PKBDS9097NVEW
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS9097NVEW/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS9097NVEW",
"aliases": [
"pankbase-consortium:EndoC-bH1_GSE155220_GC_AnalysisSet"
],
"assay_titles": [
"RNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS9097NVEW](/analysis-sets/PKBDS9097NVEW/) links to file set(s): [PKBDS5449XLCC](/measurement-sets/PKBDS5449XLCC/) 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/PKBDS9097NVEW/"
}
],
"INTERNAL_ACTION": [
{
"category": "validation error",
"detail": "Treatment [c832fd6e-e404-414f-ab72-a278895aab18](/treatments/c832fd6e-e404-414f-ab72-a278895aab18/) has schema error {'lab': '00eadba4-bed5-4ffd-a4bf-9a5c16c87cc6', 'award': '2e63d0a1-1cc1-4654-8f19-4968a5ca9618', 'amount': 0, 'status': 'in progress', 'aliases': ['pankbase-consortium:treatment_Control_Growing'], 'purpose': 'control', 'depletion': False, 'description': 'Cells cultured under standard growth conditions without treatment.', 'amount_units': 'μM', 'submitted_by': '5e3038c4-baa5-4589-b3d8-ad2fe634e826', 'schema_version': '7', 'treatment_type': 'environmental', 'treatment_term_id': 'NTR:0000001', 'creation_timestamp': '2026-02-07T00:18:03.293177+00:00', 'treatment_term_name': 'Control Growing', 'uuid': 'c832fd6e-e404-414f-ab72-a278895aab18'} should not be valid under {'required': ['treatment_term_id']}.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_schema",
"path": "/treatments/c832fd6e-e404-414f-ab72-a278895aab18/"
},
{
"category": "validation error: treatment_term_name",
"detail": "Treatment [c832fd6e-e404-414f-ab72-a278895aab18](/treatments/c832fd6e-e404-414f-ab72-a278895aab18/) has schema error 'Control Growing' is not one of ['stiffness'].",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_schema",
"path": "/treatments/c832fd6e-e404-414f-ab72-a278895aab18/"
},
{
"category": "NTR term ID",
"detail": "Treatment term for [c832fd6e-e404-414f-ab72-a278895aab18](/treatments/c832fd6e-e404-414f-ab72-a278895aab18/) has been newly requested. Treatments with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_treatment_term_id_check",
"path": "/treatments/c832fd6e-e404-414f-ab72-a278895aab18/"
},
{
"category": "mismatched status",
"detail": "Released analysis set [PKBDS9097NVEW](/analysis-sets/PKBDS9097NVEW/) has in progress subobject human beta cell lines [PKBSM8771SZOO](/human-beta-cell-line/PKBSM8771SZOO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/analysis-sets/PKBDS9097NVEW/"
}
],
"WARNING": [
{
"category": "incorrect classifications format",
"detail": "Human beta cell line [PKBSM8771SZOO](/human-beta-cell-line/PKBSM8771SZOO/) 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/PKBSM8771SZOO/"
},
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS9097NVEW](/analysis-sets/PKBDS9097NVEW/) links to file(s) [PKBFI1776MHNI](/alignment-files/PKBFI1776MHNI/), [PKBFI1384SQJA](/alignment-files/PKBFI1384SQJA/), [PKBFI0628KRDF](/alignment-files/PKBFI0628KRDF/), [PKBFI8108UYZJ](/tabular-files/PKBFI8108UYZJ/), [PKBFI6159KDHP](/tabular-files/PKBFI6159KDHP/), [PKBFI6176EUKS](/alignment-files/PKBFI6176EUKS/), [PKBFI5653KEWQ](/alignment-files/PKBFI5653KEWQ/), [PKBFI0186YESA](/alignment-files/PKBFI0186YESA/), [PKBFI3525QCYQ](/alignment-files/PKBFI3525QCYQ/), [PKBFI9001OTRA](/alignment-files/PKBFI9001OTRA/), [PKBFI7860GJUE](/tabular-files/PKBFI7860GJUE/), [PKBFI1969EFJO](/tabular-files/PKBFI1969EFJO/) that have no `derived_from`. Files in an analysis set are expected to be derived from other files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_sets_derived_from",
"path": "/analysis-sets/PKBDS9097NVEW/"
},
{
"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": "2026-02-10T20:10:41.841421+00:00",
