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chore: regen
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@cmdoret
cmdoret committed Sep 24, 2024
1 parent 64668f1 commit 1c9b9e6
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Showing 11 changed files with 379 additions and 467 deletions.
Binary file modified project/excel/modos_schema.xlsx
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8 changes: 4 additions & 4 deletions project/graphql/modos_schema.graphql
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Expand Up @@ -72,7 +72,7 @@ type ReferenceGenome
description: String
dataPath: String!
hasSequence: [ReferenceSequence]
taxonId: [Integer]
taxonId: [Uriorcurie]
sourceUri: Uri
version: String
}
Expand All @@ -92,10 +92,10 @@ type Sample
id: Uriorcurie!
name: String
description: String
cellType: String
sourceMaterial: String
cellType: Uriorcurie
sourceMaterial: Uriorcurie
sex: Sex
taxonId: [Integer]
taxonId: [Uriorcurie]
collector: [String]
}

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6 changes: 4 additions & 2 deletions project/jsonld/modos_schema.context.jsonld
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@@ -1,7 +1,7 @@
{
"comments": {
"description": "Auto generated by LinkML jsonld context generator",
"generation_date": "2024-09-23T15:24:41",
"generation_date": "2024-09-24T11:54:45",
"source": "modos_schema.yaml"
},
"@context": {
Expand Down Expand Up @@ -31,6 +31,7 @@
"sphn": "https://biomedit.ch/rdf/sphn-schema/sphn#",
"@vocab": "https://w3id.org/sdsc-ordes/modos-schema/",
"cell_type": {
"@type": "@id",
"@id": "cell_type"
},
"collector": {
Expand Down Expand Up @@ -112,14 +113,15 @@
"@id": "sex"
},
"source_material": {
"@type": "@id",
"@id": "source_material"
},
"source_uri": {
"@type": "@id",
"@id": "source_uri"
},
"taxon_id": {
"@type": "xsd:integer",
"@type": "@id",
"@id": "taxon_id"
},
"version": {
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90 changes: 20 additions & 70 deletions project/jsonld/modos_schema.jsonld
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Expand Up @@ -459,36 +459,6 @@
"meaning": "EDAM:format_3020"
}
]
},
{
"name": "CellType",
"definition_uri": "https://w3id.org/sdsc-ordes/modos-schema/CellType",
"description": "Cell type code from the cell ontology as a URI.\nSee: [https://bioregistry.io/registry/cl](https://bioregistry.io/registry/cl)\n",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"reachable_from": {
"source_ontology": "bioregistry:cl",
"source_nodes": [
"CL:0000000"
],
"relationship_types": [
"rdfs:subClassOf"
]
}
},
{
"name": "SourceMaterial",
"definition_uri": "https://w3id.org/sdsc-ordes/modos-schema/SourceMaterial",
"description": "Tissue or organ code from the UBERON ontology as a URI.\nSee: [https://bioregistry.io/registry/uberon](https://bioregistry.io/registry/uberon)\n",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"reachable_from": {
"source_ontology": "bioregistry:uberon",
"source_nodes": [
"UBERON:0001062"
],
"relationship_types": [
"rdfs:subClassOf"
]
}
}
],
"slots": [
Expand Down Expand Up @@ -551,8 +521,8 @@
"http://schema.org/hasPart"
],
"slot_uri": "http://schema.org/hasPart",
"multivalued": true,
"range": "string",
"multivalued": true,
"@type": "SlotDefinition"
},
{
Expand Down Expand Up @@ -589,13 +559,13 @@
"description": "The type of omics considered.",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/omics_type",
"multivalued": true,
"owner": "Assay",
"domain_of": [
"Assay"
],
"range": "OmicsType",
"required": true,
"multivalued": true,
"@type": "SlotDefinition"
},
{
Expand All @@ -605,12 +575,12 @@
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"is_a": "has_part",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/has_assay",
"multivalued": true,
"owner": "MODO",
"domain_of": [
"MODO"
