{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS2831NHRN/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS2831NHRN",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_AnalysisSet_RNAseq_HPAP-097"
],
"assay_titles": [
"RNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS2831NHRN](/analysis-sets/PKBDS2831NHRN/) links to file set(s): [PKBDS7621SMFT](/measurement-sets/PKBDS7621SMFT/) 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/PKBDS2831NHRN/"
},
{
"category": "inconsistent parent sample",
"detail": "Primary cell [PKBSM7378CQFK](/primary-cells/PKBSM7378CQFK/) has metadata properties (`islet_function_available`, `islet_yield`, `organ_source`, `isolation_center`, `prep_viability`, `age_units`, `hand_picked`, `purity`, `islet_histology`, `cold_ischaemia_time`, `sample_terms`, `preservation_method`, `pancreas_weight`, `rrid`, `upper_bound_age`, `lower_bound_age`, `islet_morphology`) inconsistent with its associated parent sample [PKBSM6113VWVP](/primary-islet/PKBSM6113VWVP/). 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/PKBSM7378CQFK/"
}
],
"INTERNAL_ACTION": [
{
"category": "upgrade failure",
"detail": "NameError(\"name 'ethnicities_status_mapping' is not defined\") upgrading from '16' to '17'",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_schema",
"path": "/human-donors/PKBDO1701BQMY/"
}
],
"WARNING": [
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 3 field `other_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1701BQMY](/human-donors/PKBDO1701BQMY/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1701BQMY/"
},
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS2831NHRN](/analysis-sets/PKBDS2831NHRN/) links to file(s) [PKBFI9963FGAE](/alignment-files/PKBFI9963FGAE/), [PKBFI8679ZVEC](/alignment-files/PKBFI8679ZVEC/), [PKBFI2287XVHF](/tabular-files/PKBFI2287XVHF/) 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/PKBDS2831NHRN/"
},
{
"category": "missing age",
"detail": "Primary cell [PKBSM7378CQFK](/primary-cells/PKBSM7378CQFK/) 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/PKBSM7378CQFK/"
}
]
},
"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": "2024-12-05T18:12:06.202187+00:00",
"description": "Analysis set of RNA-seq for pancreatic exocrine cell of islet biosample from human donor SAMN22562808 in the HPAP database HPAP-097",
"donors": [
{
"@id": "/human-donors/PKBDO1701BQMY/",
"accession": "PKBDO1701BQMY",
"aliases": [
"klaus-kaestner:HPAP-097"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/PKBFI9963FGAE/",
"accession": "PKBFI9963FGAE",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_AnalysisSet_RNAseq_HPAP-097_STAR-bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-04-17T21:54:59.891245+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI9963FGAE/@@download/PKBFI9963FGAE.bam"
},
{
"@id": "/alignment-files/PKBFI8679ZVEC/",
"accession": "PKBFI8679ZVEC",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_AnalysisSet_RNAseq_HPAP-097_STAR-Transbam"
],
"content_type": "transcriptome alignments",
"creation_timestamp": "2025-04-17T21:55:01.706835+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI8679ZVEC/@@download/PKBFI8679ZVEC.bam"
},
{
"@id": "/alignment-files/PKBFI5424SLWC/",
"accession": "PKBFI5424SLWC",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_AnalysisSet_RNAseq_HPAP-097_PICARD-bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-04-17T21:55:02.832776+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI5424SLWC/@@download/PKBFI5424SLWC.bam"
},
{
"@id": "/tabular-files/PKBFI9691SPXT/",
"accession": "PKBFI9691SPXT",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_AnalysisSet_RNAseq_HPAP-097_RSEM-isoform"
],
"content_type": "element quantifications",
"creation_timestamp": "2025-04-17T22:44:03.668624+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI9691SPXT/@@download/PKBFI9691SPXT.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI2287XVHF/",
"accession": "PKBFI2287XVHF",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_AnalysisSet_RNAseq_HPAP-097_STAR-log"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-04-17T22:44:00.244013+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI2287XVHF/@@download/PKBFI2287XVHF.txt.gz"
},
{
"@id": "/tabular-files/PKBFI3481PSAY/",
"accession": "PKBFI3481PSAY",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_AnalysisSet_RNAseq_HPAP-097_RNA-SeQC-metrics"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-04-17T22:44:01.821125+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI3481PSAY/@@download/PKBFI3481PSAY.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI7347AGKV/",
"accession": "PKBFI7347AGKV",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_AnalysisSet_RNAseq_HPAP-097_RSEM-gene"
],
"content_type": "element quantifications",
"creation_timestamp": "2025-04-17T22:44:02.791167+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI7347AGKV/@@download/PKBFI7347AGKV.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI0744ZHRM/",
"accession": "PKBFI0744ZHRM",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_AnalysisSet_RNAseq_HPAP-097_PICARD-metrics"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-04-17T22:44:01.078200+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI0744ZHRM/@@download/PKBFI0744ZHRM.txt.gz"
}
],
"input_file_set_for": [],
"input_file_sets": [
{
"@id": "/measurement-sets/PKBDS7621SMFT/",
"accession": "PKBDS7621SMFT",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_MeasurementSet_RNAseq_HPAP-097"
],
"file_set_type": "experimental data"
}
],
"lab": {
"@id": "/labs/klaus-kaestner/",
"title": "Klaus Kaestner, UPenn"
},
"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": "2025-01-10T10:14:20.448408+00:00",
"samples": [
{
"@id": "/primary-cells/PKBSM7378CQFK/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM7378CQFK",
"aliases": [
"klaus-kaestner:pancreaticExocrineCell_HPAP-097"
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000152/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_exocrineCell"
],
"status": "released",
"summary": "exocrine cell",
"term_name": "exocrine cell"
}
],
"status": "released",
"summary": "exocrine cell, female, Homo sapiens",
"taxa": "Homo sapiens"
}
],
"schema_version": "7",
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"submitted_files_timestamp": "2025-04-17T21:54:59.891245+00:00",
"submitter_comment": "HPAP-097",
"summary": "intermediate analysis of RNA-seq data",
"uuid": "7670f8f4-3159-4c64-ad27-954210085c6c"
}