"description": "Analysis set of EndoC‑BH1 cells with non‑silencing controls under growing conditions from GSE155220",
"donors": [
{
"@id": "/human-donors/PKBDO8293TLPA/",
"accession": "PKBDO8293TLPA",
"aliases": [
"pankbase-consortium:EndoC_donor"
],
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/PKBFI1776MHNI/",
"accession": "PKBFI1776MHNI",
"aliases": [
"pankbase-consortium:EndoC-bH1_GSE155220_GC_AnalysisSet_SRR12332870.Aligned.sortedByCoord.out.bam"
],
"content_type": "alignments",
"creation_timestamp": "2026-02-10T20:43:50.935503+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI1776MHNI/@@download/PKBFI1776MHNI.bam"
},
{
"@id": "/alignment-files/PKBFI1384SQJA/",
"accession": "PKBFI1384SQJA",
"aliases": [
"pankbase-consortium:EndoC-bH1_GSE155220_GC_AnalysisSet_SRR12332870.Aligned.toTranscriptome.out.bam"
],
"content_type": "transcriptome alignments",
"creation_timestamp": "2026-02-10T20:43:52.516087+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI1384SQJA/@@download/PKBFI1384SQJA.bam"
},
{
"@id": "/alignment-files/PKBFI0628KRDF/",
"accession": "PKBFI0628KRDF",
"aliases": [
"pankbase-consortium:EndoC-bH1_GSE155220_GC_AnalysisSet_SRR12332871.Aligned.toTranscriptome.out.bam"
],
"content_type": "transcriptome alignments",
"creation_timestamp": "2026-02-10T20:43:56.202404+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI0628KRDF/@@download/PKBFI0628KRDF.bam"
},
{
"@id": "/alignment-files/PKBFI9802QWBJ/",
"accession": "PKBFI9802QWBJ",
"aliases": [
"pankbase-consortium:EndoC-bH1_GSE155220_GC_AnalysisSet_SRR12332870.Aligned.sortedByCoord.out.md.bam"
],
"content_type": "alignments",
"creation_timestamp": "2026-02-10T20:43:53.594114+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI9802QWBJ/@@download/PKBFI9802QWBJ.bam"
},
{
"@id": "/tabular-files/PKBFI8108UYZJ/",
"accession": "PKBFI8108UYZJ",
"aliases": [
"pankbase-consortium:EndoC-bH1_GSE155220_GC_AnalysisSet_SRR12332870.Log.final.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2026-02-10T21:43:16.118730+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI8108UYZJ/@@download/PKBFI8108UYZJ.txt.gz"
},
{
"@id": "/tabular-files/PKBFI3884SSLV/",
"accession": "PKBFI3884SSLV",
"aliases": [
"pankbase-consortium:EndoC-bH1_GSE155220_GC_AnalysisSet_SRR12332870.rsem.isoforms.results"
],
"content_type": "element quantifications",
"creation_timestamp": "2026-02-10T21:43:21.997071+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI3884SSLV/@@download/PKBFI3884SSLV.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI6159KDHP/",
"accession": "PKBFI6159KDHP",
"aliases": [
"pankbase-consortium:EndoC-bH1_GSE155220_GC_AnalysisSet_SRR12332873.Log.final.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2026-02-10T21:43:40.093494+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6159KDHP/@@download/PKBFI6159KDHP.txt.gz"
},
{
"@id": "/alignment-files/PKBFI6176EUKS/",
"accession": "PKBFI6176EUKS",
"aliases": [
"pankbase-consortium:EndoC-bH1_GSE155220_GC_AnalysisSet_SRR12332871.Aligned.sortedByCoord.out.bam"
],
"content_type": "alignments",
"creation_timestamp": "2026-02-10T20:43:55.044941+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI6176EUKS/@@download/PKBFI6176EUKS.bam"
},
{
"@id": "/alignment-files/PKBFI5653KEWQ/",
"accession": "PKBFI5653KEWQ",
"aliases": [
"pankbase-consortium:EndoC-bH1_GSE155220_GC_AnalysisSet_SRR12332872.Aligned.sortedByCoord.out.bam"
],
"content_type": "alignments",
"creation_timestamp": "2026-02-10T20:43:58.468394+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI5653KEWQ/@@download/PKBFI5653KEWQ.bam"
},
{
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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
