{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1317BKCD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1317BKCD",
"aliases": [
"lior-pachter:share_seq"
],
"assay_term": {
"@id": "/assay-terms/NTR_0000739/",
"term_name": "SHARE-seq"
},
"audit": {
"ERROR": [
{
"category": "inconsistent document type",
"detail": "Signal file [IGVFFI4189XCUY](/signal-files/IGVFFI4189XCUY/) 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": "/signal-files/IGVFFI4189XCUY/"
},
{
"category": "upload status not validated",
"detail": "Signal file [IGVFFI4189XCUY](/signal-files/IGVFFI4189XCUY/) has `upload_status` pending. Files are expected to be validated.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/signal-files/IGVFFI4189XCUY/"
},
{
"category": "unexpected CCF ID",
"detail": "Tissue [IGVFSM3939SHHK](/tissues/IGVFSM3939SHHK/) has a `ccf_id` but is associated with a non-human donor. Non-human tissues are not expected to specify a common coordinate framework identifier (CCF ID).",
"level": 60,
"level_name": "ERROR",
"name": "audit_tissue_ccf_id",
"path": "/tissues/IGVFSM3939SHHK/"
},
{
"category": "inconsistent document type",
"detail": "Signal file [IGVFFI9483IBVC](/signal-files/IGVFFI9483IBVC/) 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": "/signal-files/IGVFFI9483IBVC/"
},
{
"category": "upload status not validated",
"detail": "Signal file [IGVFFI9483IBVC](/signal-files/IGVFFI9483IBVC/) has `upload_status` pending. Files are expected to be validated.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/signal-files/IGVFFI9483IBVC/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1317BKCD](/measurement-sets/IGVFDS1317BKCD/) has deleted subobject assay term [NTR_0000739](/assay-terms/NTR_0000739/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1317BKCD/"
},
{
"category": "mismatched status",
"detail": "Archived rodent donor [IGVFDO8570HWEN](/rodent-donors/IGVFDO8570HWEN/) has in progress subobject document [d8ce793f-933b-45ea-9611-1c3f80cb7e11](/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/rodent-donors/IGVFDO8570HWEN/"
},
{
"category": "mismatched status",
"detail": "Archived rodent donor [IGVFDO8570HWEN](/rodent-donors/IGVFDO8570HWEN/) has in progress subobject phenotypic feature [c81e1c40-3eb5-4636-93b4-27e3d56e276d](/phenotypic-features/c81e1c40-3eb5-4636-93b4-27e3d56e276d/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/rodent-donors/IGVFDO8570HWEN/"
},
{
"category": "mismatched status",
"detail": "Archived tissue [IGVFSM3939SHHK](/tissues/IGVFSM3939SHHK/) has in progress subobject document [d8ce793f-933b-45ea-9611-1c3f80cb7e11](/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM3939SHHK/"
},
{
"category": "mismatched status",
"detail": "Archived tissue [IGVFSM3939SHHK](/tissues/IGVFSM3939SHHK/) has in progress subobject treatment [612fd456-886b-412d-b935-c5cac7a1df21](/treatments/612fd456-886b-412d-b935-c5cac7a1df21/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM3939SHHK/"
},
{
"category": "mismatched status",
"detail": "Archived tissue [IGVFSM3939SHHK](/tissues/IGVFSM3939SHHK/) has in progress subobject phenotype term [MONDO_0015924](/phenotype-terms/MONDO_0015924/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM3939SHHK/"
},
{
"category": "NTR term ID",
"detail": "Assay term for [NTR_0000739](/assay-terms/NTR_0000739/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/assay-terms/NTR_0000739/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing multiome size",
"detail": "Measurement set [IGVFDS1317BKCD](/measurement-sets/IGVFDS1317BKCD/) has no `multiome_size`. Measurement sets from multiome assays are expected to specify a multiome size.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_related_multiome_datasets",
"path": "/measurement-sets/IGVFDS1317BKCD/"
},
