PKBDS2774MNZB
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS2774MNZB/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS2774MNZB",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment"
],
"assay_titles": [
"scRNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS2774MNZB](/analysis-sets/PKBDS2774MNZB/) links to file set(s): [PKBDS5511GGIY](/measurement-sets/PKBDS5511GGIY/) 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/PKBDS2774MNZB/"
}
],
"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/PKBDO6552HQDC/"
}
],
"WARNING": [
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS2774MNZB](/analysis-sets/PKBDS2774MNZB/) links to file(s) [PKBFI3566MZDU](/alignment-files/PKBFI3566MZDU/), [PKBFI6725AZRY](/matrix-files/PKBFI6725AZRY/), [PKBFI7296VTXD](/tabular-files/PKBFI7296VTXD/), [PKBFI9903OWJN](/tabular-files/PKBFI9903OWJN/), [PKBFI9178JYNS](/tabular-files/PKBFI9178JYNS/), [PKBFI2205TZBY](/matrix-files/PKBFI2205TZBY/), [PKBFI8838BWSJ](/matrix-files/PKBFI8838BWSJ/), [PKBFI7707HVLB](/matrix-files/PKBFI7707HVLB/), [PKBFI0564PPGA](/matrix-files/PKBFI0564PPGA/), [PKBFI1895KECO](/matrix-files/PKBFI1895KECO/), [PKBFI7590PZRF](/matrix-files/PKBFI7590PZRF/), [PKBFI4688EKRB](/matrix-files/PKBFI4688EKRB/) 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/PKBDS2774MNZB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM2833VSFN](/primary-islet/PKBSM2833VSFN/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM2833VSFN/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM2833VSFN](/primary-islet/PKBSM2833VSFN/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM2833VSFN/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6552HQDC](/human-donors/PKBDO6552HQDC/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6552HQDC/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6552HQDC](/human-donors/PKBDO6552HQDC/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6552HQDC/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6552HQDC](/human-donors/PKBDO6552HQDC/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6552HQDC/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6552HQDC](/human-donors/PKBDO6552HQDC/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6552HQDC/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6552HQDC](/human-donors/PKBDO6552HQDC/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6552HQDC/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6552HQDC](/human-donors/PKBDO6552HQDC/) is missing tier 3 field `other_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6552HQDC/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6552HQDC](/human-donors/PKBDO6552HQDC/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6552HQDC/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO6552HQDC](/human-donors/PKBDO6552HQDC/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO6552HQDC/"
}
]
},
"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": "2025-05-08T23:19:05.924984+00:00",
"description": "Analysis set of scRNA-seq for islet biosample of human donor HPAP-070 from HPAP with no_treatment (HPAP-070)",
"donors": [
{
"@id": "/human-donors/PKBDO6552HQDC/",
"accession": "PKBDO6552HQDC",
"aliases": [
"klaus-kaestner:HPAP-070"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
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"accession": "PKBFI3566MZDU",
"aliases": [
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],
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"creation_timestamp": "2025-05-15T23:57:14.515664+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI3566MZDU/@@download/PKBFI3566MZDU.bam"
},
{
"@id": "/matrix-files/PKBFI6725AZRY/",
"accession": "PKBFI6725AZRY",
"aliases": [
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],
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"creation_timestamp": "2025-05-16T16:45:25.150165+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI6725AZRY/@@download/PKBFI6725AZRY.mtx"
},
{
"@id": "/tabular-files/PKBFI7296VTXD/",
"accession": "PKBFI7296VTXD",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_.Log.final.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:34:01.027846+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI7296VTXD/@@download/PKBFI7296VTXD.txt.gz"
},
{
"@id": "/tabular-files/PKBFI9903OWJN/",
"accession": "PKBFI9903OWJN",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_.Log.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:39:18.020943+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI9903OWJN/@@download/PKBFI9903OWJN.txt.gz"
},
{
"@id": "/tabular-files/PKBFI9178JYNS/",
"accession": "PKBFI9178JYNS",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_.Log.progress.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:45:28.413294+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI9178JYNS/@@download/PKBFI9178JYNS.txt.gz"
},
{
"@id": "/alignment-files/PKBFI6473AVDY/",
"accession": "PKBFI6473AVDY",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Alignment_.before-dedup.bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-05-16T16:59:14.772787+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI6473AVDY/@@download/PKBFI6473AVDY.bam"
},
{
"@id": "/tabular-files/PKBFI8620PWIQ/",
"accession": "PKBFI8620PWIQ",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_.qc.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:22:46.746193+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI8620PWIQ/@@download/PKBFI8620PWIQ.txt.gz"
},
{
"@id": "/tabular-files/PKBFI2913LSGM/",
"accession": "PKBFI2913LSGM",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_knee.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:34:57.691941+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI2913LSGM/@@download/PKBFI2913LSGM.txt.gz"
},
{
"@id": "/matrix-files/PKBFI2205TZBY/",
"accession": "PKBFI2205TZBY",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Matrix_cellbender_FPR_0.05.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T19:10:26.509845+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI2205TZBY/@@download/PKBFI2205TZBY.h5ad"
},
{
"@id": "/tabular-files/PKBFI1887UJWZ/",
