From ab476097c4695a7807f40671de7bab5d55794eb2 Mon Sep 17 00:00:00 2001 From: Paul-Davis Date: Wed, 11 Mar 2020 16:18:05 +0000 Subject: [PATCH] Added Transposon and genotype model changes for WS277. --- wspec/models.wrm | 35 +++++++++++++++++++++++++++++++++++ wspec/models.wrm.annot | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 69 insertions(+) diff --git a/wspec/models.wrm b/wspec/models.wrm index 8d908a9d4..53b45aa6e 100644 --- a/wspec/models.wrm +++ b/wspec/models.wrm @@ -300,6 +300,7 @@ Legacy_information Text #Evidence Complementation_data Text Strain ?Strain XREF Gene + Component_of_genotype ?Genotype XREF Gene In_cluster ?Gene_cluster XREF Contains_gene // linking to Clusters in locus class RNASeq_FPKM ?Life_stage Float #Evidence GO_term ?GO_term XREF Gene ?GO_code #Evidence @@ -611,6 +612,7 @@ Marked By_variation ?Variation XREF Marked_rearrangement By_transgene ?Transgene XREF Marked_rearrangement By_other ?Text + Component_of_genotype ?Genotype XREF Rearrangement // possibility to refer to other Intervals to describe a complex rearrangement // for the worm this is not too necessary, but important for fly and mouse // or perhaps there should be another class Complex_Rear that refers to @@ -710,6 +712,30 @@ Approximate UNIQUE Float Inferred_from_GPS + +//////////////////////////////////////////////////////////////////////////////// +// +// ?Genotype class +// +//////////////////////////////////////////////////////////////////////////////// + +?Genotype Genotype_name UNIQUE ?Text // e.g. “unc-1(e103);unc-2(e234)”; eventually to be automatically generated + Genotype_synonym ?Text // To capture literal representations in the literature + Genotype_component Gene ?Gene XREF Component_of_genotype #Evidence + Variation ?Variation XREF Component_of_genotype + Rearrangement ?Rearrangement XREF Component_of_genotype + Transgene ?Transgene XREF Component_of_genotype + Other_component UNIQUE ?Text // Free text components including RNAi + Disease_info Models_disease ?DO_term XREF Disease_model_genotype + Modifies_disease ?DO_term XREF Disease_modifier_genotype + Disease_model_annotation Model_genotype ?Disease_model_annotation XREF Genotype + Modifier_genotype ?Disease_model_annotation XREF Modifier_genotype + Specis UNIQUE ?Species + Remark ?Text + Reference ?Paper XREF Genotype + + + //////////////////////////////////////////////////////////////////////////////// // // ?Lab_Location class @@ -1056,6 +1082,7 @@ Variation UNIQUE ?Variation XREF Disease_model_annotation ?Text // genetic entity that models the disease Transgene UNIQUE ?Transgene XREF Disease_model_annotation ?Text // genetic entity that models the disease Disease_relevant_gene UNIQUE ?Gene XREF Disease_model_annotation ?Text //when the genetic entity is a gene + Genotype UNIQUE ?Genotype XREF Model_genotype //to associate genotypes Modeled_by_remark UNIQUE ?Text Annotation_made_with Interacting_variation ?Variation //Addition for WS261 Interacting_transgene ?Transgene @@ -1077,6 +1104,7 @@ Modifier_strain ?Strain //(same as above) Modifier_gene ?Gene //to indicate the gene in the modifying Transgene, Variation, Strain. Modifier_molecule ?Molecule XREF Disease_model_modifier // to indicate chemical modifiers of the disease + Modifier_genotype ?Genotype XREF Modifier_genotype //to annotate genotype modifiers of disease Other_modifier ?Text //to indicate other modifiers of the disease eg. diet,radiation, surgery etc Modifier_association_type UNIQUE condition_ameliorated_by //to indicate the association type between modifiers and disease condition_exacerbated_by @@ -1257,6 +1285,8 @@ Disease_model_variation ?Variation