PKBDS6824TBCT
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS6824TBCT/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS6824TBCT",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment"
],
"assay_titles": [
"scRNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS6824TBCT](/analysis-sets/PKBDS6824TBCT/) links to file set(s): [PKBDS1526HQKR](/measurement-sets/PKBDS1526HQKR/) 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/PKBDS6824TBCT/"
}
],
"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/PKBDO7608YHRK/"
}
],
"WARNING": [
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7608YHRK](/human-donors/PKBDO7608YHRK/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7608YHRK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7608YHRK](/human-donors/PKBDO7608YHRK/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7608YHRK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7608YHRK](/human-donors/PKBDO7608YHRK/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7608YHRK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7608YHRK](/human-donors/PKBDO7608YHRK/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7608YHRK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7608YHRK](/human-donors/PKBDO7608YHRK/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7608YHRK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7608YHRK](/human-donors/PKBDO7608YHRK/) is missing tier 3 field `other_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7608YHRK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7608YHRK](/human-donors/PKBDO7608YHRK/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7608YHRK/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO7608YHRK](/human-donors/PKBDO7608YHRK/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO7608YHRK/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM5541GMAA](/primary-islet/PKBSM5541GMAA/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM5541GMAA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM5541GMAA](/primary-islet/PKBSM5541GMAA/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM5541GMAA/"
},
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS6824TBCT](/analysis-sets/PKBDS6824TBCT/) links to file(s) [PKBFI2141KNMP](/alignment-files/PKBFI2141KNMP/), [PKBFI8806WPEO](/matrix-files/PKBFI8806WPEO/), [PKBFI5247SKBT](/tabular-files/PKBFI5247SKBT/), [PKBFI8485MCYT](/tabular-files/PKBFI8485MCYT/), [PKBFI7893QXCI](/tabular-files/PKBFI7893QXCI/), [PKBFI3758CQLQ](/matrix-files/PKBFI3758CQLQ/), [PKBFI4352QRLQ](/matrix-files/PKBFI4352QRLQ/), [PKBFI9412EUTU](/matrix-files/PKBFI9412EUTU/), [PKBFI3564HSEA](/matrix-files/PKBFI3564HSEA/), [PKBFI6075DANX](/matrix-files/PKBFI6075DANX/), [PKBFI7470UWGY](/matrix-files/PKBFI7470UWGY/), [PKBFI4074EERU](/matrix-files/PKBFI4074EERU/) 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/PKBDS6824TBCT/"
}
]
},
"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": "2025-05-08T23:19:37.446920+00:00",
"description": "Analysis set of scRNA-seq for islet biosample of human donor HPAP-120 from HPAP with no_treatment (HPAP-120)",
"donors": [
{
"@id": "/human-donors/PKBDO7608YHRK/",
"accession": "PKBDO7608YHRK",
"aliases": [
"klaus-kaestner:HPAP-120"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/PKBFI2141KNMP/",
"accession": "PKBFI2141KNMP",
"aliases": [
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],
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"creation_timestamp": "2025-05-15T23:58:36.385226+00:00",
"file_format": "bam",
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},
{
"@id": "/matrix-files/PKBFI8806WPEO/",
"accession": "PKBFI8806WPEO",
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"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Matrix_matrix.mtx"
],
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"creation_timestamp": "2025-05-16T16:46:55.372872+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI8806WPEO/@@download/PKBFI8806WPEO.mtx"
},
{
"@id": "/tabular-files/PKBFI5247SKBT/",
"accession": "PKBFI5247SKBT",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_.Log.final.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:35:16.760725+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI5247SKBT/@@download/PKBFI5247SKBT.txt.gz"
},
{
"@id": "/tabular-files/PKBFI8485MCYT/",
"accession": "PKBFI8485MCYT",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_.Log.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:40:16.338333+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI8485MCYT/@@download/PKBFI8485MCYT.txt.gz"
},
{
"@id": "/tabular-files/PKBFI7893QXCI/",
"accession": "PKBFI7893QXCI",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_.Log.progress.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-15T23:46:06.821219+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI7893QXCI/@@download/PKBFI7893QXCI.txt.gz"
},
{
"@id": "/alignment-files/PKBFI4767HGWF/",
"accession": "PKBFI4767HGWF",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Alignment_.before-dedup.bam"
],
"content_type": "alignments",
"creation_timestamp": "2025-05-16T17:01:13.258737+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI4767HGWF/@@download/PKBFI4767HGWF.bam"
},
{
"@id": "/tabular-files/PKBFI8217JAFV/",
"accession": "PKBFI8217JAFV",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_.qc.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:24:26.226425+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI8217JAFV/@@download/PKBFI8217JAFV.txt.gz"
},
{
"@id": "/tabular-files/PKBFI5974HFFO/",
"accession": "PKBFI5974HFFO",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_knee.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:35:37.086831+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI5974HFFO/@@download/PKBFI5974HFFO.txt.gz"
},
{
"@id": "/matrix-files/PKBFI3758CQLQ/",
"accession": "PKBFI3758CQLQ",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Matrix_cellbender_FPR_0.05.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T19:14:08.207253+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI3758CQLQ/@@download/PKBFI3758CQLQ.h5ad"
