PKBDS2381EBAM

{
    "@context": "/terms/",
    "@id": "/analysis-sets/PKBDS2381EBAM/",
    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "PKBDS2381EBAM",
    "aliases": [
        "klaus-kaestner:scATAC_isletCells_AnalysisSet_HPAP-105"
    ],
    "assay_titles": [
        "snATAC-seq"
    ],
    "audit": {
        "ERROR": [
            {
                "category": "unexpected input file set",
                "detail": "Analysis set [PKBDS2381EBAM](/analysis-sets/PKBDS2381EBAM/) links to file set(s): [PKBDS4488JJBN](/measurement-sets/PKBDS4488JJBN/) 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/PKBDS2381EBAM/"
            },
            {
                "category": "upload status not validated",
                "detail": "Matrix file [PKBFI1253BCFK](/matrix-files/PKBFI1253BCFK/) has `upload_status` pending. Files are expected to be validated.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_upload_status",
                "path": "/matrix-files/PKBFI1253BCFK/"
            }
        ],
        "INTERNAL_ACTION": [
            {
                "category": "validation error",
                "detail": "Matrix file [PKBFI1253BCFK](/matrix-files/PKBFI1253BCFK/) has schema error 'file_size' is a required property.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_schema",
                "path": "/matrix-files/PKBFI1253BCFK/"
            }
        ],
        "WARNING": [
            {
                "category": "missing tier 2 field",
                "detail": "Human donor [PKBSM4463PMSN](/primary-islet/PKBSM4463PMSN/) is missing tier 2 field `warm_ischaemia_duration`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_desired_fields",
                "path": "/primary-islet/PKBSM4463PMSN/"
            },
            {
                "category": "missing tier 2 field",
                "detail": "Human donor [PKBDO4401GCBA](/human-donors/PKBDO4401GCBA/) is missing tier 2 field `diabetes_status_hba1c`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_desired_fields",
                "path": "/human-donors/PKBDO4401GCBA/"
            },
            {
                "category": "missing tier 2 field",
                "detail": "Human donor [PKBDO4401GCBA](/human-donors/PKBDO4401GCBA/) is missing tier 2 field `glucose_loweing_theraphy`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_desired_fields",
                "path": "/human-donors/PKBDO4401GCBA/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO4401GCBA](/human-donors/PKBDO4401GCBA/) is missing tier 3 field `phenotypic_features`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO4401GCBA/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO4401GCBA](/human-donors/PKBDO4401GCBA/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO4401GCBA/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO4401GCBA](/human-donors/PKBDO4401GCBA/) is missing tier 3 field `biological_sex`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO4401GCBA/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO4401GCBA](/human-donors/PKBDO4401GCBA/) is missing tier 3 field `diabetes_duration`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO4401GCBA/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO4401GCBA](/human-donors/PKBDO4401GCBA/) is missing tier 3 field `documents`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO4401GCBA/"
            },
            {
                "category": "missing derived from",
                "detail": "Analysis set [PKBDS2381EBAM](/analysis-sets/PKBDS2381EBAM/) links to file(s) [PKBFI1253BCFK](/matrix-files/PKBFI1253BCFK/) 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/PKBDS2381EBAM/"
            }
        ]
    },
    "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": "2024-12-23T00:24:28.594099+00:00",
    "donors": [
        {
            "@id": "/human-donors/PKBDO4401GCBA/",
            "accession": "PKBDO4401GCBA",
            "aliases": [
                "klaus-kaestner:HPAP-105"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "intermediate analysis",
    "files": [
        {
            "@id": "/matrix-files/PKBFI1253BCFK/",
            "accession": "PKBFI1253BCFK",
            "aliases": [
                "kyle-gaulton:embedding_islet_scATAC_matrixFile_HPAP-105"
            ],
            "content_type": "sparse peak count matrix",
            "creation_timestamp": "2024-12-23T09:49:25.178518+00:00",
            "file_format": "mtx",
            "href": "/matrix-files/PKBFI1253BCFK/@@download/PKBFI1253BCFK.mtx",
            "s3_uri": "s3://pankbase-files/2024/12/23/cdce2a89-92e9-4b02-baf1-d2faad581771/PKBFI1253BCFK.mtx"
        }
    ],
    "input_file_set_for": [],
    "input_file_sets": [
        {
            "@id": "/measurement-sets/PKBDS4488JJBN/",
            "accession": "PKBDS4488JJBN",
            "aliases": [
                "klaus-kaestner:scATAC_isletCells_HPAP-105"
            ],
            "file_set_type": "experimental data"
        }
    ],
    "lab": {
        "@id": "/labs/pankbase-consortium/",
        "title": "Pankbase Consortium, PanKbase"
    },
    "release_timestamp": "2025-01-10T06:30:37.127965+00:00",
    "samples": [
        {
            "@id": "/primary-islet/PKBSM4463PMSN/",
            "@type": [
                "PrimaryIslet",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "PKBSM4463PMSN",
            "aliases": [
                "klaus-kaestner:biosample_HPAP-105"
            ],
            "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/7e95dcd6-9c35-4082-9c53-09d14c5752be/",
        "title": "Parul Kudtarkar"
    },
    "submitted_files_timestamp": "2024-12-23T09:49:25.178518+00:00",
    "summary": "intermediate analysis of snATAC-seq data",
    "uuid": "82764cd7-e9e9-4184-8900-972dd49abf79"
}