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Model recombinases #72

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d7bc8f3
model part of https://github.com/pydna-group/pydna/issues/435
manulera Mar 4, 2026
a158cfb
improve constraints
manulera Mar 4, 2026
484165e
remove reverse from source
manulera Mar 4, 2026
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Binary file modified project/excel/opencloning_linkml.xlsx
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20 changes: 20 additions & 0 deletions project/graphql/opencloning_linkml.graphql
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Original file line number Diff line number Diff line change
Expand Up @@ -390,6 +390,26 @@ type Primer
sequence: String
}

type Recombinase
{
name: String
site1: String!
site2: String!
site1Name: String
site2Name: String
}

type RecombinaseSource
{
id: Integer!
type: String
outputName: String
databaseId: Integer
input: [SourceInput]
circular: Boolean
recombinases: [Recombinase]!
}

type RepositoryIdSource
{
id: Integer!
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24 changes: 23 additions & 1 deletion project/jsonld/opencloning_linkml.context.jsonld
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"comments": {
"description": "Auto generated by LinkML jsonld context generator",
"generation_date": "2025-12-06T00:30:23",
"generation_date": "2026-03-04T18:08:29",
"source": "opencloning_linkml.yaml"
},
"@context": {
Expand Down Expand Up @@ -246,6 +246,22 @@
"Type": {
"@id": "Type"
},
"site1": {
"@id": "site1"
},
"site1_name": {
"@id": "site1_name"
},
"site2": {
"@id": "site2"
},
"site2_name": {
"@id": "site2_name"
},
"recombinases": {
"@type": "opencloning_linkml:Recombinase",
"@id": "recombinases"
},
"repository_id": {
"@id": "repository_id"
},
Expand Down Expand Up @@ -405,6 +421,12 @@
"Primer": {
"@id": "Primer"
},
"Recombinase": {
"@id": "Recombinase"
},
"RecombinaseSource": {
"@id": "RecombinaseSource"
},
"RepositoryIdSource": {
"@id": "RepositoryIdSource"
},
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153 changes: 148 additions & 5 deletions project/jsonld/opencloning_linkml.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -559,11 +559,12 @@
"http://schema.org/name"
],
"slot_uri": "http://schema.org/name",
"owner": "CollectionOptionInfo",
"owner": "Recombinase",
"domain_of": [
"Primer",
"CollectionOption",
"CollectionOptionInfo"
"CollectionOptionInfo",
"Recombinase"
],
"range": "string",
"@type": "SlotDefinition"
Expand Down Expand Up @@ -1258,6 +1259,76 @@
"range": "boolean",
"@type": "SlotDefinition"
},
{
"name": "recombinase__site1",
"from_schema": "https://opencloning.github.io/OpenCloning_LinkML",
"slot_uri": "https://opencloning.github.io/OpenCloning_LinkML/site1",
"alias": "site1",
"owner": "Recombinase",
"domain_of": [
"Recombinase"
],
"range": "string",
"required": true,
"pattern": "^[A-Z]+[a-z]+[A-Z]+$",
"@type": "SlotDefinition"
},
{
"name": "recombinase__site2",
"from_schema": "https://opencloning.github.io/OpenCloning_LinkML",
"slot_uri": "https://opencloning.github.io/OpenCloning_LinkML/site2",
"alias": "site2",
"owner": "Recombinase",
"domain_of": [
"Recombinase"
],
"range": "string",
"required": true,
"pattern": "^[A-Z]+[a-z]+[A-Z]+$",
"@type": "SlotDefinition"
},
{
"name": "recombinase__site1_name",
"from_schema": "https://opencloning.github.io/OpenCloning_LinkML",
"slot_uri": "https://opencloning.github.io/OpenCloning_LinkML/site1_name",
"ifabsent": "string(\"site1\")",
"alias": "site1_name",
"owner": "Recombinase",
"domain_of": [
"Recombinase"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "recombinase__site2_name",
"from_schema": "https://opencloning.github.io/OpenCloning_LinkML",
"slot_uri": "https://opencloning.github.io/OpenCloning_LinkML/site2_name",
"ifabsent": "string(\"site2\")",
"alias": "site2_name",
"owner": "Recombinase",
"domain_of": [
"Recombinase"
],
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "recombinaseSource__recombinases",
"from_schema": "https://opencloning.github.io/OpenCloning_LinkML",
"slot_uri": "https://opencloning.github.io/OpenCloning_LinkML/recombinases",
"alias": "recombinases",
"owner": "RecombinaseSource",
"domain_of": [
"RecombinaseSource"
],
"range": "Recombinase",
"required": true,
"multivalued": true,
"inlined": true,
"inlined_as_list": true,
"@type": "SlotDefinition"
},
{
"name": "cloningStrategy__sequences",
"description": "The sequences that are used in the cloning strategy",
Expand Down Expand Up @@ -3184,6 +3255,78 @@
"class_uri": "https://opencloning.github.io/OpenCloning_LinkML/PolymeraseExtensionSource",
"@type": "ClassDefinition"
