From bbb2e5c3df9dc823df5c1ab95cca3115e86e4fc4 Mon Sep 17 00:00:00 2001 From: Paul-Davis Date: Wed, 20 May 2020 10:11:10 +0100 Subject: [PATCH] Final model tweaks and the removal of the ECO_term Attribute_of grouping tag as requested. --- wspec/models.wrm | 16 ++++------ wspec/models.wrm.annot | 72 +++++++++++++++++++++++++++++++----------- 2 files changed, 60 insertions(+), 28 deletions(-) diff --git a/wspec/models.wrm b/wspec/models.wrm index dab69c135..7e5de6aa2 100644 --- a/wspec/models.wrm +++ b/wspec/models.wrm @@ -1080,10 +1080,10 @@ ////////////////////////////////////////// ?Disease_model_annotation Disease_term UNIQUE ?DO_term XREF Disease_model_annotation Disease_of_species ?Species - Modeled_by Strain UNIQUE ?Strain XREF Models_disease_in_annotation ?Text // WS268 XREF tag modified - Variation UNIQUE ?Variation XREF Models_disease_in_annotation ?Text // WS268 XREF tag modified - Transgene UNIQUE ?Transgene XREF Models_disease_in_annotation ?Text // WS268 XREF tag modified - Disease_relevant_gene UNIQUE ?Gene XREF Models_disease_in_annotation ?Text // WS268 XREF tag modified + Modeled_by Strain UNIQUE ?Strain XREF Models_disease_in_annotation ?Text // WS278 XREF tag modified + Variation UNIQUE ?Variation XREF Models_disease_in_annotation ?Text // WS278 XREF tag modified + Transgene UNIQUE ?Transgene XREF Models_disease_in_annotation ?Text // WS278 XREF tag modified + Disease_relevant_gene UNIQUE ?Gene XREF Models_disease_in_annotation ?Text // WS278 XREF tag modified Genotype UNIQUE ?Genotype XREF Models_disease_in_annotation //to associate genotypes Modeled_by_remark UNIQUE ?Text Annotation_made_with Interacting_variation ?Variation //Addition for WS261 @@ -1098,7 +1098,7 @@ contributes_to_condition is_marker_for Evidence_code GO_code ?GO_code // will use ECO later on - ECO_term ?ECO_term XREF Disease_model_annotation + ECO_term ?ECO_term Qualifier_not // to indicate that a disease is NOT modeled by X change tag WS262 Experimental_condition Inducing_chemical ?Molecule XREF Disease_model_inducer //to indicate the disease-inducing agent Inducing_agent ?Text //e.g. diet, radiation,etc not in Molecule class @@ -1135,7 +1135,7 @@ ?GO_annotation Gene UNIQUE ?Gene XREF GO_annotation - ECO_term UNIQUE ?ECO_term XREF GO_annotation + ECO_term UNIQUE ?ECO_term GO_term UNIQUE ?GO_term XREF GO_annotation GO_code UNIQUE ?GO_code Annotation_relation UNIQUE ?RO_term XREF GO_annotation @@ -1228,8 +1228,6 @@ Related ?Text Child ?ECO_term XREF Parent Parent ?ECO_term XREF Child - Attribute_of GO_annotation ?GO_annotation XREF ECO_term - Disease_model_annotation ?Disease_model_annotation XREF ECO_term Version UNIQUE Text /////////////////////////////////////////////////////////////// @@ -3967,4 +3965,4 @@ // Add a line for the WS release the models file is going to be CVS tagged for // This give you a final shot at creating a nicely formatted CVS commit message // -// WS274 +// WS278 diff --git a/wspec/models.wrm.annot b/wspec/models.wrm.annot index d4d2b8dd0..80fc572ea 100644 --- a/wspec/models.wrm.annot +++ b/wspec/models.wrm.annot @@ -345,7 +345,9 @@ Disease_info Experimental_model ^disease-experimental-model ?DO_term OUTXREF Gene_by_biology ?Species #Evidence Potential_model ^disease-potential-model ?DO_term OUTXREF Gene_by_orthology ?Species #Evidence Disease_relevance ?Text ^note ?Species #Evidence - Disease_model_annotation ?Disease_model_annotation INXREF Disease_relevant_gene + Modifies_disease ?DO_term INXREF