Evidence
<                                     Transgene ?Transgene ?Phenotype #Evidence
<                                     RNAi      ?RNAi      ?Phenotype #Evidence
< 				    Rearrangement  ?Rearrangement  ?Phenotype  #Evidence  //KY [110602 pad]
< 	   Interaction	?Interaction	XREF	Molecule_regulator
< 	   Molecule_use  ?Text  #Evidence
---
>            Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence
>                                 Strain ?Strain ?Phenotype #Evidence
>                                 Transgene ?Transgene ?Phenotype #Evidence
>                                 RNAi ?RNAi ?Phenotype #Evidence
> 				Rearrangement ?Rearrangement ?Phenotype #Evidence  // KY [110602 pad]
> 	   Interaction ?Interaction XREF Molecule_interactor                       // Chris WS244
> 	   Molecule_use ?Text #Evidence
3481c3498
<                                 Expression_cluster ?Expression_cluster XREF WBProcess  #Evidence
---
>                                 Expression_cluster ?Expression_cluster XREF WBProcess #Evidence
3491c3508
<                 Movie ?Movie  #Evidence
---
>                 Movie ?Movie #Evidence
3494c3511
<                 Historical_gene   ?Gene #Evidence
---
>                 Historical_gene ?Gene #Evidence
3509a3527
> // WS244
gen1b[pad]2171: cvs diff -r 1.403 -r 1.406 | less
X11 forwarding request failed on channel 0
cvs diff: Diffing .
? WS244_preliminary_models.wrm
Index: models.wrm
===================================================================
RCS file: /nfs/ensembl/cvsroot/wormbase/wspec/models.wrm,v
retrieving revision 1.403
retrieving revision 1.406
diff -r1.403 -r1.406
17c17
< // Last edited on: $Date: 2014-03-14 12:38:51 $
---
> // Last edited on: $Date: 2014-05-10 09:56:35 $
62c62
<                Gene  ?Gene XREF Map
---
>                Gene ?Gene XREF Map
69c69
<                  Transgene  ?Transgene //sdm added to display gmaps //removed XREF ky 2011 
---
>                  Transgene ?Transgene //sdm added to display gmaps //removed XREF ky 2011 
78c78
<                       Multi_Position  Float #Map_error
---
>                       Multi_Position Float #Map_error
156c156
<                       Point_pe  #Colour // positive, error
---
>                       Point_pe #Colour  // positive, error
158c158
<                       Point_ne  #Colour // negative, error
---
>                       Point_ne #Colour  // negative, error
208c208
<                       Pe  #Colour // positive, error
---
>                       Pe #Colour  // positive, error
210c210
<                       Ne  #Colour // negative, error
---
>                       Ne #Colour  // negative, error
234c234
<                 Main_name  ?Gene_class XREF Other_name
---
>                 Main_name ?Gene_class XREF Other_name
250,256c250,256
<         Type  Polymorphism    SNP  Text       // Todd [171001 krb]
<                                 Status Text
<                                 SNP_assay ?PCR_product XREF SNP_locus ?Text
<                                 RFLP    Text
<                                 Transposon_insertion  Text
<                                 Detection_method Text
<         Map    UNIQUE ?Map XREF Locus #Map_position
---
>         Type Polymorphism    SNP Text        // Todd [171001 krb]
>                              Status Text
>                              SNP_assay ?PCR_product XREF SNP_locus ?Text
>                              RFLP Text
>                              Transposon_insertion Text
>                              Detection_method Text
>         Map UNIQUE ?Map XREF Locus #Map_position
278,294c278,294
<         Identity  Version UNIQUE Int
<                   Name  CGC_name        UNIQUE ?Gene_name XREF CGC_name_for #Evidence
<                         Sequence_name   UNIQUE ?Gene_name XREF Sequence_name_for // captures main CDS name without isoforms
<                       Molecular_name         ?Gene_name XREF Molecular_name_for  // for linking to full CDS names, wormpep etc.
<                         Other_name             ?Gene_name XREF Other_name_for #Evidence // other unapproved CGC-style gene names
<                         Public_name     UNIQUE ?Gene_name XREF Public_name_for // the one name that should be used
<                 DB_info Database ?Database ?Database_field ?Text
<                   Species UNIQUE ?Species
<                   History Version_change Int UNIQUE DateType UNIQUE ?Person #Gene_history_action
<                           Merged_into UNIQUE ?Gene XREF Acquires_merge
<                           Acquires_merge ?Gene XREF Merged_into
<                           Split_from UNIQUE ?Gene XREF Split_into
<                           Split_into ?Gene XREF Split_from
<                         Transposon_in_origin // for genes that are identified as having CDSs/Proteins that are Transposon in origin
<                 Status UNIQUE Live #Evidence
<                                 Suppressed #Evidence
<                                 Dead #Evidence   
---
>         Identity Version UNIQUE Int
>                  Name  CGC_name UNIQUE ?Gene_name XREF CGC_name_for #Evidence
>                        Sequence_name UNIQUE ?Gene_name XREF Sequence_name_for // captures main CDS name without isoforms
>                      Molecular_name ?Gene_name XREF Molecular_name_for      // for linking to full CDS names, wormpep etc.
>                        Other_name ?Gene_name XREF Other_name_for #Evidence    // other unapproved CGC-style gene names
>                        Public_name UNIQUE ?Gene_name XREF Public_name_for     // the one name that should be used
>                DB_info Database ?Database ?Database_field ?Text
>                  Species UNIQUE ?Species
>                  History Version_change Int UNIQUE DateType UNIQUE ?Person #Gene_history_action
>                          Merged_into UNIQUE ?Gene XREF Acquires_merge
>                          Acquires_merge ?Gene XREF Merged_into
>                          Split_from UNIQUE ?Gene XREF Split_into
>                          Split_into ?Gene XREF Split_from
>                        Transposon_in_origin // for genes that are identified as having CDSs/Proteins that are Transposon in origin
>                Status UNIQUE Live #Evidence
>                                Suppressed #Evidence
>                                Dead #Evidence   
305c305
<                 RNASeq_FPKM  ?Life_stage  Float  #Evidence
---
>                 RNASeq_FPKM ?Life_stage Float #Evidence
310c310
<                 Ortholog_other  ?Protein XREF Ortholog_gene #Evidence // to allow Orthologues links to none ?Gene genes eg remanei (ar2 Nov06)
---
>                 Ortholog_other ?Protein XREF Ortholog_gene #Evidence // to allow Orthologues links to none ?Gene genes eg remanei (ar2 Nov06)
321,323c321,323
<       Disease_info    Experimental_model ?DO_term XREF Gene_by_biology   ?Species   #Evidence             
<                       Potential_model    ?DO_term XREF Gene_by_orthology ?Species #Evidence
<                       Disease_relevance  ?Text ?Species #Evidence
---
>       Disease_info Experimental_model ?DO_term XREF Gene_by_biology ?Species #Evidence                    
>                    Potential_model ?DO_term XREF Gene_by_orthology ?Species #Evidence
>                    Disease_relevance ?Text ?Species #Evidence
353c353
<                   Positive Inside_rearr   ?Rearrangement XREF Gene_inside #Evidence
---
>                   Positive Inside_rearr ?Rearrangement XREF Gene_inside #Evidence
355c355
<                   Negative Outside_rearr  ?Rearrangement XREF Gene_outside #Evidence
---
>                   Negative Outside_rearr ?Rearrangement XREF Gene_outside #Evidence
365d364
<       
415,416c414,415
< ?Gene_name CGC_name_for       ?Gene XREF CGC_name
<            Sequence_name_for  ?Gene XREF Sequence_name
---
> ?Gene_name CGC_name_for ?Gene XREF CGC_name
>            Sequence_name_for ?Gene XREF Sequence_name
418,420c417,419
<            Other_name_for     ?Gene XREF Other_name     // main reason for this class
<            Former_member_of   ?Gene_class XREF Old_member // track old members of a class
<            Public_name_for    ?Gene XREF Public_name    // the main name for a gene
---
>            Other_name_for ?Gene XREF Other_name     // main reason for this class
>            Former_member_of ?Gene_class XREF Old_member // track old members of a class
>            Public_name_for ?Gene XREF Public_name    // the main name for a gene
471,474c470,473
<               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 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
476,479c475,478
<                          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
<                          Rearrangement  ?Rearrangement XREF Interactor #Interactor_info
---
>                          Molecule_interactor ?Molecule XREF Interaction #Interactor_info     // Molecule that regulates a gene or protein (ported from Gene_regulation Class) Modified Chris WS244
>                          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
>                          Rearrangement ?Rearrangement XREF Interactor #Interactor_info
482,518c481,518
<               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
<                                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
<               Deviation_from_expectation Text                           // A text description of the way in which the phenotype deviated from expectation in genetic interactions     
<               Neutrality_function UNIQUE Multiplicative                 // The multiplicative neutrality function defines expectation as the product of two quantified phenotypes (relative to wild type) 
<                                          Additive                       // The additive neutrality function defines expectation as the sum of two quantified phenotypes (relative to wild type) 
<                                          Minimal                        // The minimal neutrality function defines expectation as the most severe of two quantified phenotypes (relative to wild type) 
<               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
---
>               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
>                                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
>                                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
>               Deviation_from_expectation Text                          // A text description of the way in which the phenotype deviated from expectation in genetic interactions      
>               Neutrality_function UNIQUE Multiplicative                // The multiplicative neutrality function defines expectation as the product of two quantified phenotypes (relative to wild type) 
>                                          Additive                      // The additive neutrality function defines expectation as the sum of two quantified phenotypes (relative to wild type) 
>                                          Minimal                       // The minimal neutrality function defines expectation as the most severe of two quantified phenotypes (relative to wild type) 
>               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
521,525c521,525
<                                 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
---
>                                 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
527,534c527,534
<               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
<               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
---
>               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
>               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
537c537
<               Historical_gene   ?Gene #Evidence
---
>               Historical_gene ?Gene #Evidence
551,552c551,552
<                      Intragenic_effector_variation   ?Variation   XREF   Interactor
<                      Intragenic_affected_variation   ?Variation   XREF   Interactor
---
>                      Intragenic_effector_variation ?Variation XREF Interactor
>                      Intragenic_affected_variation ?Variation XREF Interactor
600c600
<                               Source_rearrangement  ?Rearrangement XREF Derived_rearrangement
---
>                               Source_rearrangement ?Rearrangement XREF Derived_rearrangement
602,603c602,603
<                 Map     ?Map XREF Rearrangement #Map_position
<               Positive Gene_inside  ?Gene  XREF Inside_rearr #Evidence
---
>                 Map ?Map XREF Rearrangement #Map_position
>               Positive Gene_inside ?Gene XREF Inside_rearr #Evidence
605c605
<                        Clone_inside  ?Clone XREF Inside_rearr ?Author
---
>                        Clone_inside ?Clone XREF Inside_rearr ?Author
607c607
<               Negative Gene_outside  ?Gene  XREF Outside_rearr #Evidence
---
>               Negative Gene_outside ?Gene XREF Outside_rearr #Evidence
618c618
<               Strain   ?Strain XREF Rearrangement
---
>               Strain ?Strain XREF Rearrangement
630,645c630,645
<        Contains  Gene  ?Gene XREF Strain
<                  Variation  ?Variation XREF Strain 
<                  Rearrangement         ?Rearrangement XREF Strain
<                    Clone ?Clone XREF In_strain                  
<                  Transgene ?Transgene XREF Strain
<        Properties  Inbreeding_state UNIQUE Selfed Text
<                                              Isofemale Text
<                                              Multifemale Text
<                                              Inbred Text 
<                    Outcrossed Text
<                    Mutagen Text
<                    Strain_history Text
<                    Date_first_frozen UNIQUE DateType
<                    CGC_received DateType
<                    Phenotype ?Phenotype XREF Strain #Phenotype_info
<                    Phenotype_not_observed ?Phenotype XREF Not_in_Strain #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes 
---
>        Contains Gene   ?Gene XREF Strain
>                 Variation ?Variation XREF Strain 
>                 Rearrangement  ?Rearrangement XREF Strain
