PKBDS2035CZMI
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS2035CZMI/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS2035CZMI",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment"
],
"assay_titles": [
"scRNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS2035CZMI](/analysis-sets/PKBDS2035CZMI/) links to file set(s): [PKBDS6188MDZJ](/measurement-sets/PKBDS6188MDZJ/) 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/PKBDS2035CZMI/"
}
],
"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/PKBDO1225NSNK/"
}
],
"WARNING": [
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO1225NSNK](/human-donors/PKBDO1225NSNK/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO1225NSNK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1225NSNK](/human-donors/PKBDO1225NSNK/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1225NSNK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1225NSNK](/human-donors/PKBDO1225NSNK/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1225NSNK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1225NSNK](/human-donors/PKBDO1225NSNK/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1225NSNK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1225NSNK](/human-donors/PKBDO1225NSNK/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1225NSNK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1225NSNK](/human-donors/PKBDO1225NSNK/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1225NSNK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1225NSNK](/human-donors/PKBDO1225NSNK/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1225NSNK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1225NSNK](/human-donors/PKBDO1225NSNK/) is missing tier 3 field `other_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1225NSNK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1225NSNK](/human-donors/PKBDO1225NSNK/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1225NSNK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO1225NSNK](/human-donors/PKBDO1225NSNK/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO1225NSNK/"
},
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS2035CZMI](/analysis-sets/PKBDS2035CZMI/) links to file(s) [PKBFI0908YOWM](/alignment-files/PKBFI0908YOWM/), [PKBFI7522MKDM](/matrix-files/PKBFI7522MKDM/), [PKBFI6257UWCE](/tabular-files/PKBFI6257UWCE/), [PKBFI9639JORI](/tabular-files/PKBFI9639JORI/), [PKBFI5015FNLT](/tabular-files/PKBFI5015FNLT/), [PKBFI9343FWZS](/matrix-files/PKBFI9343FWZS/), [PKBFI7069IGPX](/matrix-files/PKBFI7069IGPX/), [PKBFI5060RWCO](/matrix-files/PKBFI5060RWCO/), [PKBFI4676UKGP](/matrix-files/PKBFI4676UKGP/), [PKBFI7738BQSL](/matrix-files/PKBFI7738BQSL/), [PKBFI5389PDIR](/matrix-files/PKBFI5389PDIR/), [PKBFI0215IZEZ](/matrix-files/PKBFI0215IZEZ/) 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/PKBDS2035CZMI/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM5143MXFX](/primary-islet/PKBSM5143MXFX/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM5143MXFX/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM5143MXFX](/primary-islet/PKBSM5143MXFX/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM5143MXFX/"
}
]
},
"award": {
"@id": "/awards/UC4DK112217/",
"contact_pi": {
"@id": "/users/e1c8c91f-3952-45a9-9f56-442627f60c13/",
"title": "Klaus Kaestner"
},
"title": "PENN INTEGRATED HUMAN PANCREAS PROCUREMENT AND ANALYSIS PROGRAM"
},
"collections": [
"HPAP"
],
"control_for": [],
"creation_timestamp": "2025-05-08T23:19:38.188988+00:00",
"description": "Analysis set of scRNA-seq for islet biosample of human donor HPAP-122 from HPAP with no_treatment (HPAP-122)",
"donors": [
{
"@id": "/human-donors/PKBDO1225NSNK/",
"accession": "PKBDO1225NSNK",
"aliases": [
"klaus-kaestner:HPAP-122"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/PKBFI0908YOWM/",
"accession": "PKBFI0908YOWM",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Alignment_.Aligned.sortedByCoord.out.bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-05-15T23:58:41.699803+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI0908YOWM/@@download/PKBFI0908YOWM.bam"
},
{
"@id": "/matrix-files/PKBFI7522MKDM/",
"accession": "PKBFI7522MKDM",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Matrix_matrix.mtx"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T16:46:56.460994+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI7522MKDM/@@download/PKBFI7522MKDM.mtx"
},
{
"@id": "/tabular-files/PKBFI6257UWCE/",
"accession": "PKBFI6257UWCE",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_.Log.final.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:35:21.500849+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6257UWCE/@@download/PKBFI6257UWCE.txt.gz"
},
{
"@id": "/tabular-files/PKBFI9639JORI/",
"accession": "PKBFI9639JORI",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_.Log.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:40:17.802822+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI9639JORI/@@download/PKBFI9639JORI.txt.gz"
},
{
"@id": "/tabular-files/PKBFI5015FNLT/",
"accession": "PKBFI5015FNLT",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_.Log.progress.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:46:08.102388+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI5015FNLT/@@download/PKBFI5015FNLT.txt.gz"
},
{
"@id": "/alignment-files/PKBFI9035ZZRZ/",
"accession": "PKBFI9035ZZRZ",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Alignment_.before-dedup.bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-05-16T17:01:14.735182+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI9035ZZRZ/@@download/PKBFI9035ZZRZ.bam"
},
{
"@id": "/matrix-files/PKBFI9343FWZS/",
"accession": "PKBFI9343FWZS",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Matrix_cellbender_FPR_0.05.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T19:14:09.574960+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI9343FWZS/@@download/PKBFI9343FWZS.h5ad"
},
{
"@id": "/tabular-files/PKBFI5866VMOO/",
"accession": "PKBFI5866VMOO",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_.qc.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:24:27.187747+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI5866VMOO/@@download/PKBFI5866VMOO.txt.gz"
},
{
"@id": "/tabular-files/PKBFI6765ULMP/",
