{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1953KIOT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1953KIOT",
"aliases": [
"lea-starita:F9-DMS-Heavy-chain-antibody-Tile2-Replicate1-Bin3-FileSet_idan",
"igvf:my-alias"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003659/",
"term_name": "in vitro CRISPR screen assay"
},
"audit": {
"ERROR": [
{
"category": "inconsistent related donors",
"detail": "Human donor [IGVFDO1183RRBM](/human-donors/IGVFDO1183RRBM/) has [IGVFDO9571CSNU](/human-donors/IGVFDO9571CSNU/) as a related donor, but [IGVFDO9571CSNU](/human-donors/IGVFDO9571CSNU/) does not mutually specify [IGVFDO1183RRBM](/human-donors/IGVFDO1183RRBM/) as a related donor in `related_donors`. The human donors indicated in the list of related donors are expected to include a mutual link to the corresponding donor.",
"level": 60,
"level_name": "ERROR",
"name": "audit_related_donors",
"path": "/human-donors/IGVFDO1183RRBM/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO1183RRBM](/human-donors/IGVFDO1183RRBM/) has in progress subobject publication [a8e3cb8d-8edd-45b3-9ec7-956c4565054e](/publications/a8e3cb8d-8edd-45b3-9ec7-956c4565054e/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO1183RRBM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4726LPSQ](/in-vitro-systems/IGVFSM4726LPSQ/) has in progress subobject construct library set [IGVFDS1009OBGA](/construct-library-sets/IGVFDS1009OBGA/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM4726LPSQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing modification",
"detail": "Measurement set [IGVFDS1953KIOT](/measurement-sets/IGVFDS1953KIOT/) is a CRISPR screen assay but has no specified `modifications` on its `samples`: [IGVFSM4726LPSQ](/in-vitro-systems/IGVFSM4726LPSQ/). Measurement sets from CRISPR-based assays are expected to have a modification specified on their samples.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_CRISPR_screen_lacking_modifications",
"path": "/measurement-sets/IGVFDS1953KIOT/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1953KIOT](/measurement-sets/IGVFDS1953KIOT/) has no gRNA sequencing `auxiliary_sets`. CRISPR-based measurement sets, with the exception of mutagenesis assays, are expected to link to a gRNA sequencing auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS1953KIOT/"
},
{
"category": "missing protocol",
"detail": "Measurement set [IGVFDS1953KIOT](/measurement-sets/IGVFDS1953KIOT/) 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/IGVFDS1953KIOT/"
}
],
"WARNING": [
{
"category": "inconsistent preferred assay title",
"detail": "Measurement set [IGVFDS1953KIOT](/measurement-sets/IGVFDS1953KIOT/) has `assay_term` in vitro CRISPR screen assay, but `preferred_assay_title` VAMP-seq. Measurement sets are expected to specify an appropriate preferred assay title for its respective assay term.",
"level": 40,
"level_name": "WARNING",
"name": "audit_preferred_assay_title",
"path": "/measurement-sets/IGVFDS1953KIOT/"
}
]
},
"award": {
"@id": "/awards/HG011969/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/65fd52d5-dc5d-457d-9563-a301f7a15ecc/",
"title": "Lea Starita"
},
"title": "The Center for Actionable Variant Analysis; measuring variant function at scale"
},
"control_for": [],
"creation_timestamp": "2024-03-29T00:30:42.387579+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1183RRBM/",
"accession": "IGVFDO1183RRBM",
"aliases": [
"igvf:donor_of_HEK293T"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS7736VVSH/"
],
"lab": {
"@id": "/labs/doug-fowler/",
"title": "Doug Fowler, UW"
},
"notes": "This file_set previously had fcd3ad7e-baa4-4f99-b779-f104501a8df7 submitted as library_construction_platform, but the property library_construction_platform has been now removed.",
"preferred_assay_title": "VAMP-seq",
"release_timestamp": "2024-03-22T23:04:37.145369+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4726LPSQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4726LPSQ",
"aliases": [
"lea-starita:F9-DMS-Heavy-chain-antibody-Tile2-Replicate1-Bin3_idan"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS1009OBGA/",
"accession": "IGVFDS1009OBGA",
"file_set_type": "expression vector library",
"small_scale_gene_list": [
{
"@id": "/genes/ENSG00000127054/",
"geneid": "ENSG00000127054",
"name": "integrator complex subunit 11",
"summary": "INTS11 - ENSG00000127054 (Homo sapiens)",
"symbol": "INTS11"
}
],
"summary": "Expression vector library of tile tile3 of INTS11 (AA 299-461) (sequence variants)"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001184/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HEK293T"
],
"status": "released",
"summary": "HEK293T",
"term_name": "HEK293T"
}
],
"status": "released",
"summary": "HEK293T cell line, female, Homo sapiens transfected with a expression vector library (MOI of 1)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/98fb23d3-0d79-4c3d-981d-01539e6589f1/",
"title": "Idan Gabdank"
},
"summary": "VAMP-seq integrating a expression vector library of tile tile3 of INTS11 (AA 299-461) (sequence variants)",
"uuid": "ff3751eb-8590-4c56-ab5d-5b00960f510a"
}