},
{
"name": "Recombinase",
"definition_uri": "https://opencloning.github.io/OpenCloning_LinkML/Recombinase",
"from_schema": "https://opencloning.github.io/OpenCloning_LinkML",
"slots": [
"name",
"recombinase__site1",
"recombinase__site2",
"recombinase__site1_name",
"recombinase__site2_name"
],
"slot_usage": {},
"attributes": [
{
"name": "site1",
"range": "string",
"required": true,
"pattern": "^[A-Z]+[a-z]+[A-Z]+$",
"@type": "SlotDefinition"
},
{
"name": "site2",
"range": "string",
"required": true,
"pattern": "^[A-Z]+[a-z]+[A-Z]+$",
"@type": "SlotDefinition"
},
{
"name": "site1_name",
"ifabsent": "string(\"site1\")",
"range": "string",
"@type": "SlotDefinition"
},
{
"name": "site2_name",
"ifabsent": "string(\"site2\")",
"range": "string",
"@type": "SlotDefinition"
}
],
"class_uri": "https://opencloning.github.io/OpenCloning_LinkML/Recombinase",
"@type": "ClassDefinition"
},
{
"name": "RecombinaseSource",
"definition_uri": "https://opencloning.github.io/OpenCloning_LinkML/RecombinaseSource",
"description": "Represents the source of a sequence that is generated by recombination using one or more recombinases",
"from_schema": "https://opencloning.github.io/OpenCloning_LinkML",
"is_a": "AssemblySource",
"slots": [
"id",
"type",
"output_name",
"database_id",
"source__input",
"assemblySource__circular",
"recombinaseSource__recombinases"
],
"slot_usage": {},
"attributes": [
{
"name": "recombinases",
"range": "Recombinase",
"required": true,
"multivalued": true,
"inlined_as_list": true,
"@type": "SlotDefinition"
}
],
"class_uri": "https://opencloning.github.io/OpenCloning_LinkML/RecombinaseSource",
"@type": "ClassDefinition"
},
{
"name": "CloningStrategy",
"definition_uri": "https://opencloning.github.io/OpenCloning_LinkML/CloningStrategy",
Expand Down Expand Up @@ -3500,9 +3643,9 @@
],
"metamodel_version": "1.7.0",
"source_file": "opencloning_linkml.yaml",
"source_file_date": "2025-12-06T00:30:19",
"source_file_size": 25654,
"generation_date": "2025-12-06T00:30:23",
"source_file_date": "2026-03-04T18:08:25",
"source_file_size": 26405,
"generation_date": "2026-03-04T18:08:29",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/opencloning_linkml.context.jsonld",
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115 changes: 115 additions & 0 deletions project/jsonschema/opencloning_linkml.schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -611,6 +611,9 @@
{
"$ref": "#/$defs/CreLoxRecombinationSource"
},
{
"$ref": "#/$defs/RecombinaseSource"
},
{
"$ref": "#/$defs/CRISPRSource"
},
Expand Down Expand Up @@ -752,6 +755,9 @@
{
"$ref": "#/$defs/CreLoxRecombinationSource"
},
{
"$ref": "#/$defs/RecombinaseSource"
},
{
"$ref": "#/$defs/CRISPRSource"
},
Expand Down Expand Up @@ -2342,6 +2348,115 @@
"title": "Primer",
"type": "object"
},
"Recombinase": {
"additionalProperties": false,
"description": "",
"properties": {
"name": {
"description": "A human-readable name for a thing",
"type": [
"string",
"null"
]
},
"site1": {
"pattern": "^[A-Z]+[a-z]+[A-Z]+$",
"type": "string"
},
"site1_name": {
"type": [
"string",
"null"
]
},
"site2": {
"pattern": "^[A-Z]+[a-z]+[A-Z]+$",
"type": "string"
},
"site2_name": {
"type": [
"string",
"null"
]
}
},
"required": [
"site1",
"site2"
],
"title": "Recombinase",
"type": "object"
},
"RecombinaseSource": {
"additionalProperties": false,
"description": "Represents the source of a sequence that is generated by recombination using one or more recombinases",
"properties": {
"circular": {
"description": "Whether the assembly is circular or not",
"type": [
"boolean",
"null"
]
},
"database_id": {
"description": "The id of an entity in a database",
"type": [
"integer",
"null"
]
},
"id": {
"description": "A unique identifier for a thing",
"type": "integer"
},
"input": {
"description": "The inputs to this source. If the source represents external import of a sequence, it's empty.",
"items": {
"anyOf": [
{
"$ref": "#/$defs/SourceInput"
},
{
"$ref": "#/$defs/AssemblyFragment"
}
]
},
"type": [
"array",
"null"
]
},
"output_name": {
"description": "Used to specify the name of the output sequence",
"type": [
"string",
"null"
]
},
"recombinases": {
"items": {
"$ref": "#/$defs/Recombinase"
},
"type": "array"
},
"type": {
"description": "Designates the class",
"enum": [
"RecombinaseSource"
],
"type": [
"string",
"null"
]
}
},
"required": [
"recombinases",
"id"
],
"title": "RecombinaseSource",
"type": "object"
},
"RepositoryIdSource": {
"additionalProperties": false,
"description": "Represents the source of a sequence that is identified by a repository id",
Expand Down
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