Disease_modifier_gene //New tag WS278 + Models_disease_in_annotation ?Disease_model_annotation INXREF Disease_relevant_gene //New tag WS278 + Modifies_disease_in_annotation ?Disease_model_annotation INXREF Modifier_gene //New tag WS278 Molecular_info Corresponding_CDS ?CDS OUTXREF Gene #Evidence // to link to live CDSs Corresponding_CDS_history ?CDS OUTXREF Gene_history // to link to history CDSs Corresponding_transcript ?Transcript OUTXREF Gene #Evidence @@ -688,7 +690,9 @@ Clone ?Clone INXREF In_strain Transgene ?Transgene INXREF Strain Disease_info Models_disease ?DO_term INXREF Disease_model_strain - Disease_model_annotation ?Disease_model_annotation INXREF Strain + Modifies_disease ?DO_term INXREF Disease_modifier_strain //New tag + Models_disease_in_annotation ?Disease_model_annotation INXREF Strain //New tag + Modifies_disease_in_annotation ?Disease_model_annotation INXREF Modifier_strain //New tag Database ?Database ^database ?Database_field ^field ?Text ^accession Properties Inbreeding_state UNIQUE Selfed // Text Isofemale // Text @@ -1099,11 +1103,11 @@ ?Disease_model_annotation Disease_term UNIQUE ?DO_term OUTXREF Disease_model_annotation Disease_of_species ?Species - Modeled_by Strain ^modeled-by-strain UNIQUE ?Strain OUTXREF Disease_model_annotation ?Text - 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 Models_disease_in_annotation //to associate genotypes + Modeled_by Strain ^modeled-by-strain UNIQUE ?Strain OUTXREF Models_disease_in_annotation ?Text + Variation ^modeled-by-variation UNIQUE ?Variation OUTXREF Models_disease_in_annotation ?Text + Transgene ^modeled-by-transgene UNIQUE ?Transgene OUTXREF Models_disease_in_annotation ?Text + Disease_relevant_gene ^modeled-by-disease-relevant-gene UNIQUE ?Gene OUTXREF Models_disease_in_annotation ?Text + Genotype ^modeled-by-genotype UNIQUE ?Genotype OUTXREF Models_disease_in_annotation //to associate genotypes Modeled_by_remark UNIQUE ?Text Annotation_made_with Interacting_variation ?Variation //Addition for WS261 Interacting_transgene ?Transgene @@ -1116,15 +1120,16 @@ causes_condition contributes_to_condition is_marker_for - Evidence_code ?GO_code + Evidence_code GO_code ?GO_code + ECO_term ?ECO_term Qualifier_not Experimental_condition Inducing_chemical ?Molecule OUTXREF Disease_model_inducer Inducing_agent ?Text - Modifier_info Modifier_transgene ?Transgene - Modifier_variation ?Variation - Modifier_strain ?Strain - Modifier_gene ?Gene - Modifier_molecule ?Molecule OUTXREF Disease_model_modifier + Modifier_info Modifier_transgene ?Transgene OUTXREF Modifies_disease_in_annotation + Modifier_variation ?Variation OUTXREF Modifies_disease_in_annotation + Modifier_strain ?Strain OUTXREF Modifies_disease_in_annotation + Modifier_gene ?Gene OUTXREF Modifies_disease_in_annotation + Modifier_molecule ?Molecule OUTXREF Disease_model_modifier // to indicate chemical modifiers of the disease Modifier_genotype ?Genotype INXREF Modifies_disease_in_annotation //to annotate genotype modifiers of disease Other_modifier ?Text Modifier_association_type UNIQUE condition_ameliorated_by @@ -1152,6 +1157,7 @@ ?GO_annotation Gene UNIQUE ?Gene OUTXREF GO_annotation + ECO_term UNIQUE ?ECO_term GO_term UNIQUE ?GO_term OUTXREF GO_annotation GO_code UNIQUE ?GO_code Annotation_relation UNIQUE ?RO_term XREF GO_annotation @@ -1222,6 +1228,24 @@ ?GO_code Description ?Text Remark ?Text #Evidence +/////////////////////////////////////////////////////////////// +// +// ?ECO_term class - kimberly