{
"category": "missing protocol",
"detail": "Measurement set [IGVFDS1317BKCD](/measurement-sets/IGVFDS1317BKCD/) 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/IGVFDS1317BKCD/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS1317BKCD](/measurement-sets/IGVFDS1317BKCD/) 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/IGVFDS1317BKCD/"
},
{
"category": "inconsistent preferred assay title",
"detail": "Measurement set [IGVFDS1317BKCD](/measurement-sets/IGVFDS1317BKCD/) has `assay_term` SHARE-seq, but `preferred_assay_title` SHARE-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/IGVFDS1317BKCD/"
}
]
},
"award": {
"@id": "/awards/HG012077/",
"component": "mapping",
"contact_pi": {
"@id": "/users/2c33e192-e815-4384-a220-72a0992cbe24/",
"title": "Ali Mortazavi"
},
"title": "Center for Mouse Genomic Variation at Single Cell Resolution"
},
"control_for": [],
"creation_timestamp": "2023-04-27T18:51:25.830110+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO8570HWEN/",
"accession": "IGVFDO8570HWEN",
"sex": "male",
"status": "archived",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/signal-files/IGVFFI9483IBVC/",
"accession": "IGVFFI9483IBVC",
"aliases": [
"lior-pachter:raw_signal"
],
"assembly": "GRCh38",
"content_type": "raw signal",
"creation_timestamp": "2023-05-24T17:50:57.528672+00:00",
"file_format": "bigWig",
"href": "/signal-files/IGVFFI9483IBVC/@@download/IGVFFI9483IBVC.bigWig",
"s3_uri": "s3://igvf-files-dev/2023/05/24/1ba0f218-5787-4110-898f-5e3fd6b699c1/IGVFFI9483IBVC.bigWig",
"submitted_file_name": "/Users/igvf/igvf_files/raw_signal.bigWig",
"upload_status": "pending"
},
{
"@id": "/signal-files/IGVFFI4189XCUY/",
"accession": "IGVFFI4189XCUY",
"aliases": [
"lior-pachter:unstranded_signal_p_value"
],
"assembly": "GRCh38",
"content_type": "signal p-value",
"creation_timestamp": "2023-05-24T17:54:45.358751+00:00",
"file_format": "bigWig",
"href": "/signal-files/IGVFFI4189XCUY/@@download/IGVFFI4189XCUY.bigWig",
"s3_uri": "s3://igvf-files-dev/2023/05/24/33f720f7-0ad8-4c3b-b2ff-61fe273f4d2a/IGVFFI4189XCUY.bigWig",
"submitted_file_name": "/Users/igvf/igvf_files/signal_p_value.bigWig",
"upload_status": "pending"
}
],
"input_for": [],
"lab": {
"@id": "/labs/lior-pachter/",
"title": "Lior Pachter, Caltech"
},
"notes": "This meausurement_set previously linked to https://github.com/IGVF/seqspec/blob/main/assays/SHARE-seq/spec.yaml, but the property for submitting associated seqspec links has been moved to SequenceFile where it should be submitted as a link to the seqspec yaml file submitted as a ConfigurationFile instead.",
"preferred_assay_title": "SHARE-seq",
"release_timestamp": "2023-04-27T18:51:25.802339+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM3939SHHK/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3939SHHK",
"classifications": [
"tissue"
],
"disease_terms": [
{
"@id": "/phenotype-terms/MONDO_0015924/",
"term_name": "pulmonary arterial hypertension"
}
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0002369/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:adrenal gland"
],
"status": "released",
"summary": "adrenal gland",
"term_name": "adrenal gland"
}
],
"status": "archived",
"summary": "adrenal gland tissue (cellular sub pool: AT9029), male, Mus musculus B6XCast (15-25 months) associated with pulmonary arterial hypertension, treated with 10 mM leucine for 6 hours",
"taxa": "Mus musculus",
"treatments": [
{
"@id": "/treatments/612fd456-886b-412d-b935-c5cac7a1df21/",
"treatment_term_name": "leucine"
}
]
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/1e75d989-a438-4d77-a451-8a297fd3636e/",
"title": "Ian Whaling"
},
"submitted_files_timestamp": "2023-05-24T17:50:57.528672+00:00",
"summary": "SHARE-seq (SHARE-seq)",
"uuid": "269ae1c1-060c-4ef4-8903-2284689779ed"
}