Difference between revisions of "WormBase Model:Gene"
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== Model == | == Model == | ||
<pre> | <pre> | ||
+ | //////////////////////////////////////////////////////////////////////////////////////// | ||
+ | // | ||
+ | // ?Gene class - krb | ||
+ | // | ||
+ | //////////////////////////////////////////////////////////////////////////////////////// | ||
+ | |||
+ | |||
+ | ?Gene Evidence #Evidence | ||
+ | SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Gene_child | ||
+ | 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 ?Accession_number //For Darin genbank genpep ids | ||
+ | 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 | ||
+ | Made_into_transposon | ||
+ | Status UNIQUE Live #Evidence | ||
+ | Suppressed #Evidence | ||
+ | Dead #Evidence | ||
+ | Gene_info Gene_class UNIQUE ?Gene_class XREF Genes | ||
+ | Laboratory ?Laboratory | ||
+ | Cloned_by #Evidence // mt3 acreditation of person who cloned gene [060829 ar2] | ||
+ | Reference_allele ?Variation #Evidence | ||
+ | Allele ?Variation XREF Gene #Evidence | ||
+ | Possibly_affected_by ?Variation XREF Possibly_affects #Evidence | ||
+ | Legacy_information Text #Evidence | ||
+ | Complementation_data Text | ||
+ | Strain ?Strain XREF Gene | ||
+ | In_cluster ?Gene_cluster XREF Contains_gene // linking to Clusters in locus class | ||
+ | GO_term ?GO_term XREF Gene ?GO_code #Evidence | ||
+ | Contained_in_operon ?Operon XREF Contains_gene | ||
+ | Ortholog ?Gene XREF Ortholog ?Species #Evidence | ||
+ | Paralog ?Gene XREF Paralog ?Species #Evidence | ||
+ | Ortholog_other ?Protein XREF Ortholog_gene #Evidence // to allow Orthologues links to none ?Gene genes eg remanei (ar2 Nov06) | ||
+ | Structured_description Provisional_description ?Text #Evidence // Erich [020322 krb] | ||
+ | Detailed_description ?Text #Evidence // Erich [020322 krb] | ||
+ | Concise_description ?Text #Evidence // Erich [020523 krb] | ||
+ | Other_description ?Text #Evidence // Carol [050202 dl] | ||
+ | Sequence_features ?Text #Evidence // Carol [050202 dl] | ||
+ | Functional_pathway ?Text #Evidence // Carol [050202 dl] | ||
+ | Functional_physical_interaction ?Text #Evidence // Carol [050202 dl] | ||
+ | Biological_process ?Text #Evidence // Carol [050202 dl] | ||
+ | Molecular_function ?Text #Evidence // Carol [050202 dl] | ||
+ | Expression ?Text #Evidence // Carol [050202 dl] | ||
+ | Molecular_info Corresponding_CDS ?CDS XREF Gene #Evidence // to link to live CDSs | ||
+ | Corresponding_CDS_history ?CDS XREF Gene_history // to link to history CDSs | ||
+ | Corresponding_transcript ?Transcript XREF Gene #Evidence | ||
+ | Corresponding_transcript_history ?Transcript XREF Gene_history | ||
+ | Corresponding_pseudogene ?Pseudogene XREF Gene #Evidence | ||
+ | Corresponding_pseudogene_history ?Pseudogene XREF Gene_history | ||
+ | Other_sequence ?Sequence XREF Gene #Evidence // for linking to mRNAs etc. that correspond to a gene | ||
+ | Associated_feature ?Feature XREF Associated_with_gene #Evidence | ||
+ | Gene_product_binds ?Feature XREF Bound_by_product_of | ||
+ | Experimental_info RNAi_result ?RNAi XREF Gene #Evidence | ||
+ | Expr_pattern ?Expr_pattern XREF Gene | ||
+ | Drives_Transgene ?Transgene XREF Driven_by_gene | ||
+ | Transgene_product ?Transgene XREF Gene | ||
+ | Rescued_by_transgene ?Transgene | ||