WS278 +// +//////////////////////////////////////////////////////////////// + +?ECO_term Name UNIQUE ?Text + Status UNIQUE Valid + Obsolete + Alt_id ?Text + Definition UNIQUE ?Text + Synonym Broad ?Text + Exact ?Text + Narrow ?Text + Related ?Text + Child ?ECO_term OUTXREF Parent + Parent ?ECO_term INXREF Child + Version UNIQUE Text /////////////////////////////////////////////////////////////// // @@ -1297,12 +1321,17 @@ Phenotype ?Phenotype INXREF DO_term WBProcess ?WBProcess INXREF DO_term // Reference ?Paper OUTXREF DO_term + Disease_modifier_gene ?Gene OUTXREF Modifies_disease // Tag missing from original proposal WS268 Disease_model_variation ?Variation INXREF Models_disease + Disease_modifier_variation ?Variation OUTXREF Modifies_disease //New tag Disease_model_strain ?Strain INXREF Models_disease + Disease_modifier_strain ?Strain OUTXREF Modifies_disease //New tag Disease_model_transgene ?Transgene INXREF Models_disease + Disease_modifier_transgene ?Transgene OUTXREF Modifies_disease //New tag Disease_model_genotype ?Genotype INXREF Models_disease Disease_modifier_genotype ?Genotype INXREF Modifies_disease Chemical_inducer ?Molecule INXREF Induces_disease + Other_inducer ?Text //New tag Molecule_modifier ?Molecule INXREF Modifies_disease Reagent_info Associated_antibody ?Antibody INXREF Antibody_for_disease Associated_construct ?Construct INXREF Construct_for_disease @@ -2778,7 +2807,9 @@ 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 + Modifies_disease ?DO_term INXREF Disease_modifier_transgene //New tag + Models_disease_in_annotation ?Disease_model_annotation INXREF Transgene //New tag + Modifies_disease_in_annotation ?Disease_model_annotation INXREF Modifier_transgene //New tag Reference ?Paper OUTXREF Transgene Species UNIQUE ?Species Remark ?Text #Evidence @@ -2990,7 +3021,8 @@ Not_in_Strain ?Strain INXREF Phenotype_not_observed //added by Wen for Not observed phenotypes Not_in_Transgene ?Transgene INXREF Phenotype_not_observed //added by Wen for Not observed phenotypes Not_in_Rearrangement ?Rearrangement INXREF Phenotype_not_observed //added by Wen for Not observed phenotypes - Associated_with GO_term ?GO_term OUTXREF Phenotype ?GO_code #Evidence // Tag Associated_with changed by Carol + Associated_with GO_term ?GO_term + ECO_term ?ECO_term // Tag changes from GO to ECO for WS278 WBProcess ?WBProcess INXREF Phenotype DO_term ?DO_term OUTXREF Phenotype #Evidence @@ -3659,7 +3691,9 @@ Phenotype_remark ?Text #Evidence Phenotype_not_observed ?Phenotype OUTXREF Not_in_Variation #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes Disease_info Models_disease ?DO_term INXREF Disease_model_variation - Disease_model_annotation ?Disease_model_annotation INXREF Variation + Modifies_disease ?DO_term INXREF Disease_modifier_variation //New tag + Models_disease_in_annotation ?Disease_model_annotation INXREF Variation //New tag + Modifies_disease_in_annotation ?Disease_model_annotation INXREF Modifier_variation //New tag Reference ?Paper OUTXREF Allele Remark ?Text #Evidence // Method UNIQUE ?Method // Becomes :locatable/method @@ -3953,7 +3987,7 @@ // CVS tagging lines -// Add a line for the WS release the models file is going to be CVS tagged for -// This give you a final shot at creating a nicely formatted CVS commit message +// Add a line for the WS release the models file is going to be GIT tagged for +// This give you a final shot at creating a nicely formatted GIT commit message // -// WS272 +// WS278