PKBDS6993KIMS

{
    "@context": "/terms/",
    "@id": "/analysis-sets/PKBDS6993KIMS/",
    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "PKBDS6993KIMS",
    "aliases": [
        "klaus-kaestner:pancreaticAlphaCell_AnalysisSet_RNAseq_HPAP-083"
    ],
    "assay_titles": [
        "RNA-seq"
    ],
    "audit": {
        "ERROR": [
            {
                "category": "inconsistent parent sample",
                "detail": "Primary cell [PKBSM8567TLYO](/primary-cells/PKBSM8567TLYO/) has metadata properties (`islet_function_available`, `rrid`, `islet_histology`, `pancreas_weight`, `sample_terms`, `islet_yield`, `pre_shipment_culture_time`, `isolation_center`, `lower_bound_age`, `hand_picked`, `cold_ischaemia_time`, `purity`, `age_units`, `islet_morphology`, `upper_bound_age`, `preservation_method`, `prep_viability`, `organ_source`) inconsistent with its associated parent sample [PKBSM6804RYNG](/primary-islet/PKBSM6804RYNG/). Samples that are sorted from or part of a parent sample are expected to share most of the parent's metadata properties.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_sample_sorted_from_parent_child_check",
                "path": "/primary-cells/PKBSM8567TLYO/"
            },
            {
                "category": "unexpected input file set",
                "detail": "Analysis set [PKBDS6993KIMS](/analysis-sets/PKBDS6993KIMS/) links to file set(s): [PKBDS9911KOYP](/measurement-sets/PKBDS9911KOYP/) 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/PKBDS6993KIMS/"
            }
        ],
        "WARNING": [
            {
                "category": "missing age",
                "detail": "Primary cell [PKBSM8567TLYO](/primary-cells/PKBSM8567TLYO/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_biosample_age",
                "path": "/primary-cells/PKBSM8567TLYO/"
            },
            {
                "category": "missing tier 2 field",
                "detail": "Human donor [PKBDO1723DEAS](/human-donors/PKBDO1723DEAS/) is missing tier 2 field `diabetes_status_hba1c`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_desired_fields",
                "path": "/human-donors/PKBDO1723DEAS/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO1723DEAS](/human-donors/PKBDO1723DEAS/) is missing tier 3 field `phenotypic_features`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO1723DEAS/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO1723DEAS](/human-donors/PKBDO1723DEAS/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO1723DEAS/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO1723DEAS](/human-donors/PKBDO1723DEAS/) is missing tier 3 field `biological_sex`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO1723DEAS/"
            },
            {
                "category": "missing tier 3 field",
                "detail": "Human donor [PKBDO1723DEAS](/human-donors/PKBDO1723DEAS/) is missing tier 3 field `documents`.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_optional_fields",
                "path": "/human-donors/PKBDO1723DEAS/"
            },
            {
                "category": "missing files",
                "detail": "Analysis set [PKBDS6993KIMS](/analysis-sets/PKBDS6993KIMS/) has no `files`. File sets are expected to have files.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_no_files",
                "path": "/analysis-sets/PKBDS6993KIMS/"
            }
        ]
    },
    "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": "2024-12-05T18:10:10.768048+00:00",
    "description": "Analysis set of RNA-seq for pancreatic alpha cell of islet biosample from human donor SAMN19842612 in the HPAP database HPAP-083",
    "donors": [
        {
            "@id": "/human-donors/PKBDO1723DEAS/",
            "accession": "PKBDO1723DEAS",
            "aliases": [
                "klaus-kaestner:HPAP-083"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "intermediate analysis",
    "files": [],
    "input_file_set_for": [],
    "input_file_sets": [
        {
            "@id": "/measurement-sets/PKBDS9911KOYP/",
            "accession": "PKBDS9911KOYP",
            "aliases": [
                "klaus-kaestner:pancreaticAlphaCell_MeasurementSet_RNAseq_HPAP-083"
            ],
            "file_set_type": "experimental data"
        }
    ],
    "lab": {
        "@id": "/labs/klaus-kaestner/",
        "title": "Klaus Kaestner, UPenn"
    },
    "publication_identifiers": [
        "PMID:31127054",
        "PMCID:PMC6609987",
        "doi:10.2337/db19-0058",
        "PMID:36206763",
        "PMCID:PMC9742126",
        "doi:10.1016/j.cmet.2022.09.013"
    ],
    "release_timestamp": "2025-01-10T10:14:08.839693+00:00",
    "samples": [
        {
            "@id": "/primary-cells/PKBSM8567TLYO/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "PKBSM8567TLYO",
            "aliases": [
                "klaus-kaestner:pancreaticAlphaCell_HPAP-083"
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/CL_0000171/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "kyle-gaulton:sample_pancreaticAcell"
                    ],
                    "status": "released",
                    "summary": "pancreatic A cell",
                    "term_name": "pancreatic A cell"
                }
            ],
            "status": "released",
            "summary": "pancreatic A cell, male, Homo sapiens",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "7",
    "status": "released",
    "submitted_by": {
        "@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
        "title": "Ying Sun"
    },
    "submitter_comment": "HPAP-083",
    "summary": "intermediate analysis of RNA-seq data",
    "uuid": "ddb3f262-9003-45c0-a3d6-e27c63fbbeb6"
}