WS244 Models.wrm
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Jump to navigationJump to searchModel 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
