PKBDS3070RLGN
{
"@context": "/terms/",
"@id": "/measurement-sets/PKBDS3070RLGN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "PKBDS3070RLGN",
"aliases": [
"prodo:HP-22234-01_scRNAseq_assay_IL1B18hrtreatment"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released treatment [50654f26-3a37-4abc-9288-48abeb69deff](/treatments/50654f26-3a37-4abc-9288-48abeb69deff/) has deleted subobject award [U24DK13851](/awards/U24DK13851/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/treatments/50654f26-3a37-4abc-9288-48abeb69deff/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing nih certification",
"detail": "Measurement set [PKBDS3070RLGN](/measurement-sets/PKBDS3070RLGN/) has a sample [PKBSM3073NKQP](/primary-islet/PKBSM3073NKQP/) 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/PKBDS3070RLGN/"
},
{
"category": "missing protocol",
"detail": "Measurement set [PKBDS3070RLGN](/measurement-sets/PKBDS3070RLGN/) 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/PKBDS3070RLGN/"
}
],
"WARNING": [
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 2 field `diabetes_status_hba1c`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 2 field `hospital_stay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 2 field `donation_type`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `dbxrefs`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `family_history_of_diabetes`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `genetic_ethnicities`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `biological_sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_gada`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_gada_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_ia2`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_ia2_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_znt8`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `aab_znt8_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `hla_typing`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `publication_identifiers`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5181VXNQ](/human-donors/PKBDO5181VXNQ/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO5181VXNQ/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3073NKQP](/primary-islet/PKBSM3073NKQP/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3073NKQP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3073NKQP](/primary-islet/PKBSM3073NKQP/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3073NKQP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3073NKQP](/primary-islet/PKBSM3073NKQP/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3073NKQP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3073NKQP](/primary-islet/PKBSM3073NKQP/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3073NKQP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3073NKQP](/primary-islet/PKBSM3073NKQP/) is missing tier 2 field `purity`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3073NKQP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3073NKQP](/primary-islet/PKBSM3073NKQP/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3073NKQP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3073NKQP](/primary-islet/PKBSM3073NKQP/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3073NKQP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM3073NKQP](/primary-islet/PKBSM3073NKQP/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM3073NKQP/"
},
{
"category": "missing files",
"detail": "Measurement set [PKBDS3070RLGN](/measurement-sets/PKBDS3070RLGN/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/PKBDS3070RLGN/"
},
{
"category": "inconsistent assays",
"detail": "Measurement set [PKBDS3070RLGN](/measurement-sets/PKBDS3070RLGN/) has `assay_term` single-cell RNA sequencing assay, but `preferred_assay_title` scRNA-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/PKBDS3070RLGN/"
}
]
},
"award": {
"@id": "/awards/PSEUDO2/",
"contact_pi": {
"@id": "/users/29948efc-654e-4448-ade8-2fe2cd0a8d4b/",
"title": "Prodo Laboratories"
},
"title": "Prodo Laboratories Inc."
},
"control_for": [],
"creation_timestamp": "2025-01-09T23:44:06.035747+00:00",
"donors": [
{
"@id": "/human-donors/PKBDO5181VXNQ/",
"accession": "PKBDO5181VXNQ",
"aliases": [
"prodo:HP-22234-01"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/PKBDS8427QUCQ/"
],
"lab": {
"@id": "/labs/prodo-laboratories/",
"title": "Prodo Laboratories, PRODO"
},
"preferred_assay_title": "scRNA-seq",
"release_timestamp": "2025-01-10T05:47:20.868059+00:00",
"samples": [
{
"@id": "/primary-islet/PKBSM3073NKQP/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM3073NKQP",
"aliases": [
"prodo:HP-22234-01_scRNAseq_secondaryBiosample_IL1B18hrtreatment"
],
"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 depleted of Interleukin-1 beta",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/50654f26-3a37-4abc-9288-48abeb69deff/",
"purpose": "stimulation",
"summary": "Depletion of Interleukin-1 beta",
"treatment_type": "protein"
}
]
}
],
"schema_version": "17",
"sequencing_library_types": [
"polyA enriched"
],
"status": "released",
"submitted_by": {
"@id": "/users/7e95dcd6-9c35-4082-9c53-09d14c5752be/",
"title": "Parul Kudtarkar"
},
"summary": "single-cell RNA sequencing assay (scRNA-seq)",
"uuid": "0f048a05-9a08-40f8-bafb-1aea3a30efcb"
}
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