],
"range": "Assay",
"multivalued": true,
"@type": "SlotDefinition"
},
{
Expand All @@ -620,13 +590,13 @@
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"is_a": "has_part",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/has_sample",
"multivalued": true,
"owner": "DataEntity",
"domain_of": [
"Assay",
"DataEntity"
],
"range": "Sample",
"multivalued": true,
"@type": "SlotDefinition"
},
{
Expand All @@ -636,12 +606,12 @@
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"is_a": "has_part",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/has_data",
"multivalued": true,
"owner": "Assay",
"domain_of": [
"Assay"
],
"range": "DataEntity",
"multivalued": true,
"@type": "SlotDefinition"
},
{
Expand All @@ -651,12 +621,12 @@
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"is_a": "has_part",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/has_sequence",
"multivalued": true,
"owner": "ReferenceGenome",
"domain_of": [
"ReferenceGenome"
],
"range": "ReferenceSequence",
"multivalued": true,
"@type": "SlotDefinition"
},
{
Expand All @@ -666,12 +636,12 @@
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"is_a": "has_part",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/has_reference",
"multivalued": true,
"owner": "DataEntity",
"domain_of": [
"DataEntity"
],
"range": "ReferenceGenome",
"multivalued": true,
"@type": "SlotDefinition"
},
{
Expand All @@ -691,16 +661,16 @@
{
"name": "taxon_id",
"definition_uri": "https://w3id.org/sdsc-ordes/modos-schema/taxon_id",
"description": "The taxid number describing the taxonomic range of a sample.",
"description": "The NCBI taxon code describing the taxonomic range of a sample.\nSee: [https://obofoundry.org/ontology/ncbitaxon.html](https://obofoundry.org/ontology/ncbitaxon.html)\n",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/taxon_id",
"multivalued": true,
"owner": "ReferenceGenome",
"domain_of": [
"Sample",
"ReferenceGenome"
],
"range": "integer",
"range": "uriorcurie",
"multivalued": true,
"@type": "SlotDefinition"
},
{
Expand All @@ -709,12 +679,12 @@
"description": "The organization responsible for collecting a given sample.",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/collector",
"multivalued": true,
"owner": "Sample",
"domain_of": [
"Sample"
],
"range": "string",
"multivalued": true,
"@type": "SlotDefinition"
},
{
Expand Down Expand Up @@ -792,47 +762,27 @@
{
"name": "cell_type",
"definition_uri": "https://w3id.org/sdsc-ordes/modos-schema/cell_type",
"description": "The cell type name or code, if applicable.",
"description": "The cell type of the sample, if applicable.\nShould be a cell type code URI from the cell ontology.\nSee: [https://bioregistry.io/registry/cl](https://bioregistry.io/registry/cl)\n",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/cell_type",
"owner": "Sample",
"domain_of": [
"Sample"
],
"range": "string",
"any_of": [
{
"range": "CellType",
"@type": "AnonymousSlotExpression"
},
{
"range": "string",
"@type": "AnonymousSlotExpression"
}
],
"range": "uriorcurie",
"@type": "SlotDefinition"
},
{
"name": "source_material",
"definition_uri": "https://w3id.org/sdsc-ordes/modos-schema/source_material",
"description": "The biological source from which the sample was isolated (tissue, organ).",
"description": "The biological source from which the sample was isolated (tissue, organ).\nShould be a tissue or organ code URI from the UBERON ontology.\nSee: [https://bioregistry.io/registry/uberon](https://bioregistry.io/registry/uberon)\n",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/source_material",
"owner": "Sample",
"domain_of": [
"Sample"
],
"range": "string",
"any_of": [
{
"range": "SourceMaterial",
"@type": "AnonymousSlotExpression"
},
{
"range": "string",
"@type": "AnonymousSlotExpression"
}
],
"range": "uriorcurie",