>                   Clone ?Clone XREF In_strain           
>                 Transgene ?Transgene XREF Strain
>        Properties Inbreeding_state UNIQUE Selfed Text
>                                             Isofemale Text
>                                             Multifemale Text
>                                             Inbred Text 
>                   Outcrossed Text
>                   Mutagen Text
>                   Strain_history Text
>                   Date_first_frozen UNIQUE DateType
>                   CGC_received DateType
>                   Phenotype ?Phenotype XREF Strain #Phenotype_info
>                   Phenotype_not_observed ?Phenotype XREF Not_in_Strain #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes 
686,689c686,689
< ?Lab_Location Freezer         Text
<               LiquidN2        Text
<               Minus70         Text
<                 Remark                ?Text #Evidence
---
> ?Lab_Location Freezer Text
>               LiquidN2 Text
>               Minus70 Text
>                 Remark ?Text #Evidence
693c693
< // ##                 worm physical map classes                 ##
---
> //                    worm physical map classes
697a698
> //
698a700,701
> // Class extended to incorporate AddGene data for WS244
> //
701a705,709
>       Species UNIQUE ?Species
>       Reference ?Paper XREF Clone
>       Produced_by Person ?Person              // Paul D. WS244
>                   Author ?Author              // Paul D. WS244
>       Sequence ?Sequence XREF Clone
705,714c713,721
<       Position  Map ?Map XREF Clone #Map_position
<                 pMap UNIQUE  ?Contig XREF Clone  UNIQUE Int UNIQUE Int 
<                                               // pMap units are bands
<                 Clone_left_end ?Sequence      // filled by XREF
<                 Clone_right_end ?Sequence     // filled by XREF
<                 Pos_neg_data ?Pos_neg_data
<       Positive Positive_gene   ?Gene XREF Positive_clone
<                Positive_variation  ?Variation XREF Positive_clone ?Author
<                Inside_rearr    ?Rearrangement XREF Clone_inside ?Author
<                Hybridizes_to   ?Clone XREF Positive_probe ?Grid
---
>       Position Map ?Map XREF Clone #Map_position
>                  pMap UNIQUE ?Contig XREF Clone UNIQUE Int UNIQUE Int // pMap units are bands
>                  Clone_left_end ?Sequence     // filled by XREF
>                  Clone_right_end ?Sequence    // filled by XREF
>                  Pos_neg_data ?Pos_neg_data
>       Positive Positive_gene ?Gene XREF Positive_clone
>                Positive_variation ?Variation XREF Positive_clone ?Author
>                Inside_rearr ?Rearrangement XREF Clone_inside ?Author
>                Hybridizes_to ?Clone XREF Positive_probe ?Grid
716,721c723,728
<                Positive_probe  ?Clone XREF Hybridizes_to ?Grid
<                Pos_probe_weak  ?Clone XREF Hybridizes_weak ?Grid
<       Negative Negative_gene   ?Gene XREF Negative_clone
<                Negative_locus  ?Locus XREF Negative_clone ?Author
<                Outside_rearr   ?Rearrangement XREF Clone_outside ?Author
<                Negative_probe  ?Clone XREF Does_not_hybridize_to ?Grid
---
>                Positive_probe ?Clone XREF Hybridizes_to ?Grid
>                Pos_probe_weak ?Clone XREF Hybridizes_weak ?Grid
>       Negative Negative_gene ?Gene XREF Negative_clone
>                Negative_locus ?Locus XREF Negative_clone ?Author
>                Outside_rearr ?Rearrangement XREF Clone_outside ?Author
>                Negative_probe ?Clone XREF Does_not_hybridize_to ?Grid
724,725c731
<       Species UNIQUE ?Species
<       Sequence    ?Sequence XREF Clone
---
>       Mutation ?Text                                  // Paul D. WS244
727,728c733,739
<       Length  Seq_length UNIQUE Int                   // bp
<               Gel_length UNIQUE Float                 // Kb
---
>       Primer1 ?Text                                   // Paul D. WS244
>       Primer2 ?Text                                   // Paul D. WS244
>       Resistance_marker ?Text                         // Paul D. WS244
>       Length  Seq_length UNIQUE Int                   // bp
>               Gel_length UNIQUE Float                 // Kb
>               Insert UNIQUE Int                       // bp Paul D. WS244
>               Backbone UNIQUE Int                     // bp Paul D. WS244
739,740c750,751
<                         Bands   UNIQUE Int UNIQUE Int
<                         Gel ?Motif  #Lane               // Magic tag2 construct
---
>                         Bands UNIQUE Int UNIQUE Int
>                         Gel ?Motif #Lane               // Magic tag2 construct
743c754
<               In_Situ  UNIQUE Int UNIQUE Int // percent of physical chromosome
---
>               In_Situ UNIQUE Int UNIQUE Int // percent of physical chromosome
746c757
<               Flag    UNIQUE Int
---
>               Flag UNIQUE Int
749d759
<       Reference ?Paper XREF Clone
753a764
>       Used_in_RNAi ?RNAi XREF Clone           // Chris WS244
765c776,779
<         Derived_from  ?Clone
---
>       Vector_type ?Text
>         Derived_from ?Clone XREF Parent_of
>       Parent_of ?Clone XREF Derived_from
>       Ligation ?Text
768c782
<              Band_Lengths  UNIQUE Float REPEAT // in mm: if you prefer to minimise the ace format
---
>              Band_Lengths UNIQUE Float REPEAT // in mm: if you prefer to minimise the ace format
789c803
<                           Date  UNIQUE DateType
---
>                           Date UNIQUE DateType
830,831c844,845
<               Genotype  UNIQUE Text
<               Results  UNIQUE Text
---
>               Genotype UNIQUE Text
>               Results UNIQUE Text
834c848
<                               Date  UNIQUE DateType
---
>                               Date UNIQUE DateType
836,837c850,851
<               Point_1 UNIQUE Gene_1   UNIQUE ?Gene  XREF 2_point UNIQUE ?Variation XREF In_2_point
<                              Locus_1  UNIQUE ?Locus XREF 2_point UNIQUE ?Variation XREF In_2_point
---
>               Point_1 UNIQUE Gene_1 UNIQUE ?Gene XREF 2_point UNIQUE ?Variation XREF In_2_point
>                              Locus_1 UNIQUE ?Locus XREF 2_point UNIQUE ?Variation XREF In_2_point
841,842c855,856
<               Point_2 UNIQUE Gene_2   UNIQUE ?Gene  XREF 2_point UNIQUE ?Variation XREF In_2_point
<                              Locus_2  UNIQUE ?Locus XREF 2_point UNIQUE ?Variation XREF In_2_point
---
>               Point_2 UNIQUE Gene_2 UNIQUE ?Gene XREF 2_point UNIQUE ?Variation XREF In_2_point
>                              Locus_2 UNIQUE ?Locus XREF 2_point UNIQUE ?Variation XREF In_2_point
872c886
<               Simple_distance Min      UNIQUE Float 
---
>               Simple_distance Min UNIQUE Float 
874,876c888,890
<                                 Max      UNIQUE Float
<                                 Error    UNIQUE Float
<                                 Linkage  UNIQUE Text
---
>                                 Max UNIQUE Float
>                                 Error UNIQUE Float
>                                 Linkage UNIQUE Text
884,885c898,899
<               Genotype  UNIQUE Text
<               Results  UNIQUE Text
---
>               Genotype UNIQUE Text
>               Results UNIQUE Text
888,889c902,903
<                          Date  UNIQUE DateType
<               Item_1  UNIQUE  Gene_1  UNIQUE ?Gene  XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data
---
>                          Date UNIQUE DateType
>               Item_1  UNIQUE  Gene_1 UNIQUE ?Gene XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data
894c908
<               Item_2  UNIQUE  Gene_2  UNIQUE ?Gene  XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data
---
>               Item_2  UNIQUE  Gene_2 UNIQUE ?Gene XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data
906c920
<               Genotype  UNIQUE Text
---
>               Genotype UNIQUE Text
909,912c923,926
<                           Date  UNIQUE DateType
<               Selected A UNIQUE Gene_A          UNIQUE ?Gene UNIQUE ?Variation XREF In_multi_point
<                                 Locus_A         UNIQUE ?Locus UNIQUE ?Variation XREF In_multi_point
<                                 Allele_A        UNIQUE ?Variation
---
>                           Date UNIQUE DateType
>               Selected A UNIQUE Gene_A UNIQUE ?Gene UNIQUE ?Variation XREF In_multi_point
>                                 Locus_A UNIQUE ?Locus UNIQUE ?Variation XREF In_multi_point
>                                 Allele_A UNIQUE ?Variation
914,917c928,931
<                                   Transgene_A     UNIQUE ?Transgene XREF Multi_point  
<                        B UNIQUE Gene_B          UNIQUE ?Gene UNIQUE ?Variation XREF In_multi_point
<                                 Locus_B         UNIQUE ?Locus UNIQUE ?Variation XREF In_multi_point
<                                 Allele_B        UNIQUE ?Variation
---
>                                   Transgene_A UNIQUE ?Transgene XREF Multi_point      
>                        B UNIQUE Gene_B UNIQUE ?Gene UNIQUE ?Variation XREF In_multi_point
>                                 Locus_B UNIQUE ?Locus UNIQUE ?Variation XREF In_multi_point
>                                 Allele_B UNIQUE ?Variation
920c934
<               Gene  ?Gene  UNIQUE ?Variation XREF In_multi_point     // Connect to ?Gene model
---
>               Gene ?Gene UNIQUE ?Variation XREF In_multi_point       // Connect to ?Gene model
931,933c945,947
< ?Multi_counts UNIQUE Gene          UNIQUE ?Gene                XREF Multi_point UNIQUE Int #Multi_counts
<                    Locus         UNIQUE ?Locus         XREF Multi_point UNIQUE Int #Multi_counts
<                    Allele        UNIQUE ?Variation     XREF Multi_point UNIQUE Int #Multi_counts
---
> ?Multi_counts UNIQUE Gene UNIQUE ?Gene XREF Multi_point UNIQUE Int #Multi_counts
>                    Locus UNIQUE ?Locus XREF Multi_point UNIQUE Int #Multi_counts
>                    Allele UNIQUE ?Variation XREF Multi_point UNIQUE Int #Multi_counts
935c949
<                    Transgene     UNIQUE ?Transgene     XREF Multi_point UNIQUE Int #Multi_counts  
---
>                    Transgene UNIQUE ?Transgene XREF Multi_point UNIQUE Int #Multi_counts  
985,989c999,1003
<        Attributes_of Cell       ?Cell       XREF GO_term
<                      Motif      ?Motif      XREF GO_term
<                      Gene       ?Gene       XREF GO_term // will this replace CDS? [040203 krb]
<                      CDS        ?CDS        XREF GO_term
<                      Sequence   ?Sequence   XREF GO_term // Erich, [011210 krb]
---
>        Attributes_of Cell ?Cell XREF GO_term
>                      Motif ?Motif XREF GO_term
>                      Gene ?Gene XREF GO_term // will this replace CDS? [040203 krb]
>                      CDS ?CDS XREF GO_term
>                      Sequence ?Sequence XREF GO_term // Erich, [011210 krb]
991,992c1005,1006
<                      Phenotype  ?Phenotype  XREF GO_term // Erich, [020128 dl]
<                      Index Ancestor   ?GO_term XREF Descendent // Lincoln [020709 [krb]
---
>                      Phenotype ?Phenotype XREF GO_term // Erich, [020128 dl]
>                      Index Ancestor ?GO_term XREF Descendent // Lincoln [020709 [krb]
1032c1046
<          Ancestor   ?SO_term XREF Descendent
---
>          Ancestor ?SO_term XREF Descendent
1064,1066c1078,1080
<        Synonym Broad   ?Text
<                Exact   ?Text
<                Narrow  ?Text
---
>        Synonym Broad ?Text
>                Exact ?Text
>                Narrow ?Text
1077,1081c1091,1095
<        Attribute_of Gene_by_biology    ?Gene       XREF   Experimental_model
<                     Gene_by_orthology  ?Gene       XREF   Potential_model
<                     Phenotype  ?Phenotype  XREF   DO_term
<                     WBProcess  ?WBProcess  XREF   DO_term
<                     Reference  ?Paper      XREF   DO_term 
---
>        Attribute_of Gene_by_biology ?Gene XREF Experimental_model
>                     Gene_by_orthology ?Gene XREF Potential_model
>                     Phenotype ?Phenotype XREF DO_term
>                     WBProcess ?WBProcess XREF DO_term
>                     Reference ?Paper XREF DO_term 
1113,1118c1127,1132
< ?Neurodata      Send            Text    UNIQUE Int #Neuro_location   // Text=series,Int=count
<                 Send_joint      Text    UNIQUE Int #Neuro_location   // "joint" indicates polyadic synapse
<                 Receive         Text    UNIQUE Int #Neuro_location
<                 Receive_joint   Text    UNIQUE Int #Neuro_location
<                 Gap_junction    Text    UNIQUE Int #Neuro_location
<                 Evidence        #Evidence
---
> ?Neurodata      Send Text UNIQUE Int #Neuro_location   // Text=series,Int=count
>                 Send_joint Text UNIQUE Int #Neuro_location   // "joint" indicates polyadic synapse
>                 Receive Text UNIQUE Int #Neuro_location
>                 Receive_joint Text UNIQUE Int #Neuro_location
>                 Gap_junction Text UNIQUE Int #Neuro_location
>                 Evidence #Evidence
1165,1168c1179,1182
<                              Genomic_parent   UNIQUE ?Sequence XREF Nongenomic
<                              AGP_parent       UNIQUE ?Sequence XREF AGP_fragment // added to hold briggsae data [krb 020726]
<              S_child Gene_child ?Gene       XREF Sequence UNIQUE Int UNIQUE Int #SMap_info  // maximal extent of Gene objects
<                      CDS_child  ?CDS        XREF Sequence UNIQUE Int UNIQUE Int #SMap_info  // For ?CDS [031104 krb]
---
>                              Genomic_parent UNIQUE ?Sequence XREF Nongenomic
>                              AGP_parent UNIQUE ?Sequence XREF AGP_fragment // added to hold briggsae data [krb 020726]
>              S_child Gene_child ?Gene XREF Sequence UNIQUE Int UNIQUE Int #SMap_info  // maximal extent of Gene objects
>                      CDS_child ?CDS XREF Sequence UNIQUE Int UNIQUE Int #SMap_info  // For ?CDS [031104 krb]
1221c1235
<                 Interaction  ?Interaction
---
>                 Interaction ?Interaction
1260,1261c1274,1275
<                    Match_type  UNIQUE Match_with_function
