{
"@context": "/terms/",
"@id": "/measurement-sets/PKBDS7553VRIH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "PKBDS7553VRIH",
"aliases": [
"joyce-niland:SAMN12022246_scRNAseq_assay_untreated"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing nih certification",
"detail": "Measurement set [PKBDS7553VRIH](/measurement-sets/PKBDS7553VRIH/) has a sample [PKBSM1414OXUT](/primary-islet/PKBSM1414OXUT/) 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/PKBDS7553VRIH/"
},
{
"category": "missing protocol",
"detail": "Measurement set [PKBDS7553VRIH](/measurement-sets/PKBDS7553VRIH/) 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/PKBDS7553VRIH/"
}
],
"WARNING": [
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1414OXUT](/primary-islet/PKBSM1414OXUT/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1414OXUT/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1414OXUT](/primary-islet/PKBSM1414OXUT/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1414OXUT/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1414OXUT](/primary-islet/PKBSM1414OXUT/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1414OXUT/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1414OXUT](/primary-islet/PKBSM1414OXUT/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1414OXUT/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1414OXUT](/primary-islet/PKBSM1414OXUT/) is missing tier 2 field `purity`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1414OXUT/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1414OXUT](/primary-islet/PKBSM1414OXUT/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1414OXUT/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1414OXUT](/primary-islet/PKBSM1414OXUT/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1414OXUT/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM1414OXUT](/primary-islet/PKBSM1414OXUT/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM1414OXUT/"
},
{
"category": "missing files",
"detail": "Measurement set [PKBDS7553VRIH](/measurement-sets/PKBDS7553VRIH/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/PKBDS7553VRIH/"
},
{
"category": "inconsistent assays",
"detail": "Measurement set [PKBDS7553VRIH](/measurement-sets/PKBDS7553VRIH/) 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/PKBDS7553VRIH/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 2 field `diabetes_status_hba1c`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 2 field `donation_type`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `dbxrefs`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `family_history_of_diabetes`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `biological_sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `aab_gada`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `aab_gada_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `aab_ia2`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `aab_ia2_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `aab_znt8`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `aab_znt8_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO2444UOCY](/human-donors/PKBDO2444UOCY/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_optional_fields",
"path": "/human-donors/PKBDO2444UOCY/"
}
]
},
"award": {
"@id": "/awards/U24DK098085/",
"contact_pi": {
"@id": "/users/e385b015-66c4-48cd-b4f2-884af615dade/",
"title": "Joyce Niland"
},
"title": "Integrated Islet Distribution Program"
},
"control_for": [],
"creation_timestamp": "2025-01-09T23:44:53.764686+00:00",
"donors": [
{
"@id": "/human-donors/PKBDO2444UOCY/",
"accession": "PKBDO2444UOCY",
"aliases": [
"joyce-niland:SAMN12022246"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/PKBDS8427QUCQ/"
],
"lab": {
"@id": "/labs/joyce-niland/",
"title": "Joyce Niland, CoH"
},
"preferred_assay_title": "scRNA-seq",
"release_timestamp": "2025-01-10T05:46:55.641318+00:00",
"samples": [
{
"@id": "/primary-islet/PKBSM1414OXUT/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM1414OXUT",
"aliases": [
"joyce-niland:SAMN12022246_scRNAseq_secondaryBiosample_untreated"
],
"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": [
"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": "fae9d54a-34eb-43c2-a2ed-9ffa884467cb"
}