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feat: mass spectrometry data support #18

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merged 6 commits into from
Nov 28, 2024
Merged

feat: mass spectrometry data support #18

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7f9b859
feat: add data entity for mass spectrometry
cmdoret Oct 3, 2024
10a5967
chore: regen
cmdoret Oct 4, 2024
46fcc46
fix: typo in description
cmdoret Oct 11, 2024
f052f9b
refactor: consistent slot naming
cmdoret Oct 15, 2024
4a41e86
chore: regen
cmdoret Oct 15, 2024
7bd1e50
chore: regen
cmdoret Nov 8, 2024
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Binary file modified project/excel/modos_schema.xlsx
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12 changes: 12 additions & 0 deletions project/graphql/modos_schema.graphql
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ type Assay
hasSample: [Sample]
hasData: [DataEntity]
omicsType: [OmicsType]!
sampleProcessing: [Uriorcurie]
}

type DataEntity
Expand All @@ -42,6 +43,17 @@ type DataEntity
hasReference: [ReferenceGenome]
}

type MassSpectrometryResults
{
id: Uriorcurie!
name: String
description: String
dataPath: String!
dataFormat: DataFormat!
hasSample: [Sample]
hasReference: [ReferenceGenome]
}

type MODO
{
id: Uriorcurie!
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9 changes: 8 additions & 1 deletion 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": "2024-10-23T16:01:04",
"generation_date": "2024-11-08T09:56:38",
"source": "modos_schema.yaml"
},
"@context": {
Expand Down Expand Up @@ -99,6 +99,10 @@
},
"@id": "omics_type"
},
"sample_processing": {
"@type": "xsd:anyURI",
"@id": "sample_processing"
},
"sequence_md5": {
"@id": "sequence_md5"
},
Expand Down Expand Up @@ -137,6 +141,9 @@
"DataEntity": {
"@id": "DataEntity"
},
"MassSpectrometryResults": {
"@id": "MassSpectrometryResults"
},
"MODO": {
"@id": "MODO"
},
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52 changes: 46 additions & 6 deletions project/jsonld/modos_schema.jsonld
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Expand Up @@ -457,6 +457,11 @@
"text": "BCF",
"description": "Binary call format, for efficient storage of sequence variation.",
"meaning": "EDAM:format_3020"
},
{
"text": "mzTab",
"description": "tab-delimited format for mass spectrometry-based proteomics and metabolomics results.",
"meaning": "EDAM:format_3681"
}
]
}
Expand Down Expand Up @@ -614,6 +619,21 @@
"multivalued": true,
"@type": "SlotDefinition"
},
{
"name": "sample_processing",
"definition_uri": "https://w3id.org/sdsc-ordes/modos-schema/sample_processing",
"description": "Codes describing sample processing, preparation or handling steps.\nThe order of the codes should reflect the order in which the steps were performed.\nShould be codes from [MSIO](https://bioregistry.io/registry/msio) or [OBI](https://obofoundry.org/ontology/obi.html)].\n",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/sample_processing",
"list_elements_ordered": true,
"owner": "Assay",
"domain_of": [
"Assay"
],
"range": "uriorcurie",
"multivalued": true,
"@type": "SlotDefinition"
},
{
"name": "has_sequence",
"definition_uri": "https://w3id.org/sdsc-ordes/modos-schema/has_sequence",
Expand Down Expand Up @@ -661,7 +681,7 @@
{
"name": "taxon_id",
"definition_uri": "https://w3id.org/sdsc-ordes/modos-schema/taxon_id",
"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",
"description": "The NCBI taxon code from [ncbitaxon](https://obofoundry.org/ontology/ncbitaxon.html) describing the taxonomic range of a sample.\n",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/taxon_id",
"owner": "ReferenceGenome",
Expand Down Expand Up @@ -775,7 +795,7 @@
{
"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).\nShould be a tissue or organ code URI from the UBERON ontology.\nSee: [https://bioregistry.io/registry/uberon](https://bioregistry.io/registry/uberon)\n",
"description": "The biological source from which the sample was isolated (tissue, organ).\nShould be a code URI from the [UBERON](https://bioregistry.io/registry/uberon) ontology or [fairgenomes biospecimen types](https://raw.githubusercontent.com/fairgenomes/fairgenomes-semantic-model/refs/tags/v1.2/generated/ontology/fair-genomes-biospecimentypes.ttl).\n",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"slot_uri": "https://w3id.org/sdsc-ordes/modos-schema/source_material",
"owner": "Sample",
Expand Down Expand Up @@ -866,7 +886,8 @@
"description",
"has_sample",
"has_data",
"omics_type"
"omics_type",
"sample_processing"
],
"slot_usage": {},