+ | Gene_regulation Trans_regulator ?Gene_regulation XREF Trans_regulator_gene | ||
+ | Trans_target ?Gene_regulation XREF Trans_regulated_gene | ||
+ | Antibody ?Antibody XREF Gene | ||
+ | Microarray_results ?Microarray_results XREF Gene | ||
+ | Expression_cluster ?Expression_cluster XREF Gene #Evidence //Igor: create clusters of Genes from microarray exps | ||
+ | SAGE_tag ?SAGE_tag XREF Gene #SAGE_mapping_info | ||
+ | YH_bait ?YH XREF Bait_overlapping_gene ?Text// for yeast two hybrid data | ||
+ | YH_target ?YH XREF Target_overlapping_gene ?Text | ||
+ | 3d_data ?3d_data XREF Gene // for NESGC structure information | ||
+ | Interaction ?Interaction | ||
+ | Anatomy_function ?Anatomy_function XREF Gene | ||
+ | Product_binds_matrix ?Position_Matrix XREF Bound_by_gene_product #Evidence | ||
+ | Map_info Map UNIQUE ?Map XREF Gene #Map_position | ||
+ | Well_ordered // "on the line" | ||
+ | Hide_under ?Gene XREF Representative_for | ||
+ | Representative_for ?Gene XREF Hide_under | ||
+ | Positive Inside_rearr ?Rearrangement XREF Gene_inside #Evidence | ||
+ | Positive_clone ?Clone XREF Positive_gene #Evidence | ||
+ | Negative Outside_rearr ?Rearrangement XREF Gene_outside #Evidence | ||
+ | Negative_clone ?Clone XREF Negative_gene #Evidence | ||
+ | Mapping_data 2_point ?2_point_data | ||
+ | Multi_point ?Multi_pt_data | ||
+ | Pos_neg_data ?Pos_neg_data | ||
+ | Interpolated_map_position UNIQUE ?Map UNIQUE Float // for loci with CDSs but no real Map position | ||
+ | Landmark_gene // for those genes that will appear in genetic map of Genome Browser | ||
+ | Pseudo_map_position // should be added to flag those genes which have Map position tags that | ||
+ | // were 'promoted' from Interpolated_map_position tags | ||
+ | Reference ?Paper XREF Gene #Evidence | ||
+ | Remark ?Text #Evidence | ||
+ | Method UNIQUE ?Method | ||
</pre> | </pre> | ||
== Proposed Changes == | == Proposed Changes == | ||
+ | |||
+ | ==Unused tags== | ||
+ | |||
+ | Suppressed | ||
+ | |||
+ | Detailed_description | ||
+ | |||
+ | Rescued_by_transgene | ||
+ | |||
+ | 3d_data | ||
+ | |||
+ | Product_binds_matrix - Has probable uses for the future |
Latest revision as of 10:40, 4 October 2010
Curator Comments/Description
Model
//////////////////////////////////////////////////////////////////////////////////////// // // ?Gene class - krb // //////////////////////////////////////////////////////////////////////////////////////// ?Gene Evidence #Evidence SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Gene_child 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 ?Accession_number //For Darin genbank genpep ids 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 Made_into_transposon Status UNIQUE Live #Evidence Suppressed #Evidence Dead #Evidence Gene_info Gene_class UNIQUE ?Gene_class XREF Genes Laboratory ?Laboratory Cloned_by #Evidence // mt3 acreditation of person who cloned gene [060829 ar2] Reference_allele ?Variation #Evidence Allele ?Variation XREF Gene #Evidence Possibly_affected_by ?Variation XREF Possibly_affects #Evidence Legacy_information Text #Evidence Complementation_data Text Strain ?Strain XREF Gene In_cluster ?Gene_cluster XREF Contains_gene // linking to Clusters in locus class GO_term ?GO_term XREF Gene ?GO_code #Evidence Contained_in_operon ?Operon XREF Contains_gene Ortholog ?Gene