Skip to content

Commit 6d457e2

Browse files
author
Scott Christley
committed
generated files
1 parent dbe8904 commit 6d457e2

5 files changed

Lines changed: 3140 additions & 2851 deletions

File tree

‎project/jsonld/ak_schema.jsonld‎

Lines changed: 54 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -11507,6 +11507,20 @@
1150711507
"inlined": true,
1150811508
"@type": "SlotDefinition"
1150911509
},
11510+
{
11511+
"name": "aIRRKnowledgeCommons__sequence_data",
11512+
"from_schema": "https://github.com/airr-knowledge/ak-schema",
11513+
"slot_uri": "https://github.com/airr-knowledge/ak-schema/sequence_data",
11514+
"alias": "sequence_data",
11515+
"owner": "AIRRKnowledgeCommons",
11516+
"domain_of": [
11517+
"AIRRKnowledgeCommons"
11518+
],
11519+
"range": "SequenceData",
11520+
"multivalued": true,
11521+
"inlined": true,
11522+
"@type": "SlotDefinition"
11523+
},
1151011524
{
1151111525
"name": "aIRRKnowledgeCommons__conclusions",
1151211526
"from_schema": "https://github.com/airr-knowledge/ak-schema",
@@ -11617,6 +11631,32 @@
1161711631
"range": "BiologicalSexOntology",
1161811632
"@type": "SlotDefinition"
1161911633
},
11634+
{
11635+
"name": "AIRRSequencingAssay_sequencing_files",
11636+
"definition_uri": "https://github.com/airr-knowledge/ak-schema/sequencing_files",
11637+
"annotations": {
11638+
"nullable": {
11639+
"tag": "nullable",
11640+
"value": false,
11641+
"extensions": {},
11642+
"annotations": {}
11643+
}
11644+
},
11645+
"description": "Set of sequencing files produced by the sequencing run",
11646+
"from_schema": "https://github.com/airr-knowledge/ak-schema",
11647+
"is_a": "sequencing_files",
11648+
"domain": "AIRRSequencingAssay",
11649+
"slot_uri": "https://github.com/airr-knowledge/ak-schema/sequencing_files",
11650+
"alias": "sequencing_files",
11651+
"owner": "AIRRSequencingAssay",
11652+
"domain_of": [
11653+
"AIRRSequencingAssay"
11654+
],
11655+
"is_usage_slot": true,
11656+
"usage_slot_name": "sequencing_files",
11657+
"range": "AIRRSequencingData",
11658+
"@type": "SlotDefinition"
11659+
},
1162011660
{
1162111661
"name": "TCellReceptorEpitopeSpecificityMeasurement_measurement_category",
1162211662
"definition_uri": "https://github.com/airr-knowledge/ak-schema/measurement_category",
@@ -11763,6 +11803,7 @@
1176311803
"aIRRKnowledgeCommons__specimen_processings",
1176411804
"aIRRKnowledgeCommons__assays",
1176511805
"aIRRKnowledgeCommons__datasets",
11806+
"aIRRKnowledgeCommons__sequence_data",
1176611807
"aIRRKnowledgeCommons__conclusions",
1176711808
"aIRRKnowledgeCommons__chains",
1176811809
"aIRRKnowledgeCommons__ab_tcell_receptors",
@@ -11876,6 +11917,14 @@
1187611917
"inlined": true,
1187711918
"@type": "SlotDefinition"
1187811919
},
11920+
{
11921+
"name": "sequence_data",
11922+
"from_schema": "https://github.com/airr-knowledge/ak-schema",
11923+
"range": "SequenceData",
11924+
"multivalued": true,
11925+
"inlined": true,
11926+
"@type": "SlotDefinition"
11927+
},
1187911928
{
1188011929
"name": "conclusions",
1188111930
"from_schema": "https://github.com/airr-knowledge/ak-schema",
@@ -12294,13 +12343,13 @@
1229412343
"repertoire_id",
1229512344
"tcell_receptors",
1229612345
"tcell_chains",
12346+
"AIRRSequencingAssay_sequencing_files",
1229712347
"sequencing_run_id",
1229812348
"total_reads_passing_qc_filter",
1229912349
"sequencing_platform",
1230012350
"sequencing_facility",
1230112351
"sequencing_run_date",
12302-
"sequencing_kit",
12303-
"sequencing_files"
12352+
"sequencing_kit"
1230412353
],
1230512354
"slot_usage": {},
1230612355
"class_uri": "http://purl.obolibrary.org/obo/OBI_0600047",
@@ -13898,9 +13947,9 @@
1389813947
],
1389913948
"metamodel_version": "1.7.0",
1390013949
"source_file": "ak_schema.yaml",
13901-
"source_file_date": "2025-07-21T20:16:06",
13902-
"source_file_size": 204352,
13903-
"generation_date": "2025-07-21T20:16:08",
13950+
"source_file_date": "2025-08-12T23:36:47",
13951+
"source_file_size": 204647,
13952+
"generation_date": "2025-08-12T23:36:49",
1390413953
"@type": "SchemaDefinition",
1390513954
"@context": [
1390613955
"project/jsonld/ak_schema.context.jsonld",