<                                       Match_without_function
---
>                    Match_type UNIQUE Match_with_function
>                                      Match_without_function
1267,1268c1281,1282
<                    Link // Enable gene curation of link genes [020805 krb]
<         Splices    Confirmed_intron  Int Int #Splice_confirmation
---
>                    Link       // Enable gene curation of link genes [020805 krb]
>         Splices    Confirmed_intron Int Int #Splice_confirmation
1271c1285
<         Cluster_information Contains_reads       ?Sequence XREF Contained_in_cluster  // Links cluster contig and
---
>         Cluster_information Contains_reads ?Sequence XREF Contained_in_cluster  // Links cluster contig and
1383,1397c1397,1411
< ?Sequence_collection Origin   Evidence #Evidence
<                               Name ?Text // name that the author gave this collection
<                               Species UNIQUE ?Species
<                               Strain UNIQUE ?Strain
<                               Laboratory ?Laboratory
<                               DB_info Database ?Database ?Database_field ?Text
<                    History    First_WS_release Int // first WormBase release this assembly was used
<                               Latest_WS_release Int // latest release where it was used
<                               Supercedes    UNIQUE ?Sequence_collection XREF Superceded_by
<                               Superceded_by UNIQUE ?Sequence_collection XREF Supercedes
<                    Remark     ?Text
<                    Status     UNIQUE Live #Evidence
<                                      Suppressed #Evidence
<                                      Dead #Evidence   
<                    Sequences  ?Sequence
---
> ?Sequence_collection Origin Evidence #Evidence
>                           Name ?Text // name that the author gave this collection
>                           Species UNIQUE ?Species
>                           Strain UNIQUE ?Strain
>                           Laboratory ?Laboratory
>                           DB_info Database ?Database ?Database_field ?Text
>                    History First_WS_release Int // first WormBase release this assembly was used
>                            Latest_WS_release Int // latest release where it was used
>                            Supercedes UNIQUE ?Sequence_collection XREF Superceded_by
>                            Superceded_by UNIQUE ?Sequence_collection XREF Supercedes
>                    Remark ?Text
>                    Status UNIQUE Live #Evidence
>                                  Suppressed #Evidence
>                                  Dead #Evidence   
>                    Sequences ?Sequence
1409c1423
<       SMap S_parent UNIQUE Sequence   UNIQUE ?Sequence   XREF CDS_child
---
>       SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF CDS_child
1436c1450
<               Interaction  ?Interaction
---
>               Interaction ?Interaction
1451c1465
<               RNASeq_FPKM  ?Life_stage  Float  #Evidence
---
>               RNASeq_FPKM ?Life_stage Float #Evidence
1488c1502
<                       RNASeq_FPKM  ?Life_stage  Float  #Evidence
---
>                       RNASeq_FPKM ?Life_stage Float #Evidence
1528,1534c1542,1548
<                 Origin  From_laboratory UNIQUE ?Laboratory
<                         Species UNIQUE ?Species
<                 Type    UNIQUE Coding_pseudogene #Evidence //Pseudogene of a once coding loci 
<                                RNA_pseudogene #Evidence    //Pseudogene of a ncRNA loci
<                                Transposon_pseudogene #Evidence //Pseudogene of Transposon origins
<               Attributes   Transcribed #Evidence
<                            Fragment #Evidence 
---
>                 Origin From_laboratory UNIQUE ?Laboratory
>                        Species UNIQUE ?Species
>                 Type UNIQUE Coding_pseudogene #Evidence //Pseudogene of a once coding loci 
>                             RNA_pseudogene #Evidence    //Pseudogene of a ncRNA loci
>                             Transposon_pseudogene #Evidence //Pseudogene of Transposon origins
>               Attributes Transcribed #Evidence
>                          Fragment #Evidence 
1536c1550
<                 Visible Gene         UNIQUE ?Gene XREF Corresponding_pseudogene         // when Pseudogene is live
---
>                 Visible Gene UNIQUE ?Gene XREF Corresponding_pseudogene         // when Pseudogene is live
1542c1556
<                       Corresponding_transposon    UNIQUE ?Transposon XREF Corresponding_pseudogene
---
>                       Corresponding_transposon UNIQUE ?Transposon XREF Corresponding_pseudogene
1551c1565
<                       RNASeq_FPKM  ?Life_stage  Float  #Evidence
---
>                       RNASeq_FPKM ?Life_stage Float #Evidence
1599c1613
<                  Associated_motif   ?Motif   XREF Associated_transposon_family // to connect Transposon famillies to Repeat motifs ar2
---
>                  Associated_motif ?Motif XREF Associated_transposon_family // to connect Transposon famillies to Repeat motifs ar2
1634,1639c1648,1653
<                 Group_type  UNIQUE COG           COG_type #Homology_type
<                                          COG_code #COG_codes
<                                  eggNOG  eggNOG_type #Homology_type
<                                          eggNOG_code #COG_codes
<                                  InParanoid_group
<                                  OrthoMCL_group     //erich Nov06
---
>                 Group_type UNIQUE COG    COG_type #Homology_type
>                                        COG_code #COG_codes
>                                 eggNOG eggNOG_type #Homology_type
>                                        eggNOG_code #COG_codes
>                                 InParanoid_group
>                                 OrthoMCL_group     //erich Nov06
1716,1717c1730,1731
<                   Strain  UNIQUE ?Strain//added by pad, as we are moving towards multi strain readyness.
<        History    Merged_into    UNIQUE    ?Feature XREF Acquires_merge #Evidence
---
>                   Strain UNIQUE ?Strain//added by pad, as we are moving towards multi strain readyness.
>        History    Merged_into UNIQUE ?Feature XREF Acquires_merge #Evidence
1719c1733
<                   Deprecated     Text      #Evidence 
---
>                   Deprecated Text #Evidence 
1723,1725c1737,1739
<                   Defined_by_paper    ?Paper XREF Feature #Evidence
<                   Defined_by_person   ?Person
<                   Defined_by_author   ?Author
---
>                   Defined_by_paper ?Paper XREF Feature #Evidence
>                   Defined_by_person ?Person
>                   Defined_by_author ?Author
1728,1730c1742,1744
<        Associations Associated_with_gene       ?Gene       XREF Associated_feature #Evidence // richard
<                       Associated_with_CDS      ?CDS        XREF Associated_feature #Evidence  // richard
<                       Associated_with_transcript ?Transcript XREF Associated_feature #Evidence  // richard
---
>        Associations Associated_with_gene ?Gene XREF Associated_feature #Evidence // richard
>                       Associated_with_CDS ?CDS XREF Associated_feature #Evidence // richard
>                       Associated_with_transcript ?Transcript XREF Associated_feature #Evidence // richard
1733,1735c1747,1749
<                     Associated_with_variation  ?Variation  XREF Feature #Evidence  
<                     Associated_with_Position_Matrix         ?Position_Matrix XREF Associated_feature #Evidence
<                     Associated_with_operon      ?Operon XREF Associated_feature #Evidence
---
>                     Associated_with_variation ?Variation XREF Feature #Evidence
>                     Associated_with_Position_Matrix ?Position_Matrix XREF Associated_feature #Evidence
>                     Associated_with_operon ?Operon XREF Associated_feature #Evidence
1737,1738c1751,1752
<                     Associated_with_expression_pattern         ?Expr_pattern XREF Associated_feature #Evidence 
<                     Associated_with_Feature ?Feature XREF Associated_with_Feature #Evidence 
---
>                     Associated_with_expression_pattern ?Expr_pattern XREF Associated_feature #Evidence 
>                     Associated_with_Feature ?Feature XREF Associated_with_Feature #Evidence
1741c1755
<        Annotation UNIQUE ?LongText            // added for data attribution [030220 dl]
---
>        Annotation UNIQUE ?LongText // added for data attribution [030220 dl]
1753c1767
<             Strain  UNIQUE ?Strain
---
>             Strain UNIQUE ?Strain
1756,1758c1770,1772
<             Splices   Confirmed_intron  Int Int #Splice_confirmation
<                       Predicted_5 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
<                       Predicted_3 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
---
>             Splices Confirmed_intron Int Int #Splice_confirmation
>                     Predicted_5 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
>                     Predicted_3 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1)
1771c1785
<                       Position_matrix  ?Position_Matrix XREF Transcription_factor #Evidence
---
>                       Position_matrix ?Position_Matrix XREF Transcription_factor #Evidence
1785,1788c1799,1802
< ?Position_Matrix  Description  ?Text #Evidence
<                 Brief_id  UNIQUE ?Text                        // Addition Xiaodong 
<                   Type  UNIQUE Frequency
<                                Weight
---
> ?Position_Matrix  Description ?Text #Evidence
>                 Brief_id UNIQUE ?Text                 // Addition Xiaodong 
>                   Type UNIQUE Frequency
>                               Weight
1790,1792c1804,1806
<                   Site_values      Text UNIQUE Float REPEAT
<                   Threshold        Float
<                   Consensus      Text #Evidence
---
>                   Site_values Text UNIQUE Float REPEAT
>                   Threshold Float
>                   Consensus Text #Evidence
1797,1798c1811,1812
<                 Transcription_factor  UNIQUE ?Transcription_factor XREF Position_matrix #Evidence //gw3
<                   Remark ?Text  #Evidence
---
>                 Transcription_factor UNIQUE ?Transcription_factor XREF Position_matrix #Evidence //gw3
>                   Remark ?Text #Evidence
1828,1829c1842,1843
<                 NCBI_id   UNIQUE        Int
<                 Translation  UNIQUE Text
---
>                 NCBI_id UNIQUE Int
>                 Translation UNIQUE Text
1831c1845
<               Stop  UNIQUE Text 
---
>               Stop UNIQUE Text 
1848,1849c1862,1863
<                   Gene_name  ?Text
<                   Description   UNIQUE ?Text
---
>                   Gene_name ?Text
>                   Description UNIQUE ?Text
1863,1864c1877,1878
<           Homol DNA_homol ?Sequence XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int  #Homol_info
<                 Pep_homol ?Protein XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int  #Homol_info
---
>           Homol DNA_homol ?Sequence XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
>                 Pep_homol ?Protein XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
1866c1880
<                 Motif_homol ?Motif XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int  #Homol_info
---
>                 Motif_homol ?Motif XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
1879c1893
< ?Motif        Match_sequence  UNIQUE Text     // Text is the DNA or protein sequence
---
> ?Motif        Match_sequence UNIQUE Text      // Text is the DNA or protein sequence
1882,1887c1896,1901
<       Restriction     Isoschizomer ?Motif XREF Isoschizomer
<                       Offset UNIQUE Int   
<                       Cleavage UNIQUE Text  // will show the cleavage points ex: G_ACGT'C
<                       Overhang UNIQUE Int
<                       Company UNIQUE Text
<                         Redundant
---
>       Restriction Isoschizomer ?Motif XREF Isoschizomer
>                   Offset UNIQUE Int   
>                   Cleavage UNIQUE Text  // will show the cleavage points ex: G_ACGT'C
>                   Overhang UNIQUE Int
>                   Company UNIQUE Text
>                     Redundant
1896,1899c1910,1913
<       Homol   DNA_homol ?Sequence XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
<               Pep_homol ?Protein XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
<               Motif_homol ?Motif XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
<               Homol_homol ?Homol_data XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
---
>       Homol DNA_homol ?Sequence XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
>             Pep_homol ?Protein XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
>             Motif_homol ?Motif XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
>             Homol_homol ?Homol_data XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
1932,1936c1946,1950
< ?Database  Name        UNIQUE ?Text            // name of the database
<            Description UNIQUE Text             // description of database contacts
<            URL         UNIQUE Text             // Link to database home page
<            Email              Text             // Contact email 
<            URL_constructor UNIQUE Text         // rule to build URL to specific database entry page 
---
> ?Database  Name UNIQUE ?Text           // name of the database
>            Description UNIQUE Text     // description of database contacts
>            URL UNIQUE Text             // Link to database home page
>            Email Text                  // Contact email 
>            URL_constructor UNIQUE Text // rule to build URL to specific database entry page 
2021,2063c2035,2077
< ?Expr_pattern Expression_of   Gene ?Gene XREF Expr_pattern #Evidence
<                               Reflects_endogenous_expression_of ?Gene
<                               CDS        ?CDS XREF Expr_pattern // for coding genes
<                               Sequence   ?Sequence XREF Expr_pattern // for clones???