XREF Ortholog ?Species #Evidence Paralog ?Gene XREF Paralog ?Species #Evidence Ortholog_other ?Protein XREF Ortholog_gene #Evidence // to allow Orthologues links to none ?Gene genes eg remanei (ar2 Nov06) Structured_description Provisional_description ?Text #Evidence // Erich [020322 krb] Detailed_description ?Text #Evidence // Erich [020322 krb] Concise_description ?Text #Evidence // Erich [020523 krb] Other_description ?Text #Evidence // Carol [050202 dl] Sequence_features ?Text #Evidence // Carol [050202 dl] Functional_pathway ?Text #Evidence // Carol [050202 dl] Functional_physical_interaction ?Text #Evidence // Carol [050202 dl] Biological_process ?Text #Evidence // Carol [050202 dl] Molecular_function ?Text #Evidence // Carol [050202 dl] Expression ?Text #Evidence // Carol [050202 dl] Molecular_info Corresponding_CDS ?CDS XREF Gene #Evidence // to link to live CDSs Corresponding_CDS_history ?CDS XREF Gene_history // to link to history CDSs Corresponding_transcript ?Transcript XREF Gene #Evidence Corresponding_transcript_history ?Transcript XREF Gene_history Corresponding_pseudogene ?Pseudogene XREF Gene #Evidence Corresponding_pseudogene_history ?Pseudogene XREF Gene_history Other_sequence ?Sequence XREF Gene #Evidence // for linking to mRNAs etc. that correspond to a gene Associated_feature ?Feature XREF Associated_with_gene #Evidence Gene_product_binds ?Feature XREF Bound_by_product_of Experimental_info RNAi_result ?RNAi XREF Gene #Evidence Expr_pattern ?Expr_pattern XREF Gene Drives_Transgene ?Transgene XREF Driven_by_gene Transgene_product ?Transgene XREF Gene Rescued_by_transgene ?Transgene Gene_regulation Trans_regulator ?Gene_regulation XREF Trans_regulator_gene Trans_target ?Gene_regulation XREF Trans_regulated_gene Antibody ?Antibody XREF Gene Microarray_results ?Microarray_results XREF Gene Expression_cluster ?Expression_cluster XREF Gene #Evidence //Igor: create clusters of Genes from microarray exps SAGE_tag ?SAGE_tag XREF Gene #SAGE_mapping_info YH_bait ?YH XREF Bait_overlapping_gene ?Text// for yeast two hybrid data YH_target ?YH XREF Target_overlapping_gene ?Text 3d_data ?3d_data XREF Gene // for NESGC structure information Interaction ?Interaction Anatomy_function ?Anatomy_function XREF Gene Product_binds_matrix ?Position_Matrix XREF Bound_by_gene_product #Evidence Map_info Map UNIQUE ?Map XREF Gene #Map_position Well_ordered // "on the line" Hide_under ?Gene XREF Representative_for Representative_for ?Gene XREF Hide_under Positive Inside_rearr ?Rearrangement XREF Gene_inside #Evidence Positive_clone ?Clone XREF Positive_gene #Evidence Negative Outside_rearr ?Rearrangement XREF Gene_outside #Evidence Negative_clone ?Clone XREF Negative_gene #Evidence Mapping_data 2_point ?2_point_data Multi_point ?Multi_pt_data Pos_neg_data ?Pos_neg_data Interpolated_map_position UNIQUE ?Map UNIQUE Float // for loci with CDSs but no real Map position Landmark_gene // for those genes that will appear in genetic map of Genome Browser Pseudo_map_position // should be added to flag those genes which have Map position tags that // were 'promoted' from Interpolated_map_position tags Reference ?Paper XREF Gene #Evidence Remark ?Text #Evidence Method UNIQUE ?Method
Proposed Changes
Unused tags
Suppressed
Detailed_description
Rescued_by_transgene
3d_data
Product_binds_matrix - Has probable uses for the future