PKBDS2555JMEA
{
"@context": "/terms/",
"@id": "/analysis-sets/PKBDS2555JMEA/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "PKBDS2555JMEA",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP16141-01_Ruminococcusgnavus_6hr_AnalysisSet"
],
"assay_titles": [
"RNA-seq"
],
"audit": {
"ERROR": [
{
"category": "unexpected input file set",
"detail": "Analysis set [PKBDS2555JMEA](/analysis-sets/PKBDS2555JMEA/) links to file set(s): [PKBDS1198BAXP](/measurement-sets/PKBDS1198BAXP/) 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/PKBDS2555JMEA/"
}
],
"WARNING": [
{
"category": "missing tier 1 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 1 field `sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier1_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 2 field `ethnicities`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 2 field `hba1c`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 2 field `glucose_loweing_theraphy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 2 field `hospital_stay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 2 field `donation_type`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 2 field `cause_of_death`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier2_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `dbxrefs`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `phenotypic_features`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `family_history_of_diabetes`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `family_history_of_diabetes_relationship`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `genetic_ethnicities`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `genetic_sex`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `diabetes_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `c_peptide`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_gada`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_gada_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_gada_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_ia2`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_ia2_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_ia2_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_iaa`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_iaa_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_iaa_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_znt8`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_znt8_assay`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `aab_znt8_value`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `hla_typing`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `other_therapy`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `publication_identifiers`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `pancreas_tissue_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `documents`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `url`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `derived_diabetes_status`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `data_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 3 field",
"detail": "Human donor [PKBDO5743XPEP](/human-donors/PKBDO5743XPEP/) is missing tier 3 field `related_donors`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_tier3_fields",
"path": "/human-donors/PKBDO5743XPEP/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8000XBDB](/primary-islet/PKBSM8000XBDB/) is missing tier 2 field `rrid`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8000XBDB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8000XBDB](/primary-islet/PKBSM8000XBDB/) is missing tier 2 field `organ_source`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8000XBDB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8000XBDB](/primary-islet/PKBSM8000XBDB/) is missing tier 2 field `prep_viability`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8000XBDB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8000XBDB](/primary-islet/PKBSM8000XBDB/) is missing tier 2 field `warm_ischaemia_duration`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8000XBDB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8000XBDB](/primary-islet/PKBSM8000XBDB/) is missing tier 2 field `hand_picked`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8000XBDB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8000XBDB](/primary-islet/PKBSM8000XBDB/) is missing tier 2 field `pre_shipment_culture_time`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8000XBDB/"
},
{
"category": "missing tier 2 field",
"detail": "Human donor [PKBSM8000XBDB](/primary-islet/PKBSM8000XBDB/) is missing tier 2 field `islet_function_available`.",
"level": 40,
"level_name": "WARNING",
"name": "audit_desired_fields",
"path": "/primary-islet/PKBSM8000XBDB/"
},
{
"category": "missing derived from",