"accession": "PKBFI6765ULMP",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_knee.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:35:37.955357+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6765ULMP/@@download/PKBFI6765ULMP.txt.gz"
},
{
"@id": "/tabular-files/PKBFI4778XJLM/",
"accession": "PKBFI4778XJLM",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_pass.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:42:05.819441+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI4778XJLM/@@download/PKBFI4778XJLM.txt.gz"
},
{
"@id": "/tabular-files/PKBFI2800QUPE/",
"accession": "PKBFI2800QUPE",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_cellbender_cell_barcodes.csv"
],
"content_type": "sequence barcodes",
"creation_timestamp": "2025-05-16T17:52:45.186056+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI2800QUPE/@@download/PKBFI2800QUPE.csv.gz"
},
{
"@id": "/matrix-files/PKBFI7069IGPX/",
"accession": "PKBFI7069IGPX",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Matrix_cellbender_FPR_0.05_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T19:19:31.504731+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI7069IGPX/@@download/PKBFI7069IGPX.h5ad"
},
{
"@id": "/tabular-files/PKBFI9789PFEN/",
"accession": "PKBFI9789PFEN",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_cellbender_FPR_0.05_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T18:49:13.235939+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI9789PFEN/@@download/PKBFI9789PFEN.csv.gz"
},
{
"@id": "/tabular-files/PKBFI9722WGVQ/",
"accession": "PKBFI9722WGVQ",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_cellbender_FPR_0.05_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T19:46:17.196924+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI9722WGVQ/@@download/PKBFI9722WGVQ.txt.gz"
},
{
"@id": "/matrix-files/PKBFI5060RWCO/",
"accession": "PKBFI5060RWCO",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Matrix_cellbender_FPR_0.1.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T20:03:06.558598+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI5060RWCO/@@download/PKBFI5060RWCO.h5ad"
},
{
"@id": "/matrix-files/PKBFI4676UKGP/",
"accession": "PKBFI4676UKGP",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Matrix_cellbender_FPR_0.1_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T20:06:57.937860+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI4676UKGP/@@download/PKBFI4676UKGP.h5ad"
},
{
"@id": "/tabular-files/PKBFI7452OESE/",
"accession": "PKBFI7452OESE",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_cellbender_FPR_0.15_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T21:29:04.741927+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI7452OESE/@@download/PKBFI7452OESE.txt.gz"
},
{
"@id": "/tabular-files/PKBFI3207ZTBG/",
"accession": "PKBFI3207ZTBG",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_cellbender_FPR_0.1_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T20:35:32.605312+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI3207ZTBG/@@download/PKBFI3207ZTBG.csv.gz"
},
{
"@id": "/tabular-files/PKBFI3862LCXE/",
"accession": "PKBFI3862LCXE",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_cellbender_FPR_0.1_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T20:40:16.386346+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI3862LCXE/@@download/PKBFI3862LCXE.txt.gz"
},
{
"@id": "/matrix-files/PKBFI7738BQSL/",
"accession": "PKBFI7738BQSL",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Matrix_cellbender_FPR_0.15.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T21:04:05.401238+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI7738BQSL/@@download/PKBFI7738BQSL.h5ad"
},
{
"@id": "/matrix-files/PKBFI5389PDIR/",
"accession": "PKBFI5389PDIR",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Matrix_cellbender_FPR_0.15_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T21:08:27.693972+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI5389PDIR/@@download/PKBFI5389PDIR.h5ad"
},
{
"@id": "/tabular-files/PKBFI2581LOFZ/",
"accession": "PKBFI2581LOFZ",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_cellbender_FPR_0.15_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T21:24:24.266990+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI2581LOFZ/@@download/PKBFI2581LOFZ.csv.gz"
},
{
"@id": "/tabular-files/PKBFI3036TPCO/",
"accession": "PKBFI3036TPCO",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_doubletfinder_assignments.txt"
],
"content_type": "barcode to element mapping",
"creation_timestamp": "2025-05-16T21:34:35.911589+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI3036TPCO/@@download/PKBFI3036TPCO.txt.gz"
},
{
"@id": "/tabular-files/PKBFI0724JRCX/",
"accession": "PKBFI0724JRCX",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_Tabular_barcodes.tsv"
],
"content_type": "barcode to element mapping",
"creation_timestamp": "2025-05-16T21:40:37.063331+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI0724JRCX/@@download/PKBFI0724JRCX.tsv.gz"
},
{
"@id": "/matrix-files/PKBFI0215IZEZ/",
"accession": "PKBFI0215IZEZ",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-122_no_treatment_doubletFiinderMatrix_matrix.mtx"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T22:29:36.223470+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI0215IZEZ/@@download/PKBFI0215IZEZ.mtx"
}
],
"input_file_set_for": [],
"input_file_sets": [
{
"@id": "/measurement-sets/PKBDS6188MDZJ/",
"accession": "PKBDS6188MDZJ",
"aliases": [
"klaus-kaestner:HPAP_MeasurementSet_scRNAseq_HPAP-122_no_treatment"
],
"file_set_type": "experimental data"
}
],
"lab": {
"@id": "/labs/klaus-kaestner/",
"title": "Klaus Kaestner, UPenn"
},
"notes": "HPAP",
"release_timestamp": "2025-06-15T04:47:51.146350+00:00",
"samples": [
{
"@id": "/primary-islet/PKBSM5143MXFX/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM5143MXFX",
"aliases": [
"klaus-kaestner:biosample_HPAP-122"
],
"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, 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": "2025-05-15T23:35:21.500849+00:00",
"submitter_comment": "HPAP-122",
"summary": "intermediate analysis of scRNA-seq data",
"uuid": "e5d88f64-e0d3-4fc2-ab09-d08f31626083"
}
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