"@type": "SlotDefinition"
},
{
Expand All @@ -852,13 +802,13 @@
"name": "mODOCollection__entries",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/entries",
"multivalued": true,
"alias": "entries",
"owner": "MODOCollection",
"domain_of": [
"MODOCollection"
],
"range": "MODO",
"multivalued": true,
"inlined": true,
"@type": "SlotDefinition"
}
Expand Down Expand Up @@ -1077,8 +1027,8 @@
"attributes": [
{
"name": "entries",
"multivalued": true,
"range": "MODO",
"multivalued": true,
"inlined": true,
"@type": "SlotDefinition"
}
Expand All @@ -1090,9 +1040,9 @@
],
"metamodel_version": "1.7.0",
"source_file": "modos_schema.yaml",
"source_file_date": "2024-09-23T15:23:55",
"source_file_size": 8844,
"generation_date": "2024-09-23T15:24:41",
"source_file_date": "2024-09-24T11:54:35",
"source_file_size": 8488,
"generation_date": "2024-09-24T11:54:46",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/modos_schema.context.jsonld",
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38 changes: 6 additions & 32 deletions project/jsonschema/modos_schema.schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -139,11 +139,6 @@
"title": "Assay",
"type": "object"
},
"CellType": {
"description": "Cell type code from the cell ontology as a URI.\nSee: [https://bioregistry.io/registry/cl](https://bioregistry.io/registry/cl)",
"title": "CellType",
"type": "string"
},
"DataEntity": {
"additionalProperties": false,
"description": "An entity containing data.",
Expand Down Expand Up @@ -375,9 +370,9 @@
"type": "string"
},
"taxon_id": {
"description": "The taxid number describing the taxonomic range of a sample.",
"description": "The NCBI taxon code describing the taxonomic range of a sample.\nSee: [https://obofoundry.org/ontology/ncbitaxon.html](https://obofoundry.org/ontology/ncbitaxon.html)\n",
"items": {
"type": "integer"
"type": "string"
},
"type": "array"
},
Expand Down Expand Up @@ -434,15 +429,7 @@
"description": "A biological sample used in assays. Examples include a whole organism, tissue or cell line.",
"properties": {
"cell_type": {
"anyOf": [
{
"$ref": "#/$defs/CellType"
},
{
"type": "string"
}
],
"description": "The cell type name or code, if applicable.",
"description": "The cell type of the sample, if applicable.\nShould be a cell type code URI from the cell ontology.\nSee: [https://bioregistry.io/registry/cl](https://bioregistry.io/registry/cl)\n",
"type": "string"
},
"collector": {
Expand All @@ -469,21 +456,13 @@
"description": "The biological sex of a sample."
},
"source_material": {
"anyOf": [
{
"$ref": "#/$defs/SourceMaterial"
},
{
"type": "string"
}
],
"description": "The biological source from which the sample was isolated (tissue, organ).",
"description": "The biological source from which the sample was isolated (tissue, organ).\nShould be a tissue or organ code URI from the UBERON ontology.\nSee: [https://bioregistry.io/registry/uberon](https://bioregistry.io/registry/uberon)\n",
"type": "string"
},
"taxon_id": {
"description": "The taxid number describing the taxonomic range of a sample.",
"description": "The NCBI taxon code describing the taxonomic range of a sample.\nSee: [https://obofoundry.org/ontology/ncbitaxon.html](https://obofoundry.org/ontology/ncbitaxon.html)\n",
"items": {
"type": "integer"
"type": "string"
},
"type": "array"
}
Expand All @@ -503,11 +482,6 @@
"title": "Sex",
"type": "string"
},
"SourceMaterial": {
"description": "Tissue or organ code from the UBERON ontology as a URI.\nSee: [https://bioregistry.io/registry/uberon](https://bioregistry.io/registry/uberon)",
"title": "SourceMaterial",
"type": "string"
},
"VariantSet": {
"additionalProperties": false,
"description": "A data entity consisting of genomic variants relative to a reference.",
Expand Down
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