PKBDS0482ELXA
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS0482ELXA/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS0482ELXA",
"aliases": [
"klaus-kaestner:scATAC_isletCells_AnalysisSet_HPAP-062"
],
"assay_titles": [
"snATAC-seq"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Matrix file [PKBFI5481FCZQ](/matrix-files/PKBFI5481FCZQ/) has `upload_status` pending. Files are expected to be validated.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/matrix-files/PKBFI5481FCZQ/"
},
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS0482ELXA](/analysis-sets/PKBDS0482ELXA/) links to file set(s): [PKBDS1909ZJCX](/measurement-sets/PKBDS1909ZJCX/) 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/PKBDS0482ELXA/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sample",
"detail": "Primary islet [PKBSM6289WPCO](/primary-islet/PKBSM6289WPCO/) has only 1 child sample [PKBSM5345IWBE](/primary-cells/PKBSM5345IWBE/) in `parts`. Parent samples are expected to have multiple child samples.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_parent_sample_with_singular_child",
"path": "/primary-islet/PKBSM6289WPCO/"
}
],
"WARNING": [
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM6289WPCO](/primary-islet/PKBSM6289WPCO/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM6289WPCO/"
},
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS0482ELXA](/analysis-sets/PKBDS0482ELXA/) links to file(s) [PKBFI5481FCZQ](/matrix-files/PKBFI5481FCZQ/) 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/PKBDS0482ELXA/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO0742JZZH](/human-donors/PKBDO0742JZZH/) is missing tier 2 field `hba1c`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO0742JZZH/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO0742JZZH](/human-donors/PKBDO0742JZZH/) is missing tier 2 field `diabetes_status_hba1c`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO0742JZZH/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO0742JZZH](/human-donors/PKBDO0742JZZH/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO0742JZZH/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO0742JZZH](/human-donors/PKBDO0742JZZH/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO0742JZZH/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO0742JZZH](/human-donors/PKBDO0742JZZH/) is missing tier 3 field `biological_sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO0742JZZH/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO0742JZZH](/human-donors/PKBDO0742JZZH/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO0742JZZH/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO0742JZZH](/human-donors/PKBDO0742JZZH/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO0742JZZH/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO0742JZZH](/human-donors/PKBDO0742JZZH/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO0742JZZH/"
}
]
},
"award": {
"@id": "/awards/U24DK1385121/",
"component": "data coordination",
"contact_pi": {
"@id": "/users/860c4750-8d3c-40f5-8f2c-90c5e5d19e88/",
"title": "Kyle Gaulton"
},
"title": "A Data and Administrative Coordinating Center for the PanKbase Consortium"
},
"collections": [
"HPAP"
],
"control_for": [],
"creation_timestamp": "2024-12-23T00:24:10.981511+00:00",
"donors": [
{
"@id": "/human-donors/PKBDO0742JZZH/",
"accession": "PKBDO0742JZZH",
"aliases": [
"klaus-kaestner:HPAP-062"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/PKBFI5481FCZQ/",
"accession": "PKBFI5481FCZQ",
"aliases": [
"kyle-gaulton:embedding_islet_scATAC_matrixFile_HPAP-062"
],
"content_type": "sparse peak count matrix",
"creation_timestamp": "2024-12-23T09:48:55.970998+00:00",
"file_format": "mtx",
"href": "/matrix-files/PKBFI5481FCZQ/@@download/PKBFI5481FCZQ.mtx",
"s3_uri": "s3://pankbase-files/2024/12/23/8f11dbd8-5eab-4966-9730-68ffd4684c5c/PKBFI5481FCZQ.mtx"
}
],
"input_file_set_for": [],
"input_file_sets": [
{
"@id": "/measurement-sets/PKBDS1909ZJCX/",
"accession": "PKBDS1909ZJCX",
"aliases": [
"klaus-kaestner:scATAC_isletCells_HPAP-062"
],
"file_set_type": "experimental data"
}
],
"lab": {
"@id": "/labs/pankbase-consortium/",
"title": "Pankbase Consortium, PanKbase"
},
"release_timestamp": "2025-01-10T06:30:27.339463+00:00",
"samples": [
{
"@id": "/primary-islet/PKBSM6289WPCO/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM6289WPCO",
"aliases": [
"klaus-kaestner:biosample_HPAP-062"
],
"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/7e95dcd6-9c35-4082-9c53-09d14c5752be/",
"title": "Parul Kudtarkar"
},
"submitted_files_timestamp": "2024-12-23T09:48:55.970998+00:00",
"summary": "intermediate analysis of snATAC-seq data",
"uuid": "7b4e8a5b-322d-4333-8a16-d176f5232287"
}
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