‎project/jsonschema/ak_schema.schema.json‎

Lines changed: 219 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -258,6 +258,32 @@
258258
"null"
259259
]
260260
},
261+
"sequence_data": {
262+
"additionalProperties": {
263+
"anyOf": [
264+
{
265+
"anyOf": [
266+
{
267+
"$ref": "#/$defs/SequenceData__identifier_optional"
268+
},
269+
{
270+
"$ref": "#/$defs/AIRRSequencingData__identifier_optional"
271+
},
272+
{
273+
"$ref": "#/$defs/RNATranscriptomeData__identifier_optional"
274+
}
275+
]
276+
},
277+
{
278+
"type": "null"
279+
}
280+
]
281+
},
282+
"type": [
283+
"object",
284+
"null"
285+
]
286+
},
261287
"specimen_collections": {
262288
"additionalProperties": {
263289
"anyOf": [
@@ -389,15 +415,11 @@
389415
]
390416
},
391417
"sequencing_files": {
392-
"anyOf": [
393-
{
394-
"$ref": "#/$defs/SequencingData"
395-
},
396-
{
397-
"type": "null"
398-
}
399-
],
400-
"description": "Set of sequencing files produced by the sequencing run"
418+
"description": "Set of sequencing files produced by the sequencing run",
419+
"type": [
420+
"string",
421+
"null"
422+
]
401423
},
402424
"sequencing_kit": {
403425
"description": "Name, manufacturer, order and lot numbers of sequencing kit",
@@ -535,15 +557,11 @@
535557
]
536558
},
537559
"sequencing_files": {
538-
"anyOf": [
539-
{
540-
"$ref": "#/$defs/SequencingData"
541-
},
542-
{
543-
"type": "null"
544-
}
545-
],
546-
"description": "Set of sequencing files produced by the sequencing run"
560+
"description": "Set of sequencing files produced by the sequencing run",
561+
"type": [
562+
"string",
563+
"null"
564+
]
547565
},
548566
"sequencing_kit": {
549567
"description": "Name, manufacturer, order and lot numbers of sequencing kit",
@@ -727,6 +745,99 @@
727745
"title": "AIRRSequencingData",
728746
"type": "object"
729747
},
748+
"AIRRSequencingData__identifier_optional": {
749+
"additionalProperties": false,
750+
"description": "",
751+
"properties": {
752+
"akc_id": {
753+
"description": "A unique identifier for a thing in the AKC.",
754+
"type": "string"
755+
},
756+
"data_item_types": {
757+
"description": "semantic types of the data",
758+
"items": {
759+
"$ref": "#/$defs/DataItemTypeEnum"
760+
},
761+
"type": [
762+
"array",
763+
"null"
764+
]
765+
},
766+
"file_type": {
767+
"$ref": "#/$defs/FileTypeEnum",
768+
"description": "File format for the raw reads or sequences"
769+
},
770+
"filename": {
771+
"description": "File name for the raw reads or sequences. The first file in paired-read sequencing.",
772+
"type": [
773+
"string",
774+
"null"
775+
]
776+
},
777+
"index_filename": {
778+
"description": "File name for the index file",
779+
"type": [
780+
"string",
781+
"null"
782+
]
783+
},
784+
"index_length": {
785+
"description": "Read length in bases for the index file",
786+
"type": [
787+
"integer",
788+
"null"
789+
]
790+
},
791+
"paired_filename": {
792+
"description": "File name for the second file in paired-read sequencing",
793+
"type": [
794+
"string",
795+
"null"
796+
]
797+
},
798+
"paired_read_direction": {
799+
"$ref": "#/$defs/PairedReadDirectionEnum",
800+
"description": "Read direction for the second file in paired-read sequencing"
801+
},
802+
"paired_read_length": {
803+
"description": "Read length in bases for the second file in paired-read sequencing",
804+
"type": [
805+
"integer",
806+
"null"
807+
]
808+
},
809+
