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Merge pull request #253 from alliance-genome/v2.2.3_branch
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Renamed orthology to homology and added paralogy classes and fields
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@chris-grove
chris-grove authored May 18, 2024
2 parents 7af88d0 + 256face commit 2d55270
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Showing 3 changed files with 157 additions and 37 deletions.
127 changes: 113 additions & 14 deletions generated/jsonschema/allianceModel.schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -14015,15 +14015,15 @@
},
"object_gene": {
"$ref": "#/$defs/Gene",
"description": "The second gene in the orthology match pair"
"description": "The second gene in the homology match pair"
},
"obsolete": {
"description": "Entity is no longer current.",
"type": "boolean"
},
"subject_gene": {
"$ref": "#/$defs/Gene",
"description": "The first gene in the orthology match pair"
"description": "The first gene in the homology match pair"
},
"updated_by": {
"description": "The individual that last modified the entity.",
Expand Down Expand Up @@ -14075,7 +14075,7 @@
},
"object_gene": {
"$ref": "#/$defs/Gene",
"description": "The second gene in the orthology match pair"
"description": "The second gene in the homology match pair"
},
"obsolete": {
"description": "Entity is no longer current.",
Expand All @@ -14087,7 +14087,7 @@
},
"subject_gene": {
"$ref": "#/$defs/Gene",
"description": "The first gene in the orthology match pair"
"description": "The first gene in the homology match pair"
},
"updated_by": {
"description": "The individual that last modified the entity.",
Expand All @@ -14106,10 +14106,6 @@
"additionalProperties": false,
"description": "Class that holds the properties necessary to record an orthology record from DIOPT",
"properties": {
"confidence": {
"description": "Confidence of orthology match Permissible values: moderate / high / low",
"type": "string"
},
"created_by": {
"description": "The individual that created the entity.",
"type": "string"
Expand All @@ -14134,6 +14130,10 @@
"format": "date-time",
"type": "string"
},
"homology_confidence": {
"description": "Confidence of homology match Permissible values: moderate / high / low",
"type": "string"
},
"internal": {
"description": "Classifies the entity as private (for internal use) or not (for public use).",
"type": "boolean"
Expand All @@ -14147,19 +14147,19 @@
"type": "string"
},
"moderate_filter": {
"description": "Indicates whether this orthology match is displayed when the moderate filter is selected",
"description": "Indicates whether this homology match is displayed when the moderate filter is selected",
"type": "boolean"
},
"object_gene": {
"$ref": "#/$defs/Gene",
"description": "The second gene in the orthology match pair"
"description": "The second gene in the homology match pair"
},
"obsolete": {
"description": "Entity is no longer current.",
"type": "boolean"
},
"prediction_methods_matched": {
"description": "Source of the orthology match",
"description": "Source of the homology match",
"items": {
"type": "string"
},
Expand All @@ -14180,12 +14180,12 @@
"type": "array"
},
"strict_filter": {
"description": "Indicates whether this orthology match is displayed when the strict filter is selected",
"description": "Indicates whether this homology match is displayed when the strict filter is selected",
"type": "boolean"
},
"subject_gene": {
"$ref": "#/$defs/Gene",
"description": "The first gene in the orthology match pair"
"description": "The first gene in the homology match pair"
},
"updated_by": {
"description": "The individual that last modified the entity.",
Expand All @@ -14195,14 +14195,113 @@
"required": [
"is_best_score",
"is_best_reverse_score",
"confidence",
"homology_confidence",
"subject_gene",
"object_gene",
"internal"
],
"title": "GeneToGeneOrthologyGenerated",
"type": "object"
},
"GeneToGeneParalogy": {
"additionalProperties": false,
"description": "",
"properties": {
"created_by": {
"description": "The individual that created the entity.",
"type": "string"
},
"date_created": {
"description": "The date on which an entity was created. This can be applied to nodes or edges.",
"format": "date-time",
"type": "string"
},
"date_updated": {
"description": "Date on which an entity was last modified.",
"format": "date-time",
"type": "string"
},
"db_date_created": {
"description": "The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).",
"format": "date-time",
"type": "string"
},
"db_date_updated": {
"description": "Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.",
"format": "date-time",
"type": "string"
},
"homology_confidence": {
"description": "Confidence of homology match Permissible values: moderate / high / low",
"type": "string"
},
"identity": {
"description": "Identity score between the two genes",
"type": "integer"
},
"internal": {
"description": "Classifies the entity as private (for internal use) or not (for public use).",
"type": "boolean"
},
"length": {
"description": "The length of the aligned regions between two genes",
"type": "integer"
},
"object_gene": {
"$ref": "#/$defs/Gene",
"description": "The second gene in the homology match pair"
},
"obsolete": {
"description": "Entity is no longer current.",
"type": "boolean"
},
"prediction_methods_matched": {
"description": "Source of the homology match",
"items": {
"type": "string"
},
"type": "array"
},
"prediction_methods_not_called": {
"description": "Prediction methods that were not called",
"items": {
"type": "string"
},
"type": "array"
},
"prediction_methods_not_matched": {
"description": "Prediction methods not matched",
"items": {
"type": "string"
},
"type": "array"
},
"rank": {
"description": "The rank (order) of the paralog result",
"type": "integer"
},
"similarity": {
"description": "Similarity score between the two genes",
"type": "integer"
},
"subject_gene": {
"$ref": "#/$defs/Gene",
"description": "The first gene in the homology match pair"
},
"updated_by": {
"description": "The individual that last modified the entity.",
"type": "string"
}
},
"required": [
"subject_gene",
"object_gene",
"homology_confidence",
"internal"
],
"title": "GeneToGeneParalogy",
"type": "object"
},
"GenerationMethod": {
"additionalProperties": false,
"description": "",
Expand Down
2 changes: 1 addition & 1 deletion model/schema/allianceModel.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ imports:
- modCorpusAssociation
- linkml:types
- ontologyTerm
- orthology
- homology
- phenotypeAndDiseaseAnnotation
- reagent
- reference
Expand Down
65 changes: 43 additions & 22 deletions model/schema/orthology.yaml → model/schema/homology.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
id: https://github.com/alliance-genome/agr_curation_schema/ontologyTerm
name: Alliance-Schema-Orthology-Term
title: Alliance Schema Orthology Term
id: https://github.com/alliance-genome/agr_curation_schema/homology.yaml
name: Alliance-Schema-Homology
title: Alliance Schema Homology