"accession": "PKBFI1887UJWZ",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_pass.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:41:20.571932+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI1887UJWZ/@@download/PKBFI1887UJWZ.txt.gz"
},
{
"@id": "/tabular-files/PKBFI6975XGXV/",
"accession": "PKBFI6975XGXV",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_cellbender_cell_barcodes.csv"
],
"content_type": "sequence barcodes",
"creation_timestamp": "2025-05-16T17:52:00.296103+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI6975XGXV/@@download/PKBFI6975XGXV.csv.gz"
},
{
"@id": "/tabular-files/PKBFI9153JFMO/",
"accession": "PKBFI9153JFMO",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_cellbender_FPR_0.05_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T18:46:52.019142+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI9153JFMO/@@download/PKBFI9153JFMO.csv.gz"
},
{
"@id": "/matrix-files/PKBFI8838BWSJ/",
"accession": "PKBFI8838BWSJ",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Matrix_cellbender_FPR_0.05_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T19:18:49.977056+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI8838BWSJ/@@download/PKBFI8838BWSJ.h5ad"
},
{
"@id": "/tabular-files/PKBFI1940OVYU/",
"accession": "PKBFI1940OVYU",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_cellbender_FPR_0.05_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T19:45:32.802513+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI1940OVYU/@@download/PKBFI1940OVYU.txt.gz"
},
{
"@id": "/tabular-files/PKBFI3546BBRC/",
"accession": "PKBFI3546BBRC",
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"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_cellbender_FPR_0.15_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T21:28:27.352839+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI3546BBRC/@@download/PKBFI3546BBRC.txt.gz"
},
{
"@id": "/matrix-files/PKBFI7707HVLB/",
"accession": "PKBFI7707HVLB",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Matrix_cellbender_FPR_0.1_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T20:06:20.396966+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI7707HVLB/@@download/PKBFI7707HVLB.h5ad"
},
{
"@id": "/matrix-files/PKBFI0564PPGA/",
"accession": "PKBFI0564PPGA",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Matrix_cellbender_FPR_0.1.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T20:01:45.306280+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI0564PPGA/@@download/PKBFI0564PPGA.h5ad"
},
{
"@id": "/tabular-files/PKBFI2715UFCB/",
"accession": "PKBFI2715UFCB",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_cellbender_FPR_0.1_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T20:30:09.636178+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI2715UFCB/@@download/PKBFI2715UFCB.csv.gz"
},
{
"@id": "/matrix-files/PKBFI1895KECO/",
"accession": "PKBFI1895KECO",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Matrix_cellbender_FPR_0.15.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T21:02:39.557597+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI1895KECO/@@download/PKBFI1895KECO.h5ad"
},
{
"@id": "/tabular-files/PKBFI1625WBCY/",
"accession": "PKBFI1625WBCY",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_cellbender_FPR_0.1_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T20:39:40.499352+00:00",
"file_format": "txt",
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},
{
"@id": "/matrix-files/PKBFI7590PZRF/",
"accession": "PKBFI7590PZRF",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Matrix_cellbender_FPR_0.15_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T21:07:44.052736+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI7590PZRF/@@download/PKBFI7590PZRF.h5ad"
},
{
"@id": "/tabular-files/PKBFI4671HPHF/",
"accession": "PKBFI4671HPHF",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_cellbender_FPR_0.15_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T21:22:48.441969+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI4671HPHF/@@download/PKBFI4671HPHF.csv.gz"
},
{
"@id": "/tabular-files/PKBFI1638GDQE/",
"accession": "PKBFI1638GDQE",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_doubletfinder_assignments.txt"
],
"content_type": "barcode to element mapping",
"creation_timestamp": "2025-05-16T21:33:56.868477+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI1638GDQE/@@download/PKBFI1638GDQE.txt.gz"
},
{
"@id": "/tabular-files/PKBFI8377OZBH/",
"accession": "PKBFI8377OZBH",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_Tabular_barcodes.tsv"
],
"content_type": "barcode to element mapping",
"creation_timestamp": "2025-05-16T21:39:51.974066+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI8377OZBH/@@download/PKBFI8377OZBH.tsv.gz"
},
{
"@id": "/matrix-files/PKBFI4688EKRB/",
"accession": "PKBFI4688EKRB",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-070_no_treatment_doubletFiinderMatrix_matrix.mtx"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T22:25:04.649267+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI4688EKRB/@@download/PKBFI4688EKRB.mtx"
}
],
"input_file_set_for": [],
"input_file_sets": [
{
"@id": "/measurement-sets/PKBDS5511GGIY/",
"accession": "PKBDS5511GGIY",
"aliases": [
"klaus-kaestner:HPAP_MeasurementSet_scRNAseq_HPAP-070_no_treatment"
],
"file_set_type": "experimental data"
}
],
"lab": {
"@id": "/labs/klaus-kaestner/",
"title": "Klaus Kaestner, UPenn"
},
"notes": "HPAP",
"release_timestamp": "2025-06-15T04:47:23.096671+00:00",
"samples": [
{
"@id": "/primary-islet/PKBSM2833VSFN/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM2833VSFN",
"aliases": [
"klaus-kaestner:biosample_HPAP-070"
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000006/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"kyle-gaulton:sample_isletofLangerhans"
],
"status": "released",
"summary": "islet of Langerhans",
"term_name": "islet of Langerhans"
}
],
"status": "released",
"summary": "islet of Langerhans cell, male, 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": "2025-05-15T23:34:01.027846+00:00",
"submitter_comment": "HPAP-070",
"summary": "intermediate analysis of scRNA-seq data",
"uuid": "12951fde-a1f4-4c8c-ae75-c71aece7794b"
}
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