PKBDS3828MFOC
{
"@context": "/terms/",
"@id": "/measurement-sets/PKBDS3828MFOC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "PKBDS3828MFOC",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP-16125-01_Bacteroidesdorei_6hr_MeasurementSet"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003090/",
"term_name": "bulk RNA-seq assay"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing nih certification",
"detail": "Measurement set [PKBDS3828MFOC](/measurement-sets/PKBDS3828MFOC/) has a sample [PKBSM1548AZZG](/primary-islet/PKBSM1548AZZG/) 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/PKBDS3828MFOC/"
},
{
"category": "missing protocol",
"detail": "Measurement set [PKBDS3828MFOC](/measurement-sets/PKBDS3828MFOC/) has no `protocols`. Measurement sets are expected to specify the experimental protocol utilized for conducting the assay on protocols.io.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_unspecified_protocol",
"path": "/measurement-sets/PKBDS3828MFOC/"
}
],
"WARNING": [
{
"category": "missing tier 1 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 1 field `sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier1_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 2 field `ethnicities`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 2 field `hba1c`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 2 field `hospital_stay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 2 field `donation_type`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 2 field `cause_of_death`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `dbxrefs`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `family_history_of_diabetes`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `genetic_ethnicities`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `genetic_sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_gada`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_gada_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_ia2`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_ia2_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_iaa`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_iaa_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_znt8`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `aab_znt8_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `hla_typing`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `other_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `publication_identifiers`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `pancreas_tissue_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `url`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `derived_diabetes_status`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `data_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5495LYJU](/human-donors/PKBDO5495LYJU/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5495LYJU/"
},
{
"category": "missing files",
"detail": "Measurement set [PKBDS3828MFOC](/measurement-sets/PKBDS3828MFOC/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/PKBDS3828MFOC/"
},
{
"category": "inconsistent assays",
"detail": "Measurement set [PKBDS3828MFOC](/measurement-sets/PKBDS3828MFOC/) has `assay_term` bulk RNA-seq assay, but `preferred_assay_title` RNA-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/PKBDS3828MFOC/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1548AZZG](/primary-islet/PKBSM1548AZZG/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1548AZZG/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1548AZZG](/primary-islet/PKBSM1548AZZG/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1548AZZG/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1548AZZG](/primary-islet/PKBSM1548AZZG/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1548AZZG/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1548AZZG](/primary-islet/PKBSM1548AZZG/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1548AZZG/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1548AZZG](/primary-islet/PKBSM1548AZZG/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1548AZZG/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1548AZZG](/primary-islet/PKBSM1548AZZG/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1548AZZG/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1548AZZG](/primary-islet/PKBSM1548AZZG/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1548AZZG/"
}
]
},
"award": {
"@id": "/awards/U24DK138512-DK138515/",
"component": "data coordination",
"title": "A Data and Administrative Coordinating Center for the PanKbase Consortium U24DK138512-DK138515"
},
"control_for": [],
"creation_timestamp": "2026-01-05T18:14:33.938674+00:00",
"description": "Measurement set of human donor HP-16125-01, Bacteroides dorei (BD) for 6 hr",
"donors": [
{
"@id": "/human-donors/PKBDO5495LYJU/",
"accession": "PKBDO5495LYJU",
"aliases": [
"prodo:HP-16125-01"
],
"gender": "Male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/PKBDS1379VKQT/"
],
"lab": {
"@id": "/labs/pankbase-consortium/"
},
"preferred_assay_title": "RNA-seq",
"publication_identifiers": [
"PMID:31781116",
"PMCID:PMC6857727",
"doi:10.3389/fimmu.2019.02623"
],
"release_timestamp": "2026-02-06T21:43:13.752884+00:00",
"samples": [
{
"@id": "/primary-islet/PKBSM1548AZZG/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM1548AZZG",
"aliases": [
"prodo:HP-16125-01_bulkIslet_secondaryBiosample_Bacteroidesdorei_6hr"
],
"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 treated with 0 μM Bacteroides dorei for 6 hours",
"treatments": [
{
"@id": "/treatments/5699076a-80d3-4141-a60a-c1e2d8ce842a/",
"purpose": "stimulation",
"summary": "Treatment of 0 μM Bacteroides dorei for 6 hours",
"treatment_type": "protein"
}
]
}
],
"schema_version": "17",
"sequencing_library_types": [
"rRNA depleted"
],
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"uuid": "94f1adb3-76b6-40f5-8096-36c3db3dd72a"
}
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
