{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3910MZMQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3910MZMQ",
"aliases": [
"igvf:multiome_scatac_seq"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"ERROR": [
{
"category": "inconsistent document type",
"detail": "Sequence file [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/) has `file_format_specification` [d8ce793f-933b-45ea-9611-1c3f80cb7e11](/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/) with `document_type` plasmid map. File format specifications are excepted to be documents have type file format specification.",
"level": 60,
"level_name": "ERROR",
"name": "audit_file_format_specifications",
"path": "/sequence-files/IGVFFI2658WGRW/"
},
{
"category": "upload status not validated",
"detail": "Sequence file [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/) has `upload_status` pending. Files are expected to be validated.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/sequence-files/IGVFFI2658WGRW/"
},
{
"category": "missing related files",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has seqspec configuration file [IGVFFI1190FVNM](/configuration-files/IGVFFI1190FVNM/) which links to sequence file(s): [IGVFFI4710CQYT](/sequence-files/IGVFFI4710CQYT/) which do not link to this file set. All files associated with a seqspec (both sequencing and seqspec files) are expected to be linked to the same file set.",
"level": 60,
"level_name": "ERROR",
"name": "audit_files_associated_with_incorrect_fileset",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "unexpected multiome size",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has `multiome_size`. Only measurement sets from multiome assays are expected to specify a multiome size.",
"level": 60,
"level_name": "ERROR",
"name": "audit_related_multiome_datasets",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "upload status not validated",
"detail": "Configuration file [IGVFFI1190FVNM](/configuration-files/IGVFFI1190FVNM/) has `upload_status` pending. Files are expected to be validated.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/configuration-files/IGVFFI1190FVNM/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has in progress subobject in vitro system [IGVFSM2795QSOV](/in-vitro-systems/IGVFSM2795QSOV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO9208RPQQ](/human-donors/IGVFDO9208RPQQ/) has in progress subobject publication [59c63dd9-b5fb-4768-8045-ed8c0003a40c](/publications/59c63dd9-b5fb-4768-8045-ed8c0003a40c/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9208RPQQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has sequence file(s) [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/), [IGVFFI9343YZPC](/sequence-files/IGVFFI9343YZPC/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has sequence file(s): [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "missing NIH certification",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has a sample [IGVFSM2795QSOV](/in-vitro-systems/IGVFSM2795QSOV/) that lacks any `institutional_certificates` issued to the lab that submitted this file set. Measurement sets for mapping assays or controlled access characterization 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/IGVFDS3910MZMQ/"
},
{
"category": "missing protocol",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) 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/IGVFDS3910MZMQ/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "inconsistent preferred assay title",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has `assay_term` single-cell ATAC-seq, 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/IGVFDS3910MZMQ/"
}
]
},
"award": {
"@id": "/awards/HG012051/",
"component": "networks",
"contact_pi": {
"@id": "/users/7138e67a-2af5-4a48-90bc-04ea95b53c78/",
"title": "Danwei Huangfu"
},
"title": "Genomic control of gene regulatory networks governing early human lineage decisions"
},
"control_for": [
{
"@id": "/measurement-sets/IGVFDS5330YIDV/",
"accession": "IGVFDS5330YIDV",
"aliases": [
"igvf:basic_measurement_set"
]
}
],
"creation_timestamp": "2023-04-27T18:51:25.198759+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2658WGRW/",
"accession": "IGVFFI2658WGRW",
"aliases": [
"igvf:example_fastq_01",
"jay-shendure:example_fastq_01_alt_alias"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-05-23T20:29:58.899328+00:00",
"file_format": "fastq",
"file_size": 9898933494,
"href": "/sequence-files/IGVFFI2658WGRW/@@download/IGVFFI2658WGRW.fastq.gz",
"s3_uri": "s3://igvf-files-dev/2023/05/23/21cc5af6-5c36-4913-af85-440b4b61f383/IGVFFI2658WGRW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0004203/",
"term_name": "Illumina HiSeq 2000"
},
"submitted_file_name": "/path/to/sequence_file.fastq.gz",
"upload_status": "pending"
},
{
"@id": "/configuration-files/IGVFFI1190FVNM/",
"accession": "IGVFFI1190FVNM",
"aliases": [
"igvf:example_configuration_file_01"
],
"content_type": "seqspec",
"creation_timestamp": "2023-09-19T20:11:56.580713+00:00",
"file_format": "yaml",
"file_size": 1240000,
"href": "/configuration-files/IGVFFI1190FVNM/@@download/IGVFFI1190FVNM.yaml.gz",
"s3_uri": "s3://igvf-files-dev/2023/09/19/718d7475-e11b-4a1f-bdfa-899abf6c711f/IGVFFI1190FVNM.yaml",
"submitted_file_name": "/path/to/seqspec.yaml",
"upload_status": "pending"
},
{
"@id": "/sequence-files/IGVFFI9343YZPC/",
"accession": "IGVFFI9343YZPC",
"content_type": "PacBio subreads",
"controlled_access": false,
"creation_timestamp": "2023-05-08T17:16:55.623037+00:00",
"file_format": "bam",
"file_size": 235234435,
"href": "/sequence-files/IGVFFI9343YZPC/@@download/IGVFFI9343YZPC.bam",
"s3_uri": "s3://igvf-files-dev/2023/05/08/29b7f066-9d13-4663-8fe2-cd6847ec9c5c/IGVFFI9343YZPC.bam",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0004203/",
"term_name": "Illumina HiSeq 2000"
},
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/danwei-huangfu/",
"title": "Danwei Huangfu, MSKCC"
},
"multiome_size": 2,
"preferred_assay_title": "VAMP-seq",
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS2075SWXE/",
"accession": "IGVFDS2075SWXE"
}
],
"release_timestamp": "2023-04-27T18:51:25.181642+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2795QSOV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2795QSOV",
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0948BMCL/",
"accession": "IGVFDS0948BMCL",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting TF binding sites, phenotype-associated variants genome-wide associated with DiGeorge syndrome"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "in progress",
"summary": "K562 cell line, female, Homo sapiens transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/1e75d989-a438-4d77-a451-8a297fd3636e/",
"title": "Ian Whaling"
},
"submitted_files_timestamp": "2023-05-08T17:16:55.623037+00:00",
"summary": "VAMP-seq integrating a guide (sgRNA) library targeting TF binding sites, phenotype-associated variants genome-wide associated with DiGeorge syndrome",
"uuid": "5663d0c7-faee-4c10-8ef5-c827fd74ad28"
}