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Final model tweaks and the removal of the ECO_term Attribute_of group…
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…ing tag as requested.
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Paul-Davis committed May 20, 2020
1 parent 534434a commit bbb2e5c
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16 changes: 7 additions & 9 deletions wspec/models.wrm
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//////////////////////////////////////////
?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
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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
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?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
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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

///////////////////////////////////////////////////////////////
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// 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
72 changes: 53 additions & 19 deletions wspec/models.wrm.annot
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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
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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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
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?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

///////////////////////////////////////////////////////////////
//
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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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

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