PKBDS3227VCCX
{
"@context": "/terms/",
"@id": "/measurement-sets/PKBDS3227VCCX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "PKBDS3227VCCX",
"aliases": [
"klaus-kaestner:HPAP_MeasurementSet_scRNAseq_HPAP-079_no_treatment"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "validation error",
"detail": "Human donor [PKBDO6323HZHM](/human-donors/PKBDO6323HZHM/) has schema error Additional properties are not allowed ('glucose_loweing_theraphy' was unexpected).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_schema",
"path": "/human-donors/PKBDO6323HZHM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing nih certification",
"detail": "Measurement set [PKBDS3227VCCX](/measurement-sets/PKBDS3227VCCX/) has a sample [PKBSM8482JHCM](/primary-islet/PKBSM8482JHCM/) that lacks any `institutional_certificates` issued to the lab that submitted this file set. Measurement sets for mapping assays involving samples with a human origin are expected to link to the relevant institutional certificates issued to a matching lab and award.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_institutional_certification",
"path": "/measurement-sets/PKBDS3227VCCX/"
},
{
"category": "missing protocol",
"detail": "Measurement set [PKBDS3227VCCX](/measurement-sets/PKBDS3227VCCX/) has no `protocols`. Measurement sets are expected to specify the experimental protocol utilized for conducting the assay on protocols.io.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_unspecified_protocol",
"path": "/measurement-sets/PKBDS3227VCCX/"
}
],
"WARNING": [
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6323HZHM](/human-donors/PKBDO6323HZHM/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6323HZHM/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6323HZHM](/human-donors/PKBDO6323HZHM/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6323HZHM/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6323HZHM](/human-donors/PKBDO6323HZHM/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6323HZHM/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6323HZHM](/human-donors/PKBDO6323HZHM/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6323HZHM/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6323HZHM](/human-donors/PKBDO6323HZHM/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6323HZHM/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6323HZHM](/human-donors/PKBDO6323HZHM/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6323HZHM/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6323HZHM](/human-donors/PKBDO6323HZHM/) is missing tier 3 field `other_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6323HZHM/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6323HZHM](/human-donors/PKBDO6323HZHM/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6323HZHM/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6323HZHM](/human-donors/PKBDO6323HZHM/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6323HZHM/"
},
{
"category": "missing files",
"detail": "Measurement set [PKBDS3227VCCX](/measurement-sets/PKBDS3227VCCX/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/PKBDS3227VCCX/"
},
{
"category": "inconsistent assays",
"detail": "Measurement set [PKBDS3227VCCX](/measurement-sets/PKBDS3227VCCX/) has `assay_term` single-cell RNA sequencing assay, but `preferred_assay_title` scRNA-seq. Measurement sets with a preferred assay title are expected to specify an appropriate assay term.",
"level": 40,
"level_name": "WARNING",
"name": "audit_preferred_assay_title",
"path": "/measurement-sets/PKBDS3227VCCX/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8482JHCM](/primary-islet/PKBSM8482JHCM/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8482JHCM/"
}
]
},
"award": {
"@id": "/awards/U01DK123594/",
"contact_pi": {
"@id": "/users/e1c8c91f-3952-45a9-9f56-442627f60c13/",
"title": "Klaus Kaestner"
},
"title": "THE HUMAN PANCREAS ANALYSIS PROGRAM FOR TYPE 2 DIABETES"
},
"control_for": [],
"creation_timestamp": "2025-05-09T17:05:21.069440+00:00",
"description": "Measurement set of scRNA-seq for islet biosample of human donor HPAP-079 from HPAP with no_treatment (HPAP-079)",
"donors": [
{
"@id": "/human-donors/PKBDO6323HZHM/",
"accession": "PKBDO6323HZHM",
"aliases": [
"klaus-kaestner:HPAP-079"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/PKBDS4331AFFJ/",
"/analysis-sets/PKBDS1349YHGQ/"
],
"lab": {
"@id": "/labs/klaus-kaestner/",
"title": "Klaus Kaestner, UPenn"
},
"preferred_assay_title": "scRNA-seq",
"release_timestamp": "2025-06-15T04:44:34.082566+00:00",
"samples": [
{
"@id": "/primary-islet/PKBSM8482JHCM/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM8482JHCM",
"aliases": [
"klaus-kaestner:biosample_HPAP-079"
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000006/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_isletofLangerhans"
],
"status": "released",
"summary": "islet of Langerhans",
"term_name": "islet of Langerhans"
}
],
"status": "released",
"summary": "islet of Langerhans cell, female, Homo sapiens",
"taxa": "Homo sapiens"
}
],
"schema_version": "17",
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"summary": "single-cell RNA sequencing assay (scRNA-seq)",
"uuid": "f6dfa5e1-bece-40d5-9c19-70995165cff7"
}
Supported by National Institutes of Health (NIH) grants U24 DK138515, U24 DK138512
Supplemental funds from the NIH Office of Data Science Strategies
Supplemental funds from the NIH Office of Data Science Strategies