<                               Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb]
<                               Clone ?Clone XREF Expr_pattern
<                               Protein ?Protein XREF Expr_pattern
<                                 Protein_description Text   // stores information for Expr_patterns with unknown antigens [031105 krb]
<               Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
<               Expressed_in    Cell         ?Cell         XREF Expr_pattern #Qualifier
<                               Cell_group   ?Cell_group   XREF Expr_pattern #Qualifier
<                               Life_stage   ?Life_stage   XREF Expr_pattern #Qualifier
<                               Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
<                               GO_term      ?GO_term      XREF Expr_pattern #GR_condition
<                 Subcellular_localization ?Text
<               Type    Reporter_gene ?Text
<                       In_situ Text
<                       Antibody ?Text
<                       Northern Text // Wen [krb 030425]
<                         Western Text  // Wen 
<                         RT_PCR Text   // Wen
<                       Localizome ?Text //added by Wen
<                       Microarray ?Microarray_experiment
<                       Tiling_array ?Analysis
<                       EPIC      ?Text 
<               Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
<               Pattern ?Text
<               Picture ?Picture XREF Expr_pattern
<               MovieURL Text //Added by wen for link to movie URLs. 
<               Movie    ?Movie    XREF Expr_pattern  //Added by Wen to curate Expr_pattern video
<                 Remark ?Text #Evidence
<               DB_info ?Database ?Database_field Text
<                 Experiment    Laboratory ?Laboratory
<                               Author ?Author 
<                               Date UNIQUE DateType
<                               Strain UNIQUE ?Strain
<               Reference ?Paper XREF Expr_pattern
<                 Transgene ?Transgene XREF Expr_pattern
<               Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
<               Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
<                                                           // added [031120 krb]
<               Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
<               Historical_gene   ?Gene #Evidence
---
> ?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence
>                           Reflects_endogenous_expression_of ?Gene
>                           CDS ?CDS XREF Expr_pattern               // for coding genes
>                           Sequence ?Sequence XREF Expr_pattern     // for clones???
>                           Pseudogene ?Pseudogene XREF Expr_pattern // [030801 krb]
>                           Clone ?Clone XREF Expr_pattern
>                           Protein ?Protein XREF Expr_pattern
>                             Protein_description Text   // information for Expr_patterns with unknown antigens [031105 krb]
>             Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2]
>             Expressed_in Cell ?Cell XREF Expr_pattern #Qualifier
>                          Cell_group ?Cell_group XREF Expr_pattern #Qualifier
>                          Life_stage ?Life_stage XREF Expr_pattern #Qualifier
>                          Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier
>                          GO_term ?GO_term XREF Expr_pattern #GR_condition
>               Subcellular_localization ?Text
>             Type Reporter_gene ?Text
>                  In_situ Text
>                  Antibody ?Text
>                  Northern Text // Wen [krb 030425]
>                    Western Text  // Wen 
>                    RT_PCR Text   // Wen
>                  Localizome ?Text //added by Wen
>                  Microarray ?Microarray_experiment
>                  Tiling_array ?Analysis
>                  EPIC ?Text 
>             Expression_cluster ?Expression_cluster XREF Expr_pattern //added by Wen.for localizome
>             Pattern ?Text
>             Picture ?Picture XREF Expr_pattern
>             MovieURL Text //Added by wen for link to movie URLs. 
>             Movie ?Movie XREF Expr_pattern  //Added by Wen to curate Expr_pattern video
>               Remark ?Text #Evidence
>             DB_info ?Database ?Database_field Text
>               Experiment Laboratory ?Laboratory
>                        Author ?Author 
>                        Date UNIQUE DateType
>                        Strain UNIQUE ?Strain
>             Reference ?Paper XREF Expr_pattern
>               Transgene ?Transgene XREF Expr_pattern
>             Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence
>             Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining
>                                                         // added [031120 krb]
>             Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb]
>             Historical_gene ?Gene #Evidence
2068c2082
< #Qualifier Certain   Text
---
> #Qualifier Certain Text
2070c2084
<            Partial   Text    //For expression of unidentified cell in a cell group
---
>            Partial Text      //For expression of unidentified cell in a cell group
2118c2132
<                   No_original_reference    Text //proposed by Wen
---
>                   No_original_reference Text //proposed by Wen
2133c2147
<         Historical_gene   ?Gene #Evidence                     
---
>         Historical_gene ?Gene #Evidence                       
2182,2184c2196,2198
<       Fate     Cell_type  ?Text        // e.g. muscle, neuron,hypodermis, gland
<                Program ?Text           //division, differentiation, death, and differs between sexes
<                Syncitial_cell ?Cell_group XREF Nucleus //see Cell_group,
---
>       Fate Cell_type ?Text             // e.g. muscle, neuron,hypodermis, gland
>            Program ?Text               //division, differentiation, death, and differs between sexes
>            Syncitial_cell ?Cell_group XREF Nucleus //see Cell_group,
2187,2190c2201,2204
<         Remark        ?Text #Evidence
<         Lineage Parent  UNIQUE  ?Cell XREF Daughter
<                 Daughter      ?Cell XREF Parent
<                 Lineage_name    Text
---
>         Remark ?Text #Evidence
>         Lineage Parent UNIQUE ?Cell XREF Daughter
>                 Daughter ?Cell XREF Parent
>                 Lineage_name Text
2239,2243c2253,2257
< ?Anatomy_name Primary   Name_for_cell            ?Cell XREF Main_name
<                         Name_for_cell_group      ?Cell_group XREF Main_name
<                         Name_for_anatomy_term    ?Anatomy_term XREF Term
<               Secondary Synonym_for_cell         ?Cell XREF Other_name
<                         Synonym_for_cell_group   ?Cell_group XREF Other_name
---
> ?Anatomy_name Primary   Name_for_cell ?Cell XREF Main_name
>                         Name_for_cell_group ?Cell_group XREF Main_name
>                         Name_for_anatomy_term ?Anatomy_term XREF Term
>               Secondary Synonym_for_cell ?Cell XREF Other_name
>                         Synonym_for_cell_group ?Cell_group XREF Other_name
2264c2278
<                        Fate    Cell_type  ?Text        // e.g. muscle, neuron,hypodermis, gland
---
>                        Fate    Cell_type ?Text         // e.g. muscle, neuron,hypodermis, gland
2267,2269c2281,2283
<                        Lineage Parent_term  UNIQUE  ?Anatomy_term XREF Daughter_term
<                                Daughter_term      ?Anatomy_term XREF Parent_term
<                                Lineage_name    Text
---
>                        Lineage Parent_term UNIQUE ?Anatomy_term XREF Daughter_term
>                                Daughter_term ?Anatomy_term XREF Parent_term
>                                Lineage_name Text
2287,2309c2301,2323
<                 URL     Text // for storing static URLs, such as WormAtlas, WormBook
<                 Child   PART_OF_c     ?Anatomy_term   XREF    PART_OF_p
<                         IS_A_c                ?Anatomy_term   XREF    IS_A_p
<                         DESCENDENT_OF_c       ?Anatomy_term   XREF    DESCENDENT_OF_p
<                         DESC_IN_HERM_c        ?Anatomy_term   XREF    DESC_IN_HERM_p
<                         DESC_IN_MALE_c        ?Anatomy_term   XREF    DESC_IN_MALE_p
<                         DEVELOPS_FROM_c       ?Anatomy_term   XREF    DEVELOPS_FROM_p
<                       CELL_c          ?Anatomy_term   XREF    CELL_p
<                       XUNION_OF_c     ?Anatomy_term   XREF    XUNION_OF_p
<                 Parent  PART_OF_p     ?Anatomy_term   XREF    PART_OF_c
<                         IS_A_p                ?Anatomy_term   XREF    IS_A_c
<                         DESCENDENT_OF_p       ?Anatomy_term   XREF    DESCENDENT_OF_c
<                         DESC_IN_HERM_p        ?Anatomy_term   XREF    DESC_IN_HERM_c
<                         DESC_IN_MALE_p        ?Anatomy_term   XREF    DESC_IN_MALE_c
<                         DEVELOPS_FROM_p       ?Anatomy_term   XREF    DEVELOPS_FROM_c
<                       CELL_p          ?Anatomy_term   XREF    CELL_c
<                       XUNION_OF_p     ?Anatomy_term   XREF    XUNION_OF_c
<                 Attribute_of    Expr_pattern    ?Expr_pattern   XREF    Anatomy_term
<                               Expression_cluster ?Expression_cluster XREF Anatomy_term #Evidence 
<                                 GO_term ?GO_term XREF Anatomy_term ?AO_code #Evidence
<                                 Reference       ?Paper  XREF Anatomy_term
<                               Function Anatomy_function ?Anatomy_function XREF Involved
<                                        Anatomy_function_not ?Anatomy_function XREF Not_involved
---
>                 URL Text // for storing static URLs, such as WormAtlas, WormBook
>                 Child PART_OF_c       ?Anatomy_term XREF PART_OF_p
>                       IS_A_c          ?Anatomy_term XREF IS_A_p
>                       DESCENDENT_OF_c ?Anatomy_term XREF DESCENDENT_OF_p
>                       DESC_IN_HERM_c  ?Anatomy_term XREF DESC_IN_HERM_p
>                       DESC_IN_MALE_c  ?Anatomy_term XREF DESC_IN_MALE_p
>                       DEVELOPS_FROM_c ?Anatomy_term XREF DEVELOPS_FROM_p
>                     CELL_c            ?Anatomy_term XREF CELL_p
>                     XUNION_OF_c       ?Anatomy_term XREF XUNION_OF_p
>                 Parent PART_OF_p      ?Anatomy_term XREF PART_OF_c
>                        IS_A_p         ?Anatomy_term XREF IS_A_c
>                        DESCENDENT_OF_p        ?Anatomy_term XREF DESCENDENT_OF_c
>                        DESC_IN_HERM_p ?Anatomy_term XREF DESC_IN_HERM_c
>                        DESC_IN_MALE_p ?Anatomy_term XREF DESC_IN_MALE_c
>                        DEVELOPS_FROM_p        ?Anatomy_term XREF DEVELOPS_FROM_c
>                      CELL_p           ?Anatomy_term XREF CELL_c
>                      XUNION_OF_p      ?Anatomy_term XREF XUNION_OF_c
>                 Attribute_of Expr_pattern ?Expr_pattern XREF Anatomy_term
>                            Expression_cluster ?Expression_cluster XREF Anatomy_term #Evidence 
>                              GO_term ?GO_term XREF Anatomy_term ?AO_code #Evidence
>                              Reference ?Paper XREF Anatomy_term
>                            Function Anatomy_function ?Anatomy_function XREF Involved
>                                     Anatomy_function_not ?Anatomy_function XREF Not_involved
2314,2316c2328,2330
<                 Index   Ancestor ?Anatomy_term XREF Descendent  //store ancestors of relationship IS_A and PART_OF
<                         Descendent ?Anatomy_term XREF Ancestor  //store descendents of relationship IS_A and PART_OF
<                 Remark  ?Text #Evidence
---
>                 Index Ancestor ?Anatomy_term XREF Descendent  //store ancestors of relationship IS_A and PART_OF
>                       Descendent ?Anatomy_term XREF Ancestor  //store descendents of relationship IS_A and PART_OF
>                 Remark ?Text #Evidence
2377c2391
<                      Normalization    UNIQUE Float    // Normalization factor for display (defaults to 1.0)
---
>                      Normalization UNIQUE Float       // Normalization factor for display (defaults to 1.0)
2386,2404c2400,2418
< ?TreeNode       Label UNIQUE ?Text            // Tree vertex label, e.g. sequence name or taxon   
<                 Id    UNIQUE Int              // Node numbering...