"class_uri": "https://w3id.org/sdsc-ordes/modos-schema/Assay",
Expand Down Expand Up @@ -996,6 +1017,25 @@
"class_uri": "https://w3id.org/sdsc-ordes/modos-schema/VariantSet",
"@type": "ClassDefinition"
},
{
"name": "MassSpectrometryResults",
"definition_uri": "https://w3id.org/sdsc-ordes/modos-schema/MassSpectrometryResults",
"description": "A data entity consisting of quantitative results from a mass spectrometry experiment.",
"from_schema": "https://w3id.org/sdsc-ordes/modos-schema",
"is_a": "DataEntity",
"slots": [
"id",
"name",
"description",
"data_path",
"data_format",
"has_sample",
"has_reference"
],
"slot_usage": {},
"class_uri": "https://w3id.org/sdsc-ordes/modos-schema/MassSpectrometryResults",
"@type": "ClassDefinition"
},
{
"name": "Array",
"definition_uri": "https://w3id.org/sdsc-ordes/modos-schema/Array",
Expand Down Expand Up @@ -1040,9 +1080,9 @@
],
"metamodel_version": "1.7.0",
"source_file": "modos_schema.yaml",
"source_file_date": "2024-10-23T15:50:05",
"source_file_size": 8488,
"generation_date": "2024-10-23T16:01:04",
"source_file_date": "2024-11-08T09:56:24",
"source_file_size": 9291,
"generation_date": "2024-11-08T09:56:39",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/modos_schema.context.jsonld",
Expand Down
78 changes: 74 additions & 4 deletions project/jsonschema/modos_schema.schema.json
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Expand Up @@ -166,6 +166,16 @@
"$ref": "#/$defs/OmicsType"
},
"type": "array"
},
"sample_processing": {
"description": "Codes describing sample processing, preparation or handling steps.\nThe order of the codes should reflect the order in which the steps were performed.\nShould be codes from [MSIO](https://bioregistry.io/registry/msio) or [OBI](https://obofoundry.org/ontology/obi.html)].\n",
"items": {
"type": "string"
},
"type": [
"array",
"null"
]
}
},
"required": [
Expand Down Expand Up @@ -242,7 +252,8 @@
"Zarr",
"FASTA",
"VCF",
"BCF"
"BCF",
"mzTab"
],
"title": "DataFormat",
"type": "string"
Expand Down Expand Up @@ -379,6 +390,65 @@
"title": "MODO",
"type": "object"
},
"MassSpectrometryResults": {
"additionalProperties": false,
"description": "A data entity consisting of quantitative results from a mass spectrometry experiment.",
"properties": {
"data_format": {
"$ref": "#/$defs/DataFormat",
"description": "Data/file format associated with a data entity."
},
"data_path": {
"description": "The path to access a resource, on a network or local filesystem. Can be a path relative to the root of the digital object, a URL, or an absolute path.",
"type": "string"
},
"description": {
"description": "A human-readable description for a thing",
"type": [
"string",
"null"
]
},
"has_reference": {
"description": "Specifies the reference coordinate system used by an omics dataset.",
"items": {
"type": "string"
},
"type": [
"array",
"null"
]
},
"has_sample": {
"description": "Biological sample included or described by a given thing.",
"items": {
"type": "string"
},
"type": [
"array",
"null"
]
},
"id": {
"description": "A unique identifier for a thing",
"type": "string"
},
"name": {
"description": "A human-readable name for a thing",
"type": [
"string",
"null"
]
}
},
"required": [
"data_path",
"data_format",
"id"
],
"title": "MassSpectrometryResults",
"type": "object"
},
"NamedThing": {
"additionalProperties": false,
"description": "A generic grouping for any identifiable entity",
Expand Down Expand Up @@ -466,7 +536,7 @@
]
},
"taxon_id": {
"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",
"description": "The NCBI taxon code from [ncbitaxon](https://obofoundry.org/ontology/ncbitaxon.html) describing the taxonomic range of a sample.\n",
"items": {
"type": "string"
},
Expand Down Expand Up @@ -585,14 +655,14 @@
"description": "The biological sex of a sample."
},
"source_material": {
"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",
"description": "The biological source from which the sample was isolated (tissue, organ).\nShould be a code URI from the [UBERON](https://bioregistry.io/registry/uberon) ontology or [fairgenomes biospecimen types](https://raw.githubusercontent.com/fairgenomes/fairgenomes-semantic-model/refs/tags/v1.2/generated/ontology/fair-genomes-biospecimentypes.ttl).\n",
"type": [
"string",
"null"
]
},
"taxon_id": {
"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",
"description": "The NCBI taxon code from [ncbitaxon](https://obofoundry.org/ontology/ncbitaxon.html) describing the taxonomic range of a sample.\n",
"items": {
"type": "string"
},
Expand Down
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