PKBDS4712MFGY

{
    "@context": "/terms/",
    "@id": "/measurement-sets/PKBDS4712MFGY/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "PKBDS4712MFGY",
    "aliases": [
        "klaus-kaestner:scATAC_isletCells_HPAP-055"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0002764/",
        "term_name": "single-cell ATAC-seq"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sample",
                "detail": "Primary islet [PKBSM3422VIKK](/primary-islet/PKBSM3422VIKK/) has only 1 child sample [PKBSM6120HOYN](/primary-cells/PKBSM6120HOYN/) 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/PKBSM3422VIKK/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing nih certification",
                "detail": "Measurement set [PKBDS4712MFGY](/measurement-sets/PKBDS4712MFGY/) has a sample [PKBSM3422VIKK](/primary-islet/PKBSM3422VIKK/) that lacks any `institutional_certificates` issued to the lab that submitted this file set. Measurement sets for mapping assays involving samples with a human origin are expected to link to the relevant institutional certificates issued to a matching lab and award.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_institutional_certification",
                "path": "/measurement-sets/PKBDS4712MFGY/"
            }
        ],
        "WARNING": [
            {
                "category": "missing tier 2 field",
                "detail": "Human donor [PKBSM3422VIKK](/primary-islet/PKBSM3422VIKK/) is missing tier 2 field `warm_ischaemia_duration`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_desired_fields",
                "path": "/primary-islet/PKBSM3422VIKK/"
            },
            {
                "category": "missing files",
                "detail": "Measurement set [PKBDS4712MFGY](/measurement-sets/PKBDS4712MFGY/) has no `files`. File sets are expected to have files.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_no_files",
                "path": "/measurement-sets/PKBDS4712MFGY/"
            },
            {
                "category": "inconsistent assays",
                "detail": "Measurement set [PKBDS4712MFGY](/measurement-sets/PKBDS4712MFGY/) has `assay_term` single-cell ATAC-seq, but `preferred_assay_title` snATAC-seq. Measurement sets with a preferred assay title are expected to specify an appropriate assay term.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_preferred_assay_title",
                "path": "/measurement-sets/PKBDS4712MFGY/"
            },
            {
                "category": "missing tier 2 field",
                "detail": "Human donor [PKBDO1384BFXE](/human-donors/PKBDO1384BFXE/) is missing tier 2 field `diabetes_status_hba1c`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_desired_fields",
                "path": "/human-donors/PKBDO1384BFXE/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO1384BFXE](/human-donors/PKBDO1384BFXE/) is missing tier 3 field `phenotypic_features`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO1384BFXE/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO1384BFXE](/human-donors/PKBDO1384BFXE/) is missing tier 3 field `biological_sex`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO1384BFXE/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO1384BFXE](/human-donors/PKBDO1384BFXE/) is missing tier 3 field `documents`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO1384BFXE/"
            }
        ]
    },
    "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": "2024-12-06T00:03:33.671400+00:00",
    "donors": [
        {
            "@id": "/human-donors/PKBDO1384BFXE/",
            "accession": "PKBDO1384BFXE",
            "aliases": [
                "klaus-kaestner:HPAP-055"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "experimental data",
    "files": [],
    "input_file_set_for": [
        "/analysis-sets/PKBDS0470WCHR/",
        "/analysis-sets/PKBDS9039BKEI/"
    ],
    "lab": {
        "@id": "/labs/klaus-kaestner/",
        "title": "Klaus Kaestner, UPenn"
    },
    "library_construction_platform": [
        {
            "@id": "/platform-terms/EFO_0008637/",
            "term_name": "Illumina NovaSeq 6000"
        }
    ],
    "notes": "HPAP-055",
    "preferred_assay_title": "snATAC-seq",
    "protocols": [
        "https://hpap.pmacs.upenn.edu/explore/workflow/islet-molecular-phenotyping-studies?protocol=5"
    ],
    "publication_identifiers": [
        "PMID:31127054",
        "PMID:36206763"
    ],
    "release_timestamp": "2025-01-10T05:47:23.336044+00:00",
    "samples": [
        {
            "@id": "/primary-islet/PKBSM3422VIKK/",
            "@type": [
                "PrimaryIslet",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "PKBSM3422VIKK",
            "aliases": [
                "klaus-kaestner:biosample_HPAP-055"
            ],
            "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": "17",
    "sequencing_library_types": [
        "accessible DNA"
    ],
    "status": "released",
    "submitted_by": {
        "@id": "/users/7e95dcd6-9c35-4082-9c53-09d14c5752be/",
        "title": "Parul Kudtarkar"
    },
    "summary": "single-cell ATAC-seq (snATAC-seq)",
    "uuid": "fc0f3fc4-1d84-474b-ab55-c13f999f3681"
}