},
{
"@id": "/tabular-files/PKBFI8041RWYR/",
"accession": "PKBFI8041RWYR",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_pass.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T17:42:04.732063+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI8041RWYR/@@download/PKBFI8041RWYR.txt.gz"
},
{
"@id": "/tabular-files/PKBFI4474MBUP/",
"accession": "PKBFI4474MBUP",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_cellbender_cell_barcodes.csv"
],
"content_type": "sequence barcodes",
"creation_timestamp": "2025-05-16T17:52:44.118522+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI4474MBUP/@@download/PKBFI4474MBUP.csv.gz"
},
{
"@id": "/matrix-files/PKBFI4352QRLQ/",
"accession": "PKBFI4352QRLQ",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Matrix_cellbender_FPR_0.05_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T19:19:30.444710+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI4352QRLQ/@@download/PKBFI4352QRLQ.h5ad"
},
{
"@id": "/tabular-files/PKBFI9828EWCU/",
"accession": "PKBFI9828EWCU",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_cellbender_FPR_0.05_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T18:49:11.673570+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI9828EWCU/@@download/PKBFI9828EWCU.csv.gz"
},
{
"@id": "/tabular-files/PKBFI6095ZMOE/",
"accession": "PKBFI6095ZMOE",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_cellbender_FPR_0.05_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T19:46:15.569192+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6095ZMOE/@@download/PKBFI6095ZMOE.txt.gz"
},
{
"@id": "/tabular-files/PKBFI6299IFDZ/",
"accession": "PKBFI6299IFDZ",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_cellbender_FPR_0.15_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T21:29:03.624980+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI6299IFDZ/@@download/PKBFI6299IFDZ.txt.gz"
},
{
"@id": "/matrix-files/PKBFI9412EUTU/",
"accession": "PKBFI9412EUTU",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Matrix_cellbender_FPR_0.1.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T20:03:05.540541+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI9412EUTU/@@download/PKBFI9412EUTU.h5ad"
},
{
"@id": "/matrix-files/PKBFI3564HSEA/",
"accession": "PKBFI3564HSEA",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Matrix_cellbender_FPR_0.1_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T20:06:57.209719+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI3564HSEA/@@download/PKBFI3564HSEA.h5ad"
},
{
"@id": "/tabular-files/PKBFI5884RGRB/",
"accession": "PKBFI5884RGRB",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_cellbender_FPR_0.1_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T20:35:30.959333+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI5884RGRB/@@download/PKBFI5884RGRB.csv.gz"
},
{
"@id": "/tabular-files/PKBFI8165ESQH/",
"accession": "PKBFI8165ESQH",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_cellbender_FPR_0.1_report.html"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T20:40:14.486545+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI8165ESQH/@@download/PKBFI8165ESQH.txt.gz"
},
{
"@id": "/matrix-files/PKBFI6075DANX/",
"accession": "PKBFI6075DANX",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Matrix_cellbender_FPR_0.15.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T21:04:04.324655+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI6075DANX/@@download/PKBFI6075DANX.h5ad"
},
{
"@id": "/matrix-files/PKBFI7470UWGY/",
"accession": "PKBFI7470UWGY",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Matrix_cellbender_FPR_0.15_filtered.h5"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T21:08:26.652392+00:00",
"file_format": "h5ad",
"href": "/matrix-files/PKBFI7470UWGY/@@download/PKBFI7470UWGY.h5ad"
},
{
"@id": "/tabular-files/PKBFI8461WNBO/",
"accession": "PKBFI8461WNBO",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_cellbender_FPR_0.15_metrics.csv"
],
"content_type": "QC metrics",
"creation_timestamp": "2025-05-16T21:24:23.034367+00:00",
"file_format": "csv",
"href": "/tabular-files/PKBFI8461WNBO/@@download/PKBFI8461WNBO.csv.gz"
},
{
"@id": "/tabular-files/PKBFI5833EYSR/",
"accession": "PKBFI5833EYSR",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_doubletfinder_assignments.txt"
],
"content_type": "barcode to element mapping",
"creation_timestamp": "2025-05-16T21:34:34.073206+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI5833EYSR/@@download/PKBFI5833EYSR.txt.gz"
},
{
"@id": "/tabular-files/PKBFI2398QDEH/",
"accession": "PKBFI2398QDEH",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_Tabular_barcodes.tsv"
],
"content_type": "barcode to element mapping",
"creation_timestamp": "2025-05-16T21:40:35.539588+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI2398QDEH/@@download/PKBFI2398QDEH.tsv.gz"
},
{
"@id": "/matrix-files/PKBFI4074EERU/",
"accession": "PKBFI4074EERU",
"aliases": [
"klaus-kaestner:HPAP_scRNAseq_HPAP-120_no_treatment_doubletFiinderMatrix_matrix.mtx"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-05-16T22:29:35.405701+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI4074EERU/@@download/PKBFI4074EERU.mtx"
}
],
"input_file_set_for": [],
"input_file_sets": [
{
"@id": "/measurement-sets/PKBDS1526HQKR/",
"accession": "PKBDS1526HQKR",
"aliases": [
"klaus-kaestner:HPAP_MeasurementSet_scRNAseq_HPAP-120_no_treatment"
],
"file_set_type": "experimental data"
}
],
"lab": {
"@id": "/labs/klaus-kaestner/",
"title": "Klaus Kaestner, UPenn"
},
"notes": "HPAP",
"release_timestamp": "2025-06-15T04:47:43.657898+00:00",
"samples": [
{
"@id": "/primary-islet/PKBSM5541GMAA/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM5541GMAA",
"aliases": [
"klaus-kaestner:biosample_HPAP-120"
],
"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": "2025-05-15T23:35:16.760725+00:00",
"submitter_comment": "HPAP-120",
"summary": "intermediate analysis of scRNA-seq data",
"uuid": "532cbe1c-a7bf-4c18-bb6f-feb34a7ba59d"
}
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