WormBase Model:Gene
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Model
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//
// ?Gene class - krb
//
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?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