imports:
- core
Expand Down Expand Up @@ -59,79 +59,100 @@ classes:
slots:
- is_best_score
- is_best_reverse_score
- confidence
- homology_confidence
- strict_filter
- moderate_filter
- prediction_methods_matched
- prediction_methods_not_matched
- prediction_methods_not_called

GeneToGeneParalogy:
is_a: AuditedObject
slots:
- subject_gene
- object_gene
- rank
- homology_confidence
- length
- similarity
- prediction_methods_matched
- prediction_methods_not_matched
- prediction_methods_not_called
- identity

slots:

is_best_score:
description: >-
DIOPT schema highlights the best pair
Permissible values: Yes / No / Yes_Adjusted
domain: GeneToGeneOrthologyGenerated
range: VocabularyTerm
required: true

is_best_reverse_score:
description: >-
DIOPT schema highlights the best pair
Permissible values: Yes / No
domain: GeneToGeneOrthologyGenerated
range: VocabularyTerm
required: true

confidence:
homology_confidence:
description: >-
Confidence of orthology match
Confidence of homology match
Permissible values: moderate / high / low
domain: GeneToGeneOrthologyGenerated
range: VocabularyTerm
required: true

strict_filter:
description: >-
Indicates whether this orthology match is displayed when the strict filter
Indicates whether this homology match is displayed when the strict filter
is selected
domain: GeneToGeneOrthologyGenerated
range: boolean

moderate_filter:
description: >-
Indicates whether this orthology match is displayed when the moderate filter
Indicates whether this homology match is displayed when the moderate filter
is selected
domain: GeneToGeneOrthologyGenerated
range: boolean

subject_gene:
description: The first gene in the orthology match pair
domain: GeneToGeneOrthology
description: The first gene in the homology match pair
range: Gene
required: true

object_gene:
description: The second gene in the orthology match pair
domain: GeneToGeneOrthology
description: The second gene in the homology match pair
range: Gene
required: true

prediction_methods_matched:
description: Source of the orthology match
domain: GeneToGeneOrthologyGenerated
description: Source of the homology match
range: VocabularyTerm
multivalued: true

prediction_methods_not_matched:
description: Prediction methods not matched
domain: GeneToGeneOrthologyGenerated
range: VocabularyTerm
multivalued: true

prediction_methods_not_called:
description: Prediction methods that were not called
domain: GeneToGeneOrthologyGenerated
range: VocabularyTerm
multivalued: true
multivalued: true

rank:
description: The rank (order) of the paralog result
range: integer

length:
description: The length of the aligned regions between two genes
range: integer

similarity:
description: Similarity score between the two genes
range: integer

identity:
description: Identity score between the two genes
range: integer

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