<                 Description  ?Text
<               Type UNIQUE  Root               // Root ?TreeNode should be so designated!
<                              Interior
<                            Leaf
<                 Distance UNIQUE       Float           // "Evolutionary distance" or branch length
<                 Bootstrap UNIQUE      Float           // Node subtree "bootstrap" values
<                 Tree   UNIQUE   ?Tree
<               Parent UNIQUE   ?TreeNode XREF  Child
<               Child           ?TreeNode XREF  Parent
<                 Display  Hide                 // Hide the subtree (children) of this node
<                          Colour   UNIQUE #Colour // Fixes the colour of the subtree; 
<                                                  // overridden by child node settings
<                          Hide_Bootstraps         // Hide all bootstraps in subtree...
<                          Show_Bootstrap          // ... except those with the "Show_Bootstrap" tag set
<                 Contains Taxon                //    UNIQUE ?Taxon    XREF Tree_Node
<                          Cell     UNIQUE ?Cell     XREF Tree_Node
<                          Cell_group UNIQUE ?Cell_group  XREF Tree_Node 
---
> ?TreeNode       Label UNIQUE ?Text              // Tree vertex label, e.g. sequence name or taxon   
>                 Id UNIQUE Int                   // Node numbering...
>                 Description ?Text
>               Type UNIQUE Root                // Root ?TreeNode should be so designated!
>                             Interior
>                           Leaf
>                 Distance UNIQUE       Float           // "Evolutionary distance" or branch length
>                 Bootstrap UNIQUE Float          // Node subtree "bootstrap" values
>                 Tree UNIQUE ?Tree
>               Parent UNIQUE ?TreeNode XREF Child
>               Child ?TreeNode XREF Parent
>                 Display Hide                   // Hide the subtree (children) of this node
>                         Colour UNIQUE #Colour   // Fixes the colour of the subtree; 
>                                                 // overridden by child node settings
>                         Hide_Bootstraps         // Hide all bootstraps in subtree...
>                         Show_Bootstrap          // ... except those with the "Show_Bootstrap" tag set
>                 Contains Taxon                   // UNIQUE ?Taxon XREF Tree_Node
>                          Cell UNIQUE ?Cell XREF Tree_Node
>                          Cell_group UNIQUE ?Cell_group XREF Tree_Node 
2426,2433c2440,2447
<               Summary UNIQUE ?Text                                                            // concise genomic description of the transgene
<                 Synonym ?Text                                                                 // for alternative names
<                 Promoter  Driven_by_gene ?Gene XREF Drives_transgene #Evidence                        // eventually change this tag to promoter_gene
<                           Driven_by_construct  ?Text                                          // eventually change this tag to promoter_artificial
<                 Reporter  Reporter_product ?Text                                              // removed multiple tags for Reporter_product
<                           Gene ?Gene XREF Transgene_product #Evidence 
<                         3_UTR  ?Gene #Evidence
<                 Reporter_type  ?Text                                                          // added for Transcriptional fusion or Translational fusion
---
>               Summary UNIQUE ?Text                                                            // concise genomic description of the transgene
>                 Synonym ?Text                                                                   // for alternative names
>                 Promoter  Driven_by_gene ?Gene XREF Drives_transgene #Evidence                  // eventually change this tag to promoter_gene
>                           Driven_by_construct ?Text                                             // eventually change this tag to promoter_artificial
>                 Reporter  Reporter_product ?Text                                                // removed multiple tags for Reporter_product
>                           Gene ?Gene XREF Transgene_product #Evidence
>                         3_UTR ?Gene #Evidence
>                 Reporter_type ?Text                                                             // Transcriptional fusion or Translational fusion
2435c2449
<                             Fragment ?Text                                                    // new tag to collect the following as subtags, Fragment may be deleted later
---
>                             Fragment ?Text                                                    // new tag to collect the following as subtags, Fragment may be deleted later
2437,2454c2451,2468
<                               Integration_method UNIQUE ?Text                                 // changed from Integrated_by
<                               Laboratory ?Laboratory #Lab_Location                            // changed from Location
<                               Author ?Author                                                  // may eventually be deleted
<                             Person ?Person                                                    // new tag ky 2011
<                 Genetic_information  Extrachromosomal                                         // new subtag and tags
<                                      Integrated                                                       // new subtag and collects the mapping tags
<                                    Map ?Map  #Map_position  
<                                      Map_evidence #Evidence 
<                                      Mapping_data  2_point ?2_point_data                      // if no data can be removed
<                                                    Multi_point ?Multi_pt_data                 // if no data can be removed
<                                    Phenotype ?Phenotype XREF Transgene #Phenotype_info
<                                    Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info   
<                 Used_for   Expr_pattern ?Expr_pattern XREF Transgene  
<                            Marker_for   ?Text #Evidence 
<                            Interactor ?Interaction 
<                 Associated_with   Marked_rearrangement ?Rearrangement XREF By_transgene               //new tag to collect the following as subtags
<                                 Clone ?Clone XREF Transgene Text 
<                                 Strain ?Strain XREF Transgene 
---
>                               Integration_method UNIQUE ?Text                                   // changed from Integrated_by
>                               Laboratory ?Laboratory #Lab_Location                              // changed from Location
>                               Author ?Author                                                    // may eventually be deleted
>                             Person ?Person                                                    // new tag ky 2011
>                 Genetic_information Extrachromosomal                                            // new subtag and tags
>                                     Integrated                                                  // new subtag and collects the mapping tags
>                                   Map ?Map #Map_position  
>                                     Map_evidence #Evidence 
>                                     Mapping_data  2_point ?2_point_data                         // if no data can be removed
>                                                   Multi_point ?Multi_pt_data                    // if no data can be removed
>                                   Phenotype ?Phenotype XREF Transgene #Phenotype_info
>                                   Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info   
>                 Used_for Expr_pattern ?Expr_pattern XREF Transgene  
>                          Marker_for ?Text #Evidence 
>                          Interactor ?Interaction 
>                 Associated_with Marked_rearrangement ?Rearrangement XREF By_transgene           // new tag to collect the following as subtags
>                               Clone ?Clone XREF Transgene Text 
>                               Strain ?Strain XREF Transgene 
2457,2458c2471,2472
<                 Historical_gene   ?Gene #Evidence
<                 Remark ?Text #Evidence                                                                //contains a lot of construction notes
---
>                 Historical_gene ?Gene #Evidence
>                 Remark ?Text #Evidence                                                          // contains a lot of construction notes
2475,2480c2489,2495
<         Sequence_info   DNA_text Text UNIQUE Text //stores actual probe sequence for automated mapping
<                                                 // 1st Text is DNA, 2nd is probe name
<                         Sequence ?Sequence XREF RNAi  //links to a real Sequence object used in the experiment 
<                                                     // such as yk clone; not UNIQUE anymore
<                         PCR_product ?PCR_product XREF RNAi // links to a PCR_product object used in 
<                                                          // the experiment; not UNIQUE anymore
---
>         Sequence_info DNA_text Text UNIQUE Text          //stores actual probe sequence for automated mapping
>                                                        // 1st Text is DNA, 2nd is probe name
>                       Sequence ?Sequence XREF RNAi       //links to a real Sequence object used in the experiment 
>                                                        // such as yk clone; not UNIQUE anymore
>                       Clone ?Clone XREF Used_in_RNAi     // Chris WS244
>                       PCR_product ?PCR_product XREF RNAi // links to a PCR_product object used in 
>                                                        // the experiment; not UNIQUE anymore
2482,2497c2497,2512
<                       // which maps to a single place in the genome
<         Experiment      Laboratory ?Laboratory
<                         Date UNIQUE DateType
<                         Strain UNIQUE ?Strain
<                         Genotype UNIQUE ?Text   //used when no Strain object exists
<                         Treatment UNIQUE ?Text
<                         Life_stage UNIQUE ?Life_stage
<                         Temperature UNIQUE Int
<                         Delivered_by UNIQUE Bacterial_feeding      //RL [010327]
<                                             Injection              //RL [010327]
<                                             Soaking                //RL [010327]
<                                             Transgene_expression   //RL [010327]
<         Inhibits        Predicted_gene ?CDS XREF RNAi_result #Evidence // "gene" parent (unreliable)
<                         Gene ?Gene   XREF RNAi_result #Evidence           //RL [010327]
<                         Transcript ?Transcript XREF RNAi_result #Evidence // [021126 krb]
<                         Pseudogene ?Pseudogene XREF RNAi_result #Evidence // [030801 krb]
---
>                        // which maps to a single place in the genome
>         Experiment Laboratory ?Laboratory
>                    Date UNIQUE DateType
>                    Strain UNIQUE ?Strain
>                    Genotype UNIQUE ?Text   //used when no Strain object exists
>                    Treatment UNIQUE ?Text
>                    Life_stage UNIQUE ?Life_stage
>                    Temperature UNIQUE Int
>                    Delivered_by UNIQUE Bacterial_feeding      //RL [010327]
>                                        Injection              //RL [010327]
>                                        Soaking                //RL [010327]
>                                        Transgene_expression   //RL [010327]
>         Inhibits Predicted_gene ?CDS XREF RNAi_result #Evidence // "gene" parent (unreliable)
>                  Gene ?Gene XREF RNAi_result #Evidence           //RL [010327]
>                  Transcript ?Transcript XREF RNAi_result #Evidence // [021126 krb]
>                  Pseudogene ?Pseudogene XREF RNAi_result #Evidence // [030801 krb]
2517,2561c2532,2576
< #Phenotype_info               Paper_evidence ?Paper
<                       Person_evidence ?Person
<                       Curator_confirmed       ?Person
<                       Remark  ?Text   #Evidence // specific remarks about the phenotype
<                       Quantity_description ?Text #Evidence //Remark to describe what quantity describes, below
<                       Quantity        UNIQUE  Int UNIQUE      Int     #Evidence
<                       Not             #Evidence //This is being phased out but is needed for the next phase [06/08/10].
<                       Anatomy_term    ?Anatomy_term #Evidence 
<                       Penetrance              Incomplete      Text    #Evidence
<                                               Low             Text    #Evidence
<                                               High            Text    #Evidence
<                                               Complete        Text    #Evidence
<                                               Range UNIQUE Int UNIQUE Int #Evidence // Range of penetrance
<                       Recessive               #Evidence
<                       Semi_dominant           #Evidence
<                       Dominant                #Evidence
<                       Haplo_insufficient      #Evidence
<                       Caused_by ?Gene #Evidence
<                       Caused_by_other ?Text #Evidence
<                       Rescued_by_transgene ?Transgene
<                       Loss_of_function  UNIQUE        Hypomorph                               #Evidence
<                                                       Amorph                                  #Evidence
<                                                       Uncharacterised_loss_of_function        #Evidence
<                       Gain_of_function  UNIQUE        Dominant_negative       #Evidence
<                                                       Hypermorph              #Evidence
<                                                       Neomorph                #Evidence
<                                                       Uncharacterised_gain_of_function        #Evidence
<                       Other_allele_type UNIQUE  Wild_type     #Evidence
<                                                         Isoallele     #Evidence  
<                                                 Mixed         #Evidence       
<                       Affected_by     Molecule    ?Molecule    #Evidence // ?Molecule model Karen Yook
<                       Temperature_sensitive   Heat_sensitive  Text            #Evidence
<                                               Cold_sensitive  Text            #Evidence
<                       Maternal        UNIQUE  Strictly_maternal       #Evidence
<                                               With_maternal_effect    #Evidence
<                       Paternal        #Evidence
<                       Phenotype_assay Life_stage  ?Life_stage  #Evidence
<                                       Strain      ?Strain      #Evidence
<                                       Treatment   ?Text        #Evidence
<                                       Temperature ?Text        #Evidence
<                                       Genotype    ?Text        #Evidence
<                       Ease_of_scoring UNIQUE ES0_Impossible_to_score #Evidence
<                                              ES1_Very_hard_to_score #Evidence
<                                              ES2_Difficult_to_score #Evidence
<                                              ES3_Easy_to_score #Evidence
---
> #Phenotype_info       Paper_evidence ?Paper
>               Person_evidence ?Person
>               Curator_confirmed       ?Person
>               Remark ?Text #Evidence // specific remarks about the phenotype
>               Quantity_description ?Text #Evidence //Remark to describe what quantity describes, below
>               Quantity UNIQUE Int UNIQUE Int #Evidence
>               Not #Evidence //This is being phased out but is needed for the next phase [06/08/10].
