PKBDS0310UCQN
{
"@context": "/terms/",
"@id": "/measurement-sets/PKBDS0310UCQN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "PKBDS0310UCQN",
"aliases": [
"pankbase-consortium:EndoC-bH2_treated_normoglycemia_GSE212749_MeasurementSet"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003090/",
"term_name": "bulk RNA-seq assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human beta cell lines [PKBSM9768JJCM](/human-beta-cell-line/PKBSM9768JJCM/) has in progress subobject sample term [CVCL_IS71](/sample-terms/CVCL_IS71/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-beta-cell-line/PKBSM9768JJCM/"
},
{
"category": "mismatched status",
"detail": "Released human beta cell lines [PKBSM9768JJCM](/human-beta-cell-line/PKBSM9768JJCM/) has in progress subobject source [endocell](/sources/endocell/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-beta-cell-line/PKBSM9768JJCM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing nih certification",
"detail": "Measurement set [PKBDS0310UCQN](/measurement-sets/PKBDS0310UCQN/) has a sample [PKBSM9768JJCM](/human-beta-cell-line/PKBSM9768JJCM/) 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/PKBDS0310UCQN/"
},
{
"category": "missing protocol",
"detail": "Measurement set [PKBDS0310UCQN](/measurement-sets/PKBDS0310UCQN/) 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/PKBDS0310UCQN/"
}
],
"WARNING": [
{
"category": "missing tier 1 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 1 field `sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier1_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 1 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 1 field `bmi`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier1_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 1 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 1 field `diabetes_status_description`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier1_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `ethnicities`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `hba1c`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `hospital_stay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `donation_type`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 2 field `cause_of_death`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `dbxrefs`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `family_history_of_diabetes`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `genetic_ethnicities`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `genetic_sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_gada`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_gada_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_ia2`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_ia2_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_iaa`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_iaa_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_znt8`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `aab_znt8_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `hla_typing`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `other_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `publication_identifiers`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `collections`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `pancreas_tissue_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `url`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `derived_diabetes_status`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `data_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO8293TLPA](/human-donors/PKBDO8293TLPA/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO8293TLPA/"
},
{
"category": "incorrect classifications format",
"detail": "Human beta cell line [PKBSM9768JJCM](/human-beta-cell-line/PKBSM9768JJCM/) has `classifications` ['human beta cell line'] but should be [\"cell line\"]. Human beta cell lines are expected to have classifications as an array.",
"level": 40,
"level_name": "WARNING",
"name": "audit_classifications_format_check",
"path": "/human-beta-cell-line/PKBSM9768JJCM/"
},
{
"category": "missing files",
"detail": "Measurement set [PKBDS0310UCQN](/measurement-sets/PKBDS0310UCQN/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/PKBDS0310UCQN/"
},
{
"category": "inconsistent assays",
"detail": "Measurement set [PKBDS0310UCQN](/measurement-sets/PKBDS0310UCQN/) 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/PKBDS0310UCQN/"
}
]
},
"award": {
"@id": "/awards/U24DK138512-DK138515/",
"component": "data coordination",
"title": "A Data and Administrative Coordinating Center for the PanKbase Consortium U24DK138512-DK138515"
},
"control_for": [],
"creation_timestamp": "2025-10-27T19:58:37.672265+00:00",
"description": "Measurement set of EndoC-bH2 cells treated with normoglycemia from GSE212749",
"donors": [
{
"@id": "/human-donors/PKBDO8293TLPA/",
"accession": "PKBDO8293TLPA",
"aliases": [
"pankbase-consortium:EndoC_donor"
],
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/PKBDS8703ZVXP/"
],
"lab": {
"@id": "/labs/pankbase-consortium/",
"title": "Pankbase Consortium, PanKbase"
},
"preferred_assay_title": "RNA-seq",
"publication_identifiers": [
"PMID:36450253"
],
"release_timestamp": "2025-11-15T06:57:33.233075+00:00",
"samples": [
{
"@id": "/human-beta-cell-line/PKBSM9768JJCM/",
"@type": [
"HumanBetaCellLines",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM9768JJCM",
"aliases": [
"pankbase-consortium:EndoC-bH2_treated_normoglycemia_GSE212749"
],
"sample_terms": [
{
"@id": "/sample-terms/CVCL_IS71/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_EndoC-betaH2"
],
"status": "in progress",
"summary": "EndoC-bH2",
"term_name": "EndoC-bH2"
}
],
"status": "released",
"summary": "EndoC-bH2 cell line, treated with 5.5 mM Glucose for 72 hours",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/34b49ebb-9313-4e01-9fbb-649dd4abf16b/",
"purpose": "control",
"summary": "Treatment of 5.5 mM Glucose for 72 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "17",
"sequencing_library_types": [
"rRNA depleted"
],
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"summary": "bulk RNA-seq assay (RNA-seq)",
"uuid": "fcef4ea8-149f-4ba4-be00-ff132a6cdd4a"
}
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