"read_direction": {
810+
"$ref": "#/$defs/ReadDirectionEnum",
811+
"description": "Read direction for the raw reads or sequences. The first file in paired-read sequencing."
812+
},
813+
"read_length": {
814+
"description": "Read length in bases for the first file in paired-read sequencing",
815+
"type": [
816+
"integer",
817+
"null"
818+
]
819+
},
820+
"sequencing_data_id": {
821+
"description": "Persistent identifier of raw data stored in an archive (e.g. INSDC run ID). Data archive should be identified in the CURIE prefix.",
822+
"type": [
823+
"string",
824+
"null"
825+
]
826+
},
827+
"type": {
828+
"enum": [
829+
"AIRRSequencingData"
830+
],
831+
"type": [
832+
"string",
833+
"null"
834+
]
835+
}
836+
},
837+
"required": [],
838+
"title": "AIRRSequencingData",
839+
"type": "object"
840+
},
730841
"AKDataItem": {
731842
"additionalProperties": false,
732843
"description": "data item with an akc_id",
@@ -5290,6 +5401,38 @@
52905401
"title": "RNATranscriptomeData",
52915402
"type": "object"
52925403
},
5404+
"RNATranscriptomeData__identifier_optional": {
5405+
"additionalProperties": false,
5406+
"description": "",
5407+
"properties": {
5408+
"akc_id": {
5409+
"description": "A unique identifier for a thing in the AKC.",
5410+
"type": "string"
5411+
},
5412+
"data_item_types": {
5413+
"description": "semantic types of the data",
5414+
"items": {
5415+
"$ref": "#/$defs/DataItemTypeEnum"
5416+
},
5417+
"type": [
5418+
"array",
5419+
"null"
5420+
]
5421+
},
5422+
"type": {
5423+
"enum": [
5424+
"RNATranscriptomeData"
5425+
],
5426+
"type": [
5427+
"string",
5428+
"null"
5429+
]
5430+
}
5431+
},
5432+
"required": [],
5433+
"title": "RNATranscriptomeData",
5434+
"type": "object"
5435+
},
52935436
"RaceOntology": {
52945437
"description": "",
52955438
"enum": [
@@ -7320,6 +7463,38 @@
73207463
"title": "SequenceData",
73217464
"type": "object"
73227465
},
7466+
"SequenceData__identifier_optional": {
7467+
"additionalProperties": false,
7468+
"description": "sequence data items are given an akc_id",
7469+
"properties": {
7470+
"akc_id": {
7471+
"description": "A unique identifier for a thing in the AKC.",
7472+
"type": "string"
7473+
},
7474+
"data_item_types": {
7475+
"description": "semantic types of the data",
7476+
"items": {
7477+
"$ref": "#/$defs/DataItemTypeEnum"
7478+
},
7479+
"type": [
7480+
"array",
7481+
"null"
7482+
]
7483+
},
7484+
"type": {
7485+
"enum": [
7486+
"SequenceData"
7487+
],
7488+
"type": [
7489+
"string",
7490+
"null"
7491+
]
7492+
}
7493+
},
7494+
"required": [],
7495+
"title": "SequenceData",
7496+
"type": "object"
7497+
},
73237498
"SequenceDelineationV": {
73247499
"additionalProperties": false,
73257500
"description": "",
@@ -9120,6 +9295,32 @@
91209295
"null"
91219296
]
91229297
},
9298+
"sequence_data": {
9299+
"additionalProperties": {
9300+
"anyOf": [
9301+
{
9302+
"anyOf": [
9303+
{
9304+
"$ref": "#/$defs/SequenceData__identifier_optional"
9305+
},
9306+
{
9307+
"$ref": "#/$defs/AIRRSequencingData__identifier_optional"
9308+
},
9309+
{
9310+
"$ref": "#/$defs/RNATranscriptomeData__identifier_optional"
9311+
}
9312+
]
9313+
},
9314+
{
9315+
"type": "null"
9316+
}
9317+
]
9318+
},
9319+
"type": [
9320+
"object",
9321+
"null"
9322+
]
9323+
},
91239324
"specimen_collections": {
91249325
"additionalProperties": {
91259326
"anyOf": [

0 commit comments

Comments
 (0)