PKBDS8682VUMC
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS8682VUMC/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS8682VUMC",
"aliases": [
"pankbase-consortium:EndoC-bH1_treated_IFNa24hr_GSE133218_AnalysisSet"
],
"assay_titles": [
"RNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS8682VUMC](/analysis-sets/PKBDS8682VUMC/) links to file set(s): [PKBDS8443OBOR](/measurement-sets/PKBDS8443OBOR/) in `input_file_sets` that are not represented in the `derived_from` of the file sets of the files in this analysis. The analysis set input files are expected to belong to the input file sets.",
"level": 60,
"level_name": "ERROR",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/PKBDS8682VUMC/"
}
],
"WARNING": [
{
"category": "incorrect classifications format",
"detail": "Human beta cell line [PKBSM5907VASA](/human-beta-cell-line/PKBSM5907VASA/) 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/PKBSM5907VASA/"
},
{
"category": "missing files",
"detail": "Analysis set [PKBDS8682VUMC](/analysis-sets/PKBDS8682VUMC/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/analysis-sets/PKBDS8682VUMC/"
},
{
"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/"
}
]
},
"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": "2025-10-30T18:44:51.573503+00:00",
"description": "Analysis set of EndoC-bH1 cells treated with IFNa for 24hr from GSE133218",
"donors": [
{
"@id": "/human-donors/PKBDO8293TLPA/",
"accession": "PKBDO8293TLPA",
"aliases": [
"pankbase-consortium:EndoC_donor"
],
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [],
"input_file_set_for": [],
"input_file_sets": [
{
"@id": "/measurement-sets/PKBDS8443OBOR/",
"accession": "PKBDS8443OBOR",
"aliases": [
"pankbase-consortium:EndoC-bH1_treated_IFNa24hr_GSE133218_MeasurementSet"
],
"file_set_type": "experimental data"
}
],
"lab": {
"@id": "/labs/pankbase-consortium/",
"title": "Pankbase Consortium, PanKbase"
},
"publication_identifiers": [
"PMID:32444635"
],
"release_timestamp": "2025-11-15T06:59:54.123335+00:00",
"samples": [
{
"@id": "/human-beta-cell-line/PKBSM5907VASA/",
"@type": [
"HumanBetaCellLines",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM5907VASA",
"sample_terms": [
{
"@id": "/sample-terms/CVCL_909/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_EndoC-betaH1"
],
"status": "released",
"summary": "EndoC-βH1",
"term_name": "EndoC-βH1"
}
],
"status": "released",
"summary": "EndoC-βH1 cell line, treated with 2000 U/mL Interferon alpha-2 for 86400 seconds",
"taxa": "Homo sapiens",
"treatments": [
"/treatments/ff4d301b-35c2-42df-a783-2ce9ec639f22/"
]
}
],
"schema_version": "8",
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"summary": "intermediate analysis of RNA-seq data",
"uuid": "fc4a4a8b-b252-4cc7-bb9a-c603bc75d79a"
}
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