XREF Models_disease //To associate Variations to a disease Disease_model_strain ?Strain XREF Models_disease //To associate Strains to a disease Disease_model_transgene ?Transgene XREF Models_disease //To associate Transgenes to disease + Disease_model_genotype ?Genotype XREF Models_disease + Disease_modifier_genotype ?Genotype XREF Modifies_disease Chemical_inducer ?Molecule XREF Induces_disease //To associate inducing chemicals to a disease Molecule_modifier ?Molecule XREF Modifies_disease //To associate modifying chemicals to a disease Reagent_info Associated_antibody ?Antibody XREF Antibody_for_disease @@ -1820,6 +1850,8 @@ ?Transposon Evidence #Evidence + Name Public_name UNIQUE ?Text + Other_name ?Text SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Transposon Structure S_child CDS_child ?CDS XREF Transposon UNIQUE Int UNIQUE Int #SMap_info // Transposon_CDSs will now link to parent Transposons ar2 02-DEC-05 Pseudogene_child ?Pseudogene XREF Transposon UNIQUE Int UNIQUE Int #SMap_info @@ -2717,6 +2749,7 @@ Interactor ?Interaction Associated_with Marked_rearrangement ?Rearrangement XREF By_transgene Strain ?Strain XREF Transgene + Component_of_genotype ?Genotype XREF Transgene Transgene_for_disease ?DO_term XREF Associated_transgene #Evidence Disease_info Models_disease ?DO_term XREF Disease_model_transgene Disease_model_annotation ?Disease_model_annotation XREF Transgene @@ -3417,6 +3450,7 @@ Transcript ?Transcript XREF Reference #Evidence Species ?Species #Evidence Strain ?Strain XREF Reference #Evidence + Genotype ?Genotype XREF Reference Clone ?Clone XREF Reference #Evidence Expr_pattern ?Expr_pattern XREF Reference #Evidence Expr_profile ?Expr_profile XREF Reference #Evidence @@ -3531,6 +3565,7 @@ Natural_variant Origin Species UNIQUE ?Species Strain ?Strain XREF Variation #Evidence + Component_of_genotype ?Genotype XREF Variation Laboratory ?Laboratory Author ?Author // use Person when known, else use Author Person ?Person // diff --git a/wspec/models.wrm.annot b/wspec/models.wrm.annot index 7e35ce220..da440c687 100644 --- a/wspec/models.wrm.annot +++ b/wspec/models.wrm.annot @@ -38,6 +38,8 @@ // // For more details, see https://github.com/WormBase/db-prototypes/wiki/Augmented-model-file // +// For the datomic conversion INXREF is dropped in favor of the OUTXREF so use OUT where you +// want the data displayed by default. //////////////////////// // Basic map classes // @@ -321,6 +323,7 @@ Legacy_information Text #Evidence Complementation_data Text Strain ?Strain OUTXREF Gene + Component_of_genotype ?Genotype INXREF Gene In_cluster ?Gene_cluster INXREF Contains_gene // linking to Clusters in locus class RNASeq_FPKM ^rnaseq ?Life_stage ^stage Float ^fpkm #Evidence GO_term ?GO_term OUTXREF Gene ?GO_code #Evidence @@ -634,6 +637,7 @@ Marked By_variation ^marked-by-variation ?Variation OUTXREF Marked_rearrangement By_transgene ^marked-by-transgene ?Transgene OUTXREF Marked_rearrangement By_other ^marked-by-other ?Text + Component_of_genotype ?Genotype INXREF Rearrangement // possibility to refer to other Intervals to describe a complex rearrangement // for the worm this is not too necessary, but important for fly and mouse // or perhaps there should be another class Complex_Rear that refers to @@ -733,6 +737,27 @@ Approximate UNIQUE Float Inferred_from_GPS +//////////////////////////////////////////////////////////////////////////////// +// +// ?Genotype class +// +//////////////////////////////////////////////////////////////////////////////// + +?Genotype Genotype_name UNIQUE ?Text // e.g. “unc-1(e103);unc-2(e234)”; eventually to be automatically generated + Genotype_synonym ?Text // To capture literal representations in the literature + Genotype_component Gene ?Gene OUTXREF Component_of_genotype #Evidence + Variation ?Variation OUTXREF Component_of_genotype + Rearrangement ?Rearrangement OUTXREF Component_of_genotype + Transgene ?Transgene OUTXREF Component_of_genotype + Other_component UNIQUE ?Text // Free text components including RNAi + Disease_info Models_disease ?DO_term OUTXREF Disease_model_genotype + Modifies_disease ?DO_term OUTXREF Disease_modifier_genotype + Disease_model_annotation Model_genotype ?Disease_model_annotation OUTXREF Genotype + Modifier_genotype ?Disease_model_annotation OUTXREF Modifier_genotype + Specis UNIQUE ?Species + Remark ?Text + Reference ?Paper OUTXREF Genotype + //////////////////////////////////////////////////////////////////////////////// // // ?Lab_Location class @@ -1078,6 +1103,7 @@ Variation ^modeled-by-variation UNIQUE ?Variation OUTXREF Disease_model_annotation ?Text Transgene ^modeled-by-transgene UNIQUE ?Transgene OUTXREF Disease_model_annotation ?Text Disease_relevant_gene ^modeled-by-disease-relevant-gene UNIQUE ?Gene OUTXREF Disease_model_annotation ?Text + Genotype ^modeled-by-genotype UNIQUE ?Genotype INXREF Model_genotype //to associate genotypes Modeled_by_remark UNIQUE ?Text Annotation_made_with Interacting_variation ?Variation //Addition for WS261 Interacting_transgene ?Transgene @@ -1099,6 +1125,7 @@ Modifier_strain ?Strain Modifier_gene ?Gene Modifier_molecule ?Molecule OUTXREF Disease_model_modifier + Modifier_genotype ?Genotype INXREF Modifier_genotype //to annotate genotype modifiers of disease Other_modifier ?Text Modifier_association_type UNIQUE condition_ameliorated_by condition_exacerbated_by @@ -1273,6 +1300,8 @@ Disease_model_variation ?Variation INXREF Models_disease Disease_model_strain ?Strain INXREF Models_disease Disease_model_transgene ?Transgene INXREF Models_disease + Disease_model_genotype ?Genotype INXREF Models_disease + Disease_modifier_genotype ?Genotype INXREF Modifies_disease Chemical_inducer ?Molecule INXREF Induces_disease Molecule_modifier ?Molecule INXREF Modifies_disease Reagent_info Associated_antibody ?Antibody INXREF Antibody_for_disease @@ -1838,6 +1867,8 @@ ?Transposon Evidence #Evidence + Name Public_name UNIQUE ?Text + Other_name ?Text // SMap S_parent UNIQUE Sequence UNIQUE ?Sequence NOXREF Transposon // Structure S_child CDS_child ?CDS OUTXREF Transposon UNIQUE Int ^start UNIQUE Int ^end #SMap_info // Transposon_CDSs will now link to parent Transposons ar2 02-DEC-05 // Pseudogene_child ?Pseudogene OUTXREF Transposon UNIQUE Int ^start UNIQUE Int ^end #SMap_info @@ -2744,6 +2775,7 @@ Interactor ?Interaction INXREF Transgene Associated_with Marked_rearrangement ?Rearrangement INXREF By_transgene Strain ?Strain OUTXREF Transgene + Component_of_genotype ?Genotype INXREF Transgene Transgene_for_disease ?DO_term OUTXREF Associated_transgene #Evidence Disease_info Models_disease ?DO_term INXREF Disease_model_transgene Disease_model_annotation ?Disease_model_annotation INXREF Transgene @@ -3442,6 +3474,7 @@ Transcript ?Transcript INXREF Reference #Evidence Species ?Species #Evidence Strain ?Strain INXREF Reference #Evidence + Genotype ?Genotype INXREF Reference Clone ?Clone INXREF Reference #Evidence Expr_pattern ?Expr_pattern INXREF Reference #Evidence Expr_profile ?Expr_profile INXREF Reference #Evidence @@ -3556,6 +3589,7 @@ Natural_variant Origin Species UNIQUE ?Species Strain ?Strain OUTXREF Variation #Evidence + Component_of_genotype ?Genotype INXREF Variation Laboratory ?Laboratory Author ?Author // use Person when known, else use Author Person ?Person //