>               Anatomy_term ?Anatomy_term #Evidence 
>                 Penetrance Incomplete Text #Evidence
>                            Low Text #Evidence
>                            High Text #Evidence
>                            Complete Text #Evidence
>                          Range UNIQUE Int UNIQUE Int #Evidence // Range of penetrance
>                 Recessive #Evidence
>                 Semi_dominant #Evidence
>                 Dominant #Evidence
>                 Haplo_insufficient #Evidence
>               Caused_by ?Gene #Evidence
>               Caused_by_other ?Text #Evidence
>               Rescued_by_transgene ?Transgene
>                 Loss_of_function UNIQUE Hypomorph #Evidence
>                                         Amorph #Evidence
>                                         Uncharacterised_loss_of_function #Evidence
>                 Gain_of_function UNIQUE Dominant_negative #Evidence
>                                         Hypermorph #Evidence
>                                         Neomorph #Evidence
>                                         Uncharacterised_gain_of_function #Evidence
>                 Other_allele_type UNIQUE Wild_type #Evidence
>                                          Isoallele #Evidence  
>                                        Mixed #Evidence       
>               Affected_by Molecule ?Molecule #Evidence // ?Molecule model Karen Yook
>                 Temperature_sensitive Heat_sensitive Text #Evidence
>                                       Cold_sensitive Text #Evidence
>                 Maternal UNIQUE Strictly_maternal #Evidence
>                                 With_maternal_effect #Evidence
>                 Paternal #Evidence
>               Phenotype_assay Life_stage ?Life_stage #Evidence
>                               Strain ?Strain #Evidence
>                               Treatment ?Text #Evidence
>                               Temperature ?Text #Evidence
>                               Genotype ?Text #Evidence
>               Ease_of_scoring UNIQUE ES0_Impossible_to_score #Evidence
>                                      ES1_Very_hard_to_score #Evidence
>                                      ES2_Difficult_to_score #Evidence
>                                      ES3_Easy_to_score #Evidence
2584c2599
<            Interaction  ?Interaction
---
>            Interaction ?Interaction
2594,2597c2609,2612
< ?Phenotype Description UNIQUE ?Text   #Evidence
<          Name        Primary_name     UNIQUE  ?Phenotype_name XREF Primary_name_for   #Evidence
<                        Synonym                ?Phenotype_name XREF Synonym_for        #Evidence
<                        Short_name     ?Phenotype_name XREF Short_name_for     #Evidence
---
> ?Phenotype Description UNIQUE ?Text #Evidence
>          Name Primary_name UNIQUE ?Phenotype_name XREF Primary_name_for #Evidence
>                 Synonym       ?Phenotype_name XREF Synonym_for #Evidence
>                 Short_name ?Phenotype_name XREF Short_name_for #Evidence
2603,2617c2618,2632
<            Attribute_of       RNAi    ?RNAi XREF Phenotype
<                             Variation ?Variation XREF Phenotype
<                               Transgene       ?Transgene XREF Phenotype       // Added by Carol
<                             Anatomy_function ?Anatomy_function XREF Phenotype
<                             Interaction ?Interaction XREF Interaction_phenotype
<                             Rearrangement ?Rearrangement XREF Phenotype
<                             Strain ?Strain XREF Phenotype
<                             Not_in_RNAi ?RNAi XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
<                             Not_in_Variation ?Variation XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
<                             Not_in_Strain ?Strain XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
<                             Not_in_Transgene ?Transgene XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
<                             Not_in_Rearrangement ?Rearrangement XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
<          Associated_with    GO_term   ?GO_term   XREF Phenotype   ?GO_code  #Evidence // Tag Associated_with changed by Carol
<                             WBProcess ?WBProcess XREF Phenotype
<                             DO_term ?DO_term #Evidence
---
>            Attribute_of RNAi ?RNAi XREF Phenotype
>                       Variation ?Variation XREF Phenotype
>                         Transgene ?Transgene XREF Phenotype   // Added by Carol
>                       Anatomy_function ?Anatomy_function XREF Phenotype
>                       Interaction ?Interaction XREF Interaction_phenotype
>                       Rearrangement ?Rearrangement XREF Phenotype
>                       Strain ?Strain XREF Phenotype
>                       Not_in_RNAi ?RNAi XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
>                       Not_in_Variation ?Variation XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
>                       Not_in_Strain ?Strain XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
>                       Not_in_Transgene ?Transgene XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
>                       Not_in_Rearrangement ?Rearrangement XREF Phenotype_not_observed //added by Wen for Not observed phenotypes
>          Associated_with GO_term ?GO_term XREF Phenotype ?GO_code #Evidence   // Tag Associated_with changed by Carol
>                          WBProcess ?WBProcess XREF Phenotype
>                          DO_term ?DO_term #Evidence
2640c2655
<       Description UNIQUE ?Text     #Evidence
---
>       Description UNIQUE ?Text #Evidence
2642,2646c2657,2661
<       History    Merged_into      UNIQUE ?Operon XREF Acquires_merge #Evidence
<                  Acquires_merge   ?Operon XREF Merged_into #Evidence
<                  Split_from       UNIQUE ?Operon XREF Split_into #Evidence
<                  Split_into       ?Operon XREF Split_from #Evidence
<                  Deprecated       Text   #Evidence //pad - for operons no longer believed.
---
>       History Merged_into UNIQUE ?Operon XREF Acquires_merge #Evidence
>               Acquires_merge ?Operon XREF Merged_into #Evidence
>               Split_from UNIQUE ?Operon XREF Split_into #Evidence
>               Split_into ?Operon XREF Split_from #Evidence
>               Deprecated Text #Evidence //pad - for operons no longer believed.
2671c2686
< //    ##              Classes for microarray data      ##
---
> //                    Classes for microarray data
2681,2686c2696,2701
< ?Microarray     Chip_type UNIQUE ?Text  //SMD, Affymetrix, etc.
<                 Chip_info  ?Text        //Describes batch number of the chip, etc.
<                 Reference  ?Paper       //Describes design of the chip
<               URL Text                //to link to manufacturers site.
<                 Remark     ?Text        #Evidence
<                 Microarray_experiment   ?Microarray_experiment XREF Microarray
---
> ?Microarray Chip_type UNIQUE ?Text  //SMD, Affymetrix, etc.
>             Chip_info ?Text         //Describes batch number of the chip, etc.
>             Reference ?Paper        //Describes design of the chip
>           URL Text                //to link to manufacturers site.
>             Remark ?Text #Evidence
>             Microarray_experiment ?Microarray_experiment XREF Microarray
2697,2707c2712,2722
<                       Sequence_info UNIQUE PCR_product     UNIQUE ?PCR_product     XREF Microarray_results
<                                              Oligo_set       UNIQUE ?Oligo_set       XREF Microarray_results
<                         Gene          ?Gene     XREF Microarray_results #Evidence   // should be mapped during the build
<                         CDS         ?CDS        XREF Microarray_results #Evidence   // should be mapped during the build
<                         Transcript    ?Transcript XREF Microarray_results #Evidence   // should be mapped during the build
<                       Pseudogene    ?Pseudogene XREF Microarray_results #Evidence   // should be mapped during the build
<                       Microarray    ?Microarray
<                         Results       ?Microarray_experiment UNIQUE #Microarray_data
<                         Range         Min UNIQUE Float UNIQUE ?Microarray_experiment  // mix observed ratio or frequency in all experiments and corresponding experiment
<                                       Max UNIQUE Float UNIQUE ?Microarray_experiment  // max observed ratio or frequency in all experiments and corresponding experiment 
<                         Remark        ?Text   #Evidence
---
>                       Sequence_info UNIQUE PCR_product UNIQUE ?PCR_product XREF Microarray_results
>                                              Oligo_set UNIQUE ?Oligo_set XREF Microarray_results
>                         Gene ?Gene XREF Microarray_results #Evidence               // should be mapped during the build
>                         CDS ?CDS XREF Microarray_results #Evidence                 // should be mapped during the build
>                         Transcript ?Transcript XREF Microarray_results #Evidence   // should be mapped during the build
>                       Pseudogene ?Pseudogene XREF Microarray_results #Evidence   // should be mapped during the build
>                       Microarray ?Microarray
>                         Results ?Microarray_experiment UNIQUE #Microarray_data
>                         Range Min UNIQUE Float UNIQUE ?Microarray_experiment  // mix observed ratio or frequency in all experiments and corresponding experiment
>                               Max UNIQUE Float UNIQUE ?Microarray_experiment  // max observed ratio or frequency in all experiments and corresponding experiment 
>                         Remark ?Text #Evidence
2717,2728c2732,2743
< #Microarray_data        Result          A_vs_B_log_ratio        UNIQUE Float                 // relative abundance               
<                                         A_vs_B_SD               UNIQUE Float                 // standard deviation over a set of experiments
<                                         Frequency               UNIQUE Float                 // absolute abundance in ppm - [14-Mar-06 ar2] Igor wants a float (absolute?)
<                                         Number_of_experiments   UNIQUE Int
<                                         Range_within_paper      UNIQUE Float UNIQUE Float    // min and max observed ratio or frequency in all experiments from a paper
<                         Confidence      Confidence_level        UNIQUE Float                 // Igor [031020
<                                       P_value  UNIQUE Float
<                                         Presence UNIQUE PA                                   // present always
<                                                         PS                                   // present sometimes - marginal call
<                                                         NP                                   // never present
<                       Expression_cluster ?Expression_cluster XREF Microarray_results       // one way XREF used to populate Cluster Class (prev ?Cluster)
<                         Remark          Text #Evidence
---
> #Microarray_data Result A_vs_B_log_ratio UNIQUE Float                 // relative abundance               
>                         A_vs_B_SD UNIQUE Float                        // standard deviation over a set of experiments
>                         Frequency UNIQUE Float                        // absolute abundance in ppm - [14-Mar-06 ar2] Igor wants a float (absolute?)
>                         Number_of_experiments UNIQUE Int
>                         Range_within_paper UNIQUE Float UNIQUE Float  // min and max observed ratio or frequency in all experiments from a paper
>                  Confidence Confidence_level UNIQUE Float             // Igor [031020
>                           P_value UNIQUE Float
>                             Presence UNIQUE PA                        // present always
>                                             PS                        // present sometimes - marginal call
>                                             NP                        // never present
>                Expression_cluster ?Expression_cluster XREF Microarray_results       // one way XREF used to populate Cluster Class (prev ?Cluster)
>                  Remark Text #Evidence
2741,2745c2756,2760
<                         Sample  Sample_A     UNIQUE      ?Condition     //for PCR product-base (SMD-type) chips
<                                 Sample_B     UNIQUE      ?Condition     //for PCR product-base (SMD-type) chips
<                                 Microarray_sample UNIQUE ?Condition     //for oligo-based (Affymetrix-type) chips
<                         Reference  ?Paper XREF Microarray_experiment
<                         Remark     Text        #Evidence
---
>                         Sample Sample_A UNIQUE ?Condition     //for PCR product-base (SMD-type) chips
>                                Sample_B UNIQUE ?Condition     //for PCR product-base (SMD-type) chips
>                                Microarray_sample UNIQUE ?Condition     //for oligo-based (Affymetrix-type) chips
>                         Reference ?Paper XREF Microarray_experiment
>                         Remark Text #Evidence
2763c2778
<               Overlaps_CDS        ?CDS        XREF Corresponding_oligo_set #Evidence
---
>               Overlaps_CDS ?CDS XREF Corresponding_oligo_set #Evidence
2766c2781
<               Remark Text    #Evidence
---
>               Remark Text #Evidence
2781c2796
< ?Expression_cluster  Description  ?Text                                            // refers to Biological meaning of this cluster group
---
> ?Expression_cluster  Description ?Text                                       // refers to Biological meaning of this cluster group
2783,2786c2798,2801
<                    Algorithm    Text                                       // refers to the algorithm that was used to get this clustering result.
<                    Reference    ?Paper XREF Expression_cluster
<                    Based_on_WB_Release     Int //Wen - to identify clusters not mapped if authors did not provide probe information.
<                    Microarray_results ?Microarray_results  Text #Evidence  //refers to all experimental results included in the cluster.
---
>                    Algorithm Text                                          // refers to the algorithm that was used to get this clustering result.