"detail": "Analysis set [PKBDS2555JMEA](/analysis-sets/PKBDS2555JMEA/) links to file(s) [PKBFI1241GNZV](/alignment-files/PKBFI1241GNZV/), [PKBFI3248KWHP](/alignment-files/PKBFI3248KWHP/), [PKBFI2091LUIJ](/tabular-files/PKBFI2091LUIJ/) 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/PKBDS2555JMEA/"
}
]
},
"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": "2026-01-05T18:50:26.485969+00:00",
"description": "Analysis set of RNA-seq for human donor HP-16141-01, Ruminococcus gnavus (RG) for 6 hr",
"donors": [
{
"@id": "/human-donors/PKBDO5743XPEP/",
"accession": "PKBDO5743XPEP",
"aliases": [
"prodo:HP16141-01"
],
"gender": "Male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/alignment-files/PKBFI1241GNZV/",
"accession": "PKBFI1241GNZV",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP16141-01_Ruminococcusgnavus_6hr_AnalysisSet.SAMN11785372.Aligned.toTranscriptome.out.bam"
],
"content_type": "transcriptome alignments",
"creation_timestamp": "2026-01-08T19:43:33.737848+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI1241GNZV/@@download/PKBFI1241GNZV.bam"
},
{
"@id": "/alignment-files/PKBFI8903OPYD/",
"accession": "PKBFI8903OPYD",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP16141-01_Ruminococcusgnavus_6hr_AnalysisSet.SAMN11785372.Aligned.sortedByCoord.out.md.bam"
],
"content_type": "alignments",
"creation_timestamp": "2026-01-08T19:43:34.807513+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI8903OPYD/@@download/PKBFI8903OPYD.bam"
},
{
"@id": "/alignment-files/PKBFI3248KWHP/",
"accession": "PKBFI3248KWHP",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP16141-01_Ruminococcusgnavus_6hr_AnalysisSet.SAMN11785372.Aligned.sortedByCoord.out.bam"
],
"content_type": "alignments",
"creation_timestamp": "2026-01-08T19:43:32.606920+00:00",
"file_format": "bam",
"href": "/alignment-files/PKBFI3248KWHP/@@download/PKBFI3248KWHP.bam"
},
{
"@id": "/tabular-files/PKBFI3312TXYQ/",
"accession": "PKBFI3312TXYQ",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP16141-01_Ruminococcusgnavus_6hr_AnalysisSet.SAMN11785372.metrics.tsv"
],
"content_type": "QC metrics",
"creation_timestamp": "2026-01-08T20:05:07.057990+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI3312TXYQ/@@download/PKBFI3312TXYQ.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI3650JCMP/",
"accession": "PKBFI3650JCMP",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP16141-01_Ruminococcusgnavus_6hr_AnalysisSet.SAMN11785372.rsem.isoforms.results"
],
"content_type": "element quantifications",
"creation_timestamp": "2026-01-08T20:05:09.892619+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI3650JCMP/@@download/PKBFI3650JCMP.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI2091LUIJ/",
"accession": "PKBFI2091LUIJ",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP16141-01_Ruminococcusgnavus_6hr_AnalysisSet.SAMN11785372.Log.final.out"
],
"content_type": "QC metrics",
"creation_timestamp": "2026-01-08T20:05:05.231228+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI2091LUIJ/@@download/PKBFI2091LUIJ.txt.gz"
},
{
"@id": "/tabular-files/PKBFI3117PHKO/",
"accession": "PKBFI3117PHKO",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP16141-01_Ruminococcusgnavus_6hr_AnalysisSet.SAMN11785372.rsem.genes.results"
],
"content_type": "element quantifications",
"creation_timestamp": "2026-01-08T20:05:08.577621+00:00",
"file_format": "tsv",
"href": "/tabular-files/PKBFI3117PHKO/@@download/PKBFI3117PHKO.tsv.gz"
},
{
"@id": "/tabular-files/PKBFI8747FHEB/",
"accession": "PKBFI8747FHEB",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP16141-01_Ruminococcusgnavus_6hr_AnalysisSet.SAMN11785372.Aligned.sortedByCoord.out.md.marked_dup_metrics.txt"
],
"content_type": "QC metrics",
"creation_timestamp": "2026-01-08T20:05:06.228935+00:00",
"file_format": "txt",
"href": "/tabular-files/PKBFI8747FHEB/@@download/PKBFI8747FHEB.txt.gz"
}
],
"input_file_set_for": [],
"input_file_sets": [
{
"@id": "/measurement-sets/PKBDS1198BAXP/",
"accession": "PKBDS1198BAXP",
"aliases": [
"pankbase-consortium:bulkIslets_GSE131320_HP16141-01_Ruminococcusgnavus_6hr_MeasurementSet"
],
"file_set_type": "experimental data"
}
],
"lab": {
"@id": "/labs/pankbase-consortium/"
},
"publication_identifiers": [
"PMID:31781116",
"PMCID:PMC6857727",
"doi:10.3389/fimmu.2019.02623"
],
"release_timestamp": "2026-03-03T18:32:52.845299+00:00",
"samples": [
{
"@id": "/primary-islet/PKBSM8000XBDB/",
"@type": [
"PrimaryIslet",
"Biosample",
"Sample",
"Item"
],
"accession": "PKBSM8000XBDB",
"aliases": [
"prodo:HP16141-01_bulkIslet_secondaryBiosample_Ruminococcusgnavus_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 Ruminococcus gnavus for 6 hours",
"treatments": [
"/treatments/627990c0-6271-4ef2-be52-2c3e4c4d56d8/"
]
}
],
"schema_version": "8",
"status": "released",
"submitted_by": {
"@id": "/users/5e3038c4-baa5-4589-b3d8-ad2fe634e826/",
"title": "Ying Sun"
},
"submitted_files_timestamp": "2026-01-08T19:43:32.606920+00:00",
"uuid": "79c44c8d-92b0-47f6-937d-0faf0b46deb9"
}
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
