PKBDS2528IZBJ
{
"@context": "/terms/",
"@id": "/measurement-sets/PKBDS2528IZBJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "PKBDS2528IZBJ",
"aliases": [
"klaus-kaestner:pancreaticBetaCell_MeasurementSet_RNAseq_HPAP-053"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003090/",
"term_name": "bulk RNA-seq assay"
},
"audit": {
"ERROR": [
{
"category": "inconsistent parent sample",
"detail": "Primary cell [PKBSM8203DDOR](/primary-cells/PKBSM8203DDOR/) has metadata properties (`islet_function_available`, `rrid`, `islet_histology`, `pancreas_weight`, `sample_terms`, `islet_yield`, `pre_shipment_culture_time`, `isolation_center`, `lower_bound_age`, `hand_picked`, `cold_ischaemia_time`, `purity`, `age_units`, `islet_morphology`, `upper_bound_age`, `preservation_method`, `prep_viability`, `organ_source`) inconsistent with its associated parent sample [PKBSM7427WNPD](/primary-islet/PKBSM7427WNPD/). Samples that are sorted from or part of a parent sample are expected to share most of the parent's metadata properties.",
"level": 60,
"level_name": "ERROR",
"name": "audit_sample_sorted_from_parent_child_check",
"path": "/primary-cells/PKBSM8203DDOR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing nih certification",
"detail": "Measurement set [PKBDS2528IZBJ](/measurement-sets/PKBDS2528IZBJ/) has a sample [PKBSM8203DDOR](/primary-cells/PKBSM8203DDOR/) 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/PKBDS2528IZBJ/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Measurement set [PKBDS2528IZBJ](/measurement-sets/PKBDS2528IZBJ/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/PKBDS2528IZBJ/"
},
{
"category": "inconsistent assays",
"detail": "Measurement set [PKBDS2528IZBJ](/measurement-sets/PKBDS2528IZBJ/) has `assay_term` bulk RNA-seq assay, but `preferred_assay_title` RNA-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/PKBDS2528IZBJ/"
},
{
"category": "missing age",
"detail": "Primary cell [PKBSM8203DDOR](/primary-cells/PKBSM8203DDOR/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/PKBSM8203DDOR/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO4941ZRUK](/human-donors/PKBDO4941ZRUK/) is missing tier 2 field `diabetes_status_hba1c`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO4941ZRUK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO4941ZRUK](/human-donors/PKBDO4941ZRUK/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO4941ZRUK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO4941ZRUK](/human-donors/PKBDO4941ZRUK/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO4941ZRUK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO4941ZRUK](/human-donors/PKBDO4941ZRUK/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO4941ZRUK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO4941ZRUK](/human-donors/PKBDO4941ZRUK/) is missing tier 3 field `biological_sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO4941ZRUK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO4941ZRUK](/human-donors/PKBDO4941ZRUK/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO4941ZRUK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO4941ZRUK](/human-donors/PKBDO4941ZRUK/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO4941ZRUK/"
}
]
},
"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"
},
"collections": [
"HPAP"
],
"control_for": [],
"creation_timestamp": "2024-12-05T18:07:03.729024+00:00",
"description": "RNA-seq for pancreatic beta cell of islet biosample from human donor SAMN19776483 in the HPAP database HPAP-053",
"donors": [
{
"@id": "/human-donors/PKBDO4941ZRUK/",
"accession": "PKBDO4941ZRUK",
"aliases": [
"klaus-kaestner:HPAP-053"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/PKBDS9455QFKO/"
],
"lab": {
"@id": "/labs/klaus-kaestner/",
"title": "Klaus Kaestner, UPenn"
},
"library_construction_platform": [
{
"@id": "/platform-terms/EFO_0008637/",
"term_name": "Illumina NovaSeq 6000"
}
],
"preferred_assay_title": "RNA-seq",
"protocols": [
"https://hpap.pmacs.upenn.edu/explore/workflow/islet-molecular-phenotyping-studies?protocol=6"
],
"publication_identifiers": [
"PMID:31127054",
"PMCID:PMC6609987",
"doi:10.2337/db19-0058",
"PMID:36206763",
"PMCID:PMC9742126",
"doi:10.1016/j.cmet.2022.09.013"
],
"release_timestamp": "2025-01-10T05:46:40.564547+00:00",
"samples": [
{
"@id": "/primary-cells/PKBSM8203DDOR/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM8203DDOR",
"aliases": [
"klaus-kaestner:pancreaticBetaCell_HPAP-053"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000169/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_typeBpancreaticCell"
],
"status": "released",
"summary": "type B pancreatic cell",
"term_name": "type B pancreatic cell"
}
],
"status": "released",
"summary": "type B pancreatic cell, female, Homo sapiens",
"taxa": "Homo sapiens"
}
],
"schema_version": "17",
"sequencing_library_types": [
"rRNA depleted"
],
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"submitter_comment": "HPAP-053",
"summary": "bulk RNA-seq assay (RNA-seq)",
"uuid": "3c4abd4a-f0c9-4c6f-8f81-ae749aa4953a"
}
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