>                    Reference ?Paper XREF Expression_cluster
>                    Based_on_WB_Release Int                                 // Wen - if authors did not provide probe information.
>                    Microarray_results ?Microarray_results Text #Evidence   // refers to all experimental results included in the cluster.
2788,2789c2803,2805
<                    Gene ?Gene XREF Expression_cluster Text #Evidence       //Igor: populated during build based on Microarray_results mapping
<                    Attribute_of Microarray_experiment ?Microarray_experiment  XREF Expression_cluster //Wen
---
>                    Gene ?Gene XREF Expression_cluster Text #Evidence       // Igor - populated during build based on Microarray_results mapping
>                    Attribute_of Microarray_experiment ?Microarray_experiment XREF Expression_cluster // Wen
>                                 Mass_spectrometry ?Mass_spec_experiment XREF Expression_cluster      // Wen WS244
2793,2798c2809,2814
<                                 Expr_pattern ?Expr_pattern XREF Expression_cluster #Evidence          //Wen originally for Localizome
<                      Regulation   Regulated_by_gene ?Gene                  //Wen WS228
<                                   Regulated_by_treatment Text                //Wen WS228
<                                   Regulated_by_molecule ?Molecule            //Wen WS228
<                      Associated_with  Life_stage ?Life_stage                 //Wen WS228
<                                       GO_term ?GO_term                       //Wen WS228
---
>                                 Expr_pattern ?Expr_pattern XREF Expression_cluster #Evidence          // Wen originally for Localizome
>                      Regulation   Regulated_by_gene ?Gene                    // Wen WS228
>                                   Regulated_by_treatment Text                // Wen WS228
>                                   Regulated_by_molecule ?Molecule            // Wen WS228
>                      Associated_with  Life_stage ?Life_stage                 // Wen WS228
>                                       GO_term ?GO_term                       // Wen WS228
2805c2821
< //      SAGE_tag model
---
> //      SAGE_tag class
2810,2819c2826,2835
<                 Tag_sequence            UNIQUE Text     //tag sequence including the restriction site
<                 Anchoring_enzyme        UNIQUE ?Motif   //NlaIII most commonly
<                 Tag_length              UNIQUE Int      //14 most commonly
<                 Most_three_prime        // added for tags which are the most 3' in a transcript
<                 Unambiguously_mapped    //boolean; describes whether tag is unambiguously mapped to one SAGE transcript or to splice isoforms of the same gene at the same genomic location
<                 Corresponds_to  Predicted_CDS   ?CDS XREF SAGE_tag #SAGE_mapping_info
<                                 Gene            ?Gene XREF SAGE_tag #SAGE_mapping_info
<                                 Transcript      ?Transcript XREF SAGE_tag #SAGE_mapping_info
<                                 Pseudogene      ?Pseudogene XREF SAGE_tag #SAGE_mapping_info
<                 Results ?SAGE_experiment UNIQUE #SAGE_data //contains SAGE data for all experiments using the tag
---
>                 Tag_sequence UNIQUE Text         // tag sequence including the restriction site
>                 Anchoring_enzyme UNIQUE ?Motif   // NlaIII most commonly
>                 Tag_length UNIQUE Int            // 14 most commonly
>                 Most_three_prime                 // added for tags which are the most 3' in a transcript
>                 Unambiguously_mapped             // boolean; describes whether tag is unambiguously mapped to one SAGE transcript or to splice isoforms of the same gene at the same genomic location
>                 Corresponds_to  Predicted_CDS ?CDS XREF SAGE_tag #SAGE_mapping_info
>                                 Gene ?Gene XREF SAGE_tag #SAGE_mapping_info
>                                 Transcript ?Transcript XREF SAGE_tag #SAGE_mapping_info
>                                 Pseudogene ?Pseudogene XREF SAGE_tag #SAGE_mapping_info
>                 Results ?SAGE_experiment UNIQUE #SAGE_data              //contains SAGE data for all experiments using the tag
2821c2837
<                 Method UNIQUE ?Method  //for GFF dumping
---
>                 Method UNIQUE ?Method
2823,2826c2839,2842
< #SAGE_mapping_info Transcript_source      UNIQUE ?Text            //Coding RNA, Mitochondrial, Other...
<                    Position               UNIQUE Int              //the number of the SAGE anchoring enzyme restriction site from the 3' end of the cDNA molecule
<                    Strand                 UNIQUE Sense            //sense/antisense
<                                                  Antisense
---
> #SAGE_mapping_info Transcript_source UNIQUE ?Text   //Coding RNA, Mitochondrial, Other...
>                    Position UNIQUE Int              //the number of the SAGE anchoring enzyme restriction site from the 3' end of the cDNA molecule
>                    Strand UNIQUE Sense              //sense/antisense
>                                  Antisense
2830,2839c2846,2855
< #SAGE_data      Result          Frequency               UNIQUE Int      //tag count
<                                 Total_tag_count         UNIQUE Int      //sum of all tag counts in the experiment
<                                 Relative_abundance      UNIQUE Float    //Frequency/Total_tag_count
<                                 Significance            UNIQUE Float
<                                 Confidence_level        UNIQUE Float
<                                 Standard_deviation      UNIQUE Float
<                                 Number_of_experiments   UNIQUE Int
<               Expression_cluster ?Expression_cluster XREF SAGE_tag    //Replaces ?Cluster connection
<                 Sequence_quality  UNIQUE Float            //most commonly cumulative phred scores associated with the tag 
<                                               // sequences; not in ?SAGE_tag since it will vary from experiment to experiment
---
> #SAGE_data Result Frequency UNIQUE Int              // tag count
>                   Total_tag_count UNIQUE Int        // sum of all tag counts in the experiment
>                   Relative_abundance UNIQUE Float   // Frequency/Total_tag_count
>                   Significance UNIQUE Float
>                   Confidence_level UNIQUE Float
>                   Standard_deviation UNIQUE Float
>                   Number_of_experiments UNIQUE Int
>          Expression_cluster ?Expression_cluster XREF SAGE_tag    //Replaces ?Cluster connection
>            Sequence_quality UNIQUE Float            //most commonly cumulative phred scores associated with the tag 
>                                                   // sequences; not in ?SAGE_tag since it will vary from experiment to experiment
2849c2865
< ?SAGE_experiment Sample  UNIQUE  ?Condition XREF SAGE_experiment
---
> ?SAGE_experiment Sample UNIQUE ?Condition XREF SAGE_experiment
2851c2867
<                  Reference  ?Paper XREF SAGE_experiment
---
>                  Reference ?Paper XREF SAGE_experiment
2872,2896c2888,2912
< ?3d_data Evidence              #Evidence
<          DB_info  Database ?Database ?Database_field ?Text
<          CDS      ?CDS XREF 3d_data
<        Protein  ?Protein XREF 3d_data
<        Gene     ?Gene XREF 3d_data
<          Status                Selected
<                                Cloned
<                                Expressed
<                                Soluble
<                                Purified
<                                Crystallized
<                                Diffraction_quality_crystals    //Diffraction-quality Crystals
<                                Diffraction
<                                NMR_assigned                    //NMR assigned
<                                HSQC
<                                Crystal_structure               //Crystal Structure
<                                NMR_structure                   //NMR Structure
<                                In_PDB                          //In PDB
<                                Work_stopped                    //Work Stopped
<                                Test_target                     //Test Target
<                                Other
<          Origin                Location UNIQUE NESGC           //3d data sources can be added as new sub-tags to the model in the future
<                                First_imported UNIQUE DateType
<                                Last_updated UNIQUE DateType
<          Remark                ?Text #Evidence
---
> ?3d_data Evidence #Evidence
>          DB_info Database ?Database ?Database_field ?Text
>          CDS ?CDS XREF 3d_data
>        Protein ?Protein XREF 3d_data
>        Gene ?Gene XREF 3d_data
>          Status Selected
>                 Cloned
>                 Expressed
>                 Soluble
>                 Purified
>                 Crystallized
>                 Diffraction_quality_crystals    //Diffraction-quality Crystals
>                 Diffraction
>                 NMR_assigned                    //NMR assigned
>                 HSQC
>                 Crystal_structure               //Crystal Structure
>                 NMR_structure                   //NMR Structure
>                 In_PDB                          //In PDB
>                 Work_stopped                    //Work Stopped
>                 Test_target                     //Test Target
>                 Other
>          Origin Location UNIQUE NESGC           //3d data sources can be added as new sub-tags to the model in the future
>                 First_imported UNIQUE DateType
>                 Last_updated UNIQUE DateType
>          Remark ?Text #Evidence
2911c2927
< ?Person PostgreSQL_id UNIQUE Text     // for linking to internal RDB // Text instead of Int so it says WBperson####
---
> ?Person PostgreSQL_id UNIQUE Text         // for linking to internal RDB // Text instead of Int so it says WBperson####
2913,2919c2929,2935
<         Name    First_name    UNIQUE  Text    // prefered first name
<                 Middle_name   Text            // middle name(s)
<                 Last_name     UNIQUE  ?Person_name XREF Last_name_of    // prefered last name
<                 Standard_name UNIQUE  ?Person_name XREF Standard_name_of   // name to be used for displays
<                                               // default is "First_name Last_name"
<               Full_name     UNIQUE  ?Person_name XREF Full_name_of // field for storing long name [030321 krb]
<                 Also_known_as   ?Person_name XREF Other_name_of // new XREF added [030310 krb]
---
>         Name    First_name UNIQUE Text    // prefered first name
>                 Middle_name Text          // middle name(s)
>                 Last_name UNIQUE ?Person_name XREF Last_name_of    // prefered last name
>                 Standard_name UNIQUE ?Person_name XREF Standard_name_of   // name to be used for displays
>                                           // default is "First_name Last_name"
>               Full_name UNIQUE ?Person_name XREF Full_name_of // field for storing long name [030321 krb]
>                 Also_known_as ?Person_name XREF Other_name_of // new XREF added [030310 krb]
2935c2951
<       Lineage Supervised    ?Person XREF Supervised_by #Role
---
>       Lineage Supervised ?Person XREF Supervised_by #Role
2937c2953
<                 Worked_with   ?Person XREF Worked_with #Role
---
>                 Worked_with ?Person XREF Worked_with #Role
2946c2962
< #Address  Street_address Text        // multiple lines including town, state, zip/postcode, whatever
---
> #Address  Street_address Text           // multiple lines including town, state, zip/postcode, whatever
2949,2955c2965,2971
<           Email Text                 // multiple emails allowed
<           Main_phone    Text         // phone number for the institution, I presume
<           Lab_phone     Text
<           Office_phone  Text
<           Other_phone   Text UNIQUE Text  // second text can be used to indicate type
<           Fax           Text 
<           Web_page      Text    // web page is part of the address info I think
---
>           Email Text                    // multiple emails allowed
>           Main_phone Text               // phone number for the institution, I presume
>           Lab_phone Text
>           Office_phone Text
>           Other_phone Text UNIQUE Text  // second text can be used to indicate type
>           Fax Text 
>           Web_page Text                 // web page is part of the address info I think
2967,2977c2983,2993
< #Role   Assistant_professor    DateType    UNIQUE    DateType
<       Phd             DateType UNIQUE DateType
<         Postdoc               DateType UNIQUE DateType
<         Masters               DateType UNIQUE DateType
<         Undergrad     DateType UNIQUE DateType
<         Highschool    DateType UNIQUE DateType
<         Sabbatical    DateType UNIQUE DateType
<         Lab_visitor   DateType UNIQUE DateType
<         Collaborated  DateType UNIQUE DateType
<         Research_staff  DateType UNIQUE DateType
<         Unknown               DateType UNIQUE DateType
---
> #Role Assistant_professor DateType UNIQUE DateType
>       Phd DateType UNIQUE DateType
>       Postdoc DateType UNIQUE DateType
>       Masters DateType UNIQUE DateType
>       Undergrad DateType UNIQUE DateType
>       Highschool DateType UNIQUE DateType
>       Sabbatical DateType UNIQUE DateType
>       Lab_visitor DateType UNIQUE DateType
>       Collaborated DateType UNIQUE DateType
>       Research_staff DateType UNIQUE DateType
>       Unknown DateType UNIQUE DateType
2988c3004
< ?Person_name Name Full_name_of     ?Person XREF Full_name
---
> ?Person_name Name Full_name_of ?Person XREF Full_name
2990,2991c3006,3007
<                 Last_name_of     ?Person XREF Last_name
<                 Other_name_of    ?Person XREF Also_known_as // added [030310 krb]
---
>                 Last_name_of ?Person XREF Last_name
>                 Other_name_of ?Person XREF Also_known_as // added [030310 krb]
3007c3023
<                 Fax   Text
---
>                 Fax Text
3029,3039c3045,3055
<        Erratum_in      ?Paper XREF Erratum_for
<        Erratum_for     ?Paper XREF Erratum_in
<        Reference       Title UNIQUE ?Text
<                        Journal UNIQUE ?Text     //we are cleaning up Journal names and considering retiring the class
<                        Publisher UNIQUE Text
<                        Editor ?Text            //used for books put in as objects
<                        Page  UNIQUE  Text 
<                        Volume UNIQUE Text
<                        Publication_date UNIQUE ?Text         //YYYY-MM-DD or YYYY-MM, replaces DateType which led to erroneous pub dates
<                        Contained_in ?Paper XREF Contains       // old form
<                        Contains ?Paper XREF Contained_in
---
>        Erratum_in ?Paper XREF Erratum_for
>        Erratum_for ?Paper XREF Erratum_in
>        Reference Title UNIQUE ?Text
>                  Journal UNIQUE ?Text     //we are cleaning up Journal names and considering retiring the class
>                  Publisher UNIQUE Text
>                  Editor ?Text            //used for books put in as objects
>                  Page UNIQUE Text 
>                  Volume UNIQUE Text
>                  Publication_date UNIQUE ?Text         //YYYY-MM-DD or YYYY-MM, replaces DateType which led to erroneous pub dates
>                  Contained_in ?Paper XREF Contains       // old form
>                  Contains ?Paper XREF Contained_in
3048,3071c3064,3087
<        Type    Journal_article        #Evidence
<                Review        #Evidence
<                Comment        #Evidence
<                News        #Evidence
<                Letter        #Evidence
<                Editorial        #Evidence
<                Congresses        #Evidence
<                Historical_article        #Evidence
<                Biography        #Evidence
<                Interview        #Evidence
<                Lectures        #Evidence
<                Interactive_tutorial        #Evidence
<                Retracted_publication        #Evidence
<                Technical_report        #Evidence
<                Directory        #Evidence
<                Monograph        #Evidence
<                Published_erratum        #Evidence
<                Meeting_abstract        #Evidence
<                Gazette_article        #Evidence
<                Book_chapter        #Evidence
<                Book        #Evidence
<                Email        #Evidence
<                WormBook        #Evidence
<                Other        #Evidence
---
>        Type    Journal_article #Evidence
>                Review #Evidence
>                Comment #Evidence
>                News #Evidence
>                Letter #Evidence
>                Editorial #Evidence
>                Congresses #Evidence
>                Historical_article #Evidence
>                Biography #Evidence
>                Interview #Evidence
>                Lectures #Evidence
>                Interactive_tutorial #Evidence
>                Retracted_publication #Evidence
>                Technical_report #Evidence
>                Directory #Evidence
>                Monograph #Evidence
>                Published_erratum #Evidence
>                Meeting_abstract #Evidence
>                Gazette_article #Evidence
>                Book_chapter #Evidence
>                Book #Evidence
>                Email #Evidence
>                WormBook #Evidence
>                Other #Evidence
3106c3122
<        Remark  ?Text   #Evidence
---
>        Remark ?Text #Evidence
3148,3151c3164,3167
< #GR_condition          Life_stage               ?Life_stage      
<                        Cell                     ?Cell
<                        Cell_group               ?Cell_group
<                      Anatomy_term             ?Anatomy_term //Added by wen 02132006
---
> #GR_condition          Life_stage ?Life_stage      
>                        Cell ?Cell
>                        Cell_group ?Cell_group
>                      Anatomy_term ?Anatomy_term //Added by wen 02132006
3161,3163c3177,3179
<          Name Public_name     UNIQUE ?Variation_name XREF Public_name_for
<               Other_name      ?Variation_name XREF Other_name_for #Evidence
<                 Rearrangement ?Rearrangement  XREF Variation // some alleles are really rearrangements                
---
>          Name Public_name UNIQUE ?Variation_name XREF Public_name_for
>               Other_name ?Variation_name XREF Other_name_for #Evidence
>                 Rearrangement ?Rearrangement XREF Variation // some alleles are really rearrangements         
3171,3172c3187,3188
<                                            Insertion    UNIQUE Text      #Evidence
<                                            Deletion     UNIQUE Text      #Evidence  
---
>                                            Insertion UNIQUE Text #Evidence
>                                            Deletion UNIQUE Text #Evidence  
3191,3192c3207,3208
<                 Author  ?Author // use Person when known, else use Author
<                   Person  ?Person //
---
>                 Author ?Author // use Person when known, else use Author
>                   Person ?Person //
3210,3215c3226,3231
<          Affects Gene          ?Gene       XREF Allele #Molecular_change      //#Molecular_change mh6 define precise changes [060217 ar2]
<                  Predicted_CDS ?CDS        XREF Variation #Molecular_change
<                  Transcript    ?Transcript XREF Variation #Molecular_change
<                  Pseudogene    ?Pseudogene XREF Variation #Molecular_change
<                  Feature       ?Feature    XREF Associated_with_variation
<                  Interactor    ?Interaction
---
>          Affects Gene ?Gene XREF Allele #Molecular_change      //#Molecular_change mh6 define precise changes [060217 ar2]
>                  Predicted_CDS ?CDS XREF Variation #Molecular_change
>                  Transcript ?Transcript XREF Variation #Molecular_change
>                  Pseudogene ?Pseudogene XREF Variation #Molecular_change
>                  Feature ?Feature XREF Associated_with_variation
>                  Interactor ?Interaction
3217c3233
<            Isolation Date    DateType
---
>            Isolation Date DateType
3223c3239
<                    Derivative   ?Variation XREF Derived_from
---
>                    Derivative ?Variation XREF Derived_from
3233c3249
<                   Map ?Map   XREF Variation #Map_position
---
>                   Map ?Map XREF Variation #Map_position
3235,3237c3251,3253
<                     Mapping_data 2_point         ?2_point_data
<                                  Multi_point     ?Multi_pt_data
<                                  Pos_neg_data    ?Pos_neg_data
---
>                     Mapping_data 2_point ?2_point_data
>                                  Multi_point ?Multi_pt_data
>                                  Pos_neg_data ?Pos_neg_data
3239,3240c3255,3256
<                                  In_2_point      ?2_point_data
<                                  In_multi_point  ?Multi_pt_data
---
>                                  In_2_point ?2_point_data
>                                  In_multi_point ?Multi_pt_data
3249,3250c3265,3266
<                                        Opal_UGA  Text #Evidence
<                        Missense Text  #Evidence                               // text fields stored details of codon change
---
>                                        Opal_UGA Text #Evidence
>                        Missense Text #Evidence                                // text fields stored details of codon change
3257c3273
<            Remark  ?Text #Evidence
---
>            Remark ?Text #Evidence
3259c3275
<            Supporting_data Movie   ?Movie   XREF Variation #Evidence  //Carol [060421 ar2] 
---
>            Supporting_data Movie ?Movie XREF Variation #Evidence  //Carol [060421 ar2] 
3262,3263c3278,3279
< ?Variation_name Other_name_for     ?Variation XREF Other_name // main reason for this class
<                 Public_name_for    ?Variation XREF Public_name // the main name for a gene
---
> ?Variation_name Other_name_for ?Variation XREF Other_name // main reason for this class
>                 Public_name_for ?Variation XREF Public_name // the main name for a gene
3267,3268c3283,3284
< #Molecular_change   Missense Int    Text #Evidence
<                     Silent   Text   #Evidence
---
> #Molecular_change   Missense Int Text #Evidence
>                     Silent Text #Evidence
3271c3287
<                                     Opal_UGA  Text #Evidence
---
>                                     Opal_UGA Text #Evidence
3275c3291
<                     Splice_site UNIQUE  Donor    Text #Evidence
---
>                     Splice_site UNIQUE  Donor Text #Evidence
3343,3344c3359,3360
<                       Ionisation_source     UNIQUE MALDI
<                                                    ESI
---
>                       Ionisation_source UNIQUE MALDI
>                                                ESI
3354a3371
>                       Expression_cluster ?Expression_cluster XREF Mass_spectrometry       // Wen WS244
3372,3373c3389,3390
< #Mass_spec_data  XCorr   UNIQUE Float   // SEQUEST score
<                  DeltaCN UNIQUE Float   // SEQUEST score
---
> #Mass_spec_data  XCorr UNIQUE Float      // SEQUEST score
>                  DeltaCN UNIQUE Float    // SEQUEST score
3375,3376c3392,3393
<                  Sp_rank UNIQUE Int  // SEQUEST score
<                  Sp_score UNIQUE Float  // SEQUEST score
---
>                  Sp_rank UNIQUE Int      // SEQUEST score
>                  Sp_score UNIQUE Float   // SEQUEST score
3380c3397
<                  Matches Protein ?Protein  XREF  Contains_peptide    // matched protein
---
>                  Matches Protein ?Protein XREF Contains_peptide    // matched protein
3393c3410
<                  Subproject     ?Analysis XREF Project
---
>                  Subproject ?Analysis XREF Project
3411,3430c3428,3447
< ?Condition Life_stage      ?Life_stage
<          Sex             UNIQUE Hermaphrodite
<                                 Male
<                                 Female        //not all worms are elegans!
<                                 Unknown
<          Food            Text
<          Exposure_time   Text
<          Species         UNIQUE ?Species
<          Strain          ?Strain // added for Microarry_result [030127 krb]
<          Preparation     ?Text // added for Microarray_result [030127 krb]
<            Temperature     Float // Int -> Float WS236
<            Genotype        ?Text
<            Other           ?Text
<            Relationship    Contains        ?Condition XREF Contained_in
<                            Contained_in    ?Condition XREF Contains
<                            Precedes        ?Condition XREF Follows
<                            Follows         ?Condition XREF Precedes
<            Reference       ?Paper  //Defines the condition.
<          Tissue          ?Anatomy_term   // added for Experiment (Microarray_results)
<            Treatment       ?Text // added for Experiment (Microarray_results)
---
> ?Condition Life_stage ?Life_stage
>          Sex UNIQUE Hermaphrodite
>                     Male
>                     Female    //not all worms are elegans!
>                     Unknown
>          Food Text
>          Exposure_time Text
>          Species UNIQUE ?Species
>          Strain ?Strain // added for Microarry_result [030127 krb]
>          Preparation ?Text // added for Microarray_result [030127 krb]
>            Temperature Float // Int -> Float WS236
>            Genotype ?Text
>            Other ?Text
>            Relationship Contains ?Condition XREF Contained_in
>                         Contained_in ?Condition XREF Contains
>                         Precedes ?Condition XREF Follows
>                         Follows ?Condition XREF Precedes
>            Reference ?Paper  //Defines the condition.
>          Tissue ?Anatomy_term   // added for Experiment (Microarray_results)
>            Treatment ?Text // added for Experiment (Microarray_results)
3432,3433c3449,3450
<          Analysis        ?Analysis XREF Sample 
<            Remark          ?Text #Evidence
---
>          Analysis ?Analysis XREF Sample 
>            Remark ?Text #Evidence
3446c3463
<            Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule //Wen WS228
---
>            Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule    // Wen WS228
3448,3454c3465,3471
<            Affects_phenotype_of     Variation ?Variation ?Phenotype #Evidence
<                                     Strain    ?Strain    ?Phenotype #Evidence
<                                     Transgene ?Transgene ?Phenotype #Evidence
<                                     RNAi      ?RNAi      ?Phenotype #Evidence
<                                   Rearrangement  ?Rearrangement  ?Phenotype  #Evidence  //KY [110602 pad]
<          Interaction  ?Interaction    XREF    Molecule_regulator
<          Molecule_use  ?Text  #Evidence
---
>            Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence
>                                 Strain ?Strain ?Phenotype #Evidence
>                                 Transgene ?Transgene ?Phenotype #Evidence
>                                 RNAi ?RNAi ?Phenotype #Evidence
>                               Rearrangement ?Rearrangement ?Phenotype #Evidence  // KY [110602 pad]
>          Interaction ?Interaction XREF Molecule_interactor                       // Chris WS244
>          Molecule_use ?Text #Evidence
3481c3498
<                                 Expression_cluster ?Expression_cluster XREF WBProcess  #Evidence
---
>                                 Expression_cluster ?Expression_cluster XREF WBProcess #Evidence
3491c3508
<                 Movie ?Movie  #Evidence
---
>                 Movie ?Movie #Evidence
3494c3511
<                 Historical_gene   ?Gene #Evidence
---
>                 Historical_gene ?Gene #Evidence
3509a3527
> // WS244