{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3532HUSQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3532HUSQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3532HUSQ](/measurement-sets/IGVFDS3532HUSQ/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS3532HUSQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3532HUSQ](/measurement-sets/IGVFDS3532HUSQ/) has sequence file(s) [IGVFFI9011JZSP](/sequence-files/IGVFFI9011JZSP/), [IGVFFI1757ZMTH](/sequence-files/IGVFFI1757ZMTH/), [IGVFFI5236DVMS](/sequence-files/IGVFFI5236DVMS/), [IGVFFI5093CIBV](/sequence-files/IGVFFI5093CIBV/), [IGVFFI4336OOGL](/sequence-files/IGVFFI4336OOGL/), [IGVFFI9902DTNW](/sequence-files/IGVFFI9902DTNW/), [IGVFFI9425XFLN](/sequence-files/IGVFFI9425XFLN/), [IGVFFI5937UKNN](/sequence-files/IGVFFI5937UKNN/), [IGVFFI2645LXDJ](/sequence-files/IGVFFI2645LXDJ/), [IGVFFI7697CPHD](/sequence-files/IGVFFI7697CPHD/), [IGVFFI2608UIFP](/sequence-files/IGVFFI2608UIFP/), [IGVFFI4499KBGC](/sequence-files/IGVFFI4499KBGC/), [IGVFFI8226JTAF](/sequence-files/IGVFFI8226JTAF/), [IGVFFI5134PITR](/sequence-files/IGVFFI5134PITR/), [IGVFFI8035JAYZ](/sequence-files/IGVFFI8035JAYZ/), [IGVFFI4708YAVO](/sequence-files/IGVFFI4708YAVO/), [IGVFFI8167CDYG](/sequence-files/IGVFFI8167CDYG/), [IGVFFI4202SXOX](/sequence-files/IGVFFI4202SXOX/), [IGVFFI6430CSSG](/sequence-files/IGVFFI6430CSSG/), [IGVFFI7953IKDE](/sequence-files/IGVFFI7953IKDE/), [IGVFFI7788LKMY](/sequence-files/IGVFFI7788LKMY/), [IGVFFI2668LZJW](/sequence-files/IGVFFI2668LZJW/), [IGVFFI2203XIZT](/sequence-files/IGVFFI2203XIZT/), [IGVFFI7865JYFJ](/sequence-files/IGVFFI7865JYFJ/), [IGVFFI6234VYOB](/sequence-files/IGVFFI6234VYOB/), [IGVFFI7852SUZC](/sequence-files/IGVFFI7852SUZC/), [IGVFFI2450ULEZ](/sequence-files/IGVFFI2450ULEZ/), [IGVFFI2640KDXP](/sequence-files/IGVFFI2640KDXP/), [IGVFFI6368TQSJ](/sequence-files/IGVFFI6368TQSJ/), [IGVFFI0892EAHG](/sequence-files/IGVFFI0892EAHG/), [IGVFFI3015OBRV](/sequence-files/IGVFFI3015OBRV/), [IGVFFI6740EQGP](/sequence-files/IGVFFI6740EQGP/), [IGVFFI2693TTKH](/sequence-files/IGVFFI2693TTKH/), [IGVFFI3895LVSP](/sequence-files/IGVFFI3895LVSP/), [IGVFFI5717NMGE](/sequence-files/IGVFFI5717NMGE/), [IGVFFI0505WQCE](/sequence-files/IGVFFI0505WQCE/), [IGVFFI5997HFUY](/sequence-files/IGVFFI5997HFUY/), [IGVFFI3373KOZN](/sequence-files/IGVFFI3373KOZN/), [IGVFFI3648SBAZ](/sequence-files/IGVFFI3648SBAZ/), [IGVFFI7637WAPF](/sequence-files/IGVFFI7637WAPF/), [IGVFFI1380XBAY](/sequence-files/IGVFFI1380XBAY/), [IGVFFI7847SIPQ](/sequence-files/IGVFFI7847SIPQ/), [IGVFFI3892YYBS](/sequence-files/IGVFFI3892YYBS/), [IGVFFI3983GSVX](/sequence-files/IGVFFI3983GSVX/), [IGVFFI6303CIJR](/sequence-files/IGVFFI6303CIJR/), [IGVFFI2828PORV](/sequence-files/IGVFFI2828PORV/), [IGVFFI4961ENEV](/sequence-files/IGVFFI4961ENEV/), [IGVFFI9480LVQQ](/sequence-files/IGVFFI9480LVQQ/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS3532HUSQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3532HUSQ](/measurement-sets/IGVFDS3532HUSQ/) has sequence file(s): [IGVFFI9011JZSP](/sequence-files/IGVFFI9011JZSP/), [IGVFFI1757ZMTH](/sequence-files/IGVFFI1757ZMTH/), [IGVFFI5236DVMS](/sequence-files/IGVFFI5236DVMS/), [IGVFFI5093CIBV](/sequence-files/IGVFFI5093CIBV/), [IGVFFI4336OOGL](/sequence-files/IGVFFI4336OOGL/), [IGVFFI9902DTNW](/sequence-files/IGVFFI9902DTNW/), [IGVFFI9425XFLN](/sequence-files/IGVFFI9425XFLN/), [IGVFFI5937UKNN](/sequence-files/IGVFFI5937UKNN/), [IGVFFI2645LXDJ](/sequence-files/IGVFFI2645LXDJ/), [IGVFFI7697CPHD](/sequence-files/IGVFFI7697CPHD/), [IGVFFI2608UIFP](/sequence-files/IGVFFI2608UIFP/), [IGVFFI4499KBGC](/sequence-files/IGVFFI4499KBGC/), [IGVFFI8226JTAF](/sequence-files/IGVFFI8226JTAF/), [IGVFFI5134PITR](/sequence-files/IGVFFI5134PITR/), [IGVFFI8035JAYZ](/sequence-files/IGVFFI8035JAYZ/), [IGVFFI4708YAVO](/sequence-files/IGVFFI4708YAVO/), [IGVFFI8167CDYG](/sequence-files/IGVFFI8167CDYG/), [IGVFFI4202SXOX](/sequence-files/IGVFFI4202SXOX/), [IGVFFI6430CSSG](/sequence-files/IGVFFI6430CSSG/), [IGVFFI7953IKDE](/sequence-files/IGVFFI7953IKDE/), [IGVFFI7788LKMY](/sequence-files/IGVFFI7788LKMY/), [IGVFFI2668LZJW](/sequence-files/IGVFFI2668LZJW/), [IGVFFI2203XIZT](/sequence-files/IGVFFI2203XIZT/), [IGVFFI7865JYFJ](/sequence-files/IGVFFI7865JYFJ/), [IGVFFI6234VYOB](/sequence-files/IGVFFI6234VYOB/), [IGVFFI7852SUZC](/sequence-files/IGVFFI7852SUZC/), [IGVFFI2450ULEZ](/sequence-files/IGVFFI2450ULEZ/), [IGVFFI2640KDXP](/sequence-files/IGVFFI2640KDXP/), [IGVFFI6368TQSJ](/sequence-files/IGVFFI6368TQSJ/), [IGVFFI0892EAHG](/sequence-files/IGVFFI0892EAHG/), [IGVFFI3015OBRV](/sequence-files/IGVFFI3015OBRV/), [IGVFFI6740EQGP](/sequence-files/IGVFFI6740EQGP/), [IGVFFI2693TTKH](/sequence-files/IGVFFI2693TTKH/), [IGVFFI3895LVSP](/sequence-files/IGVFFI3895LVSP/), [IGVFFI5717NMGE](/sequence-files/IGVFFI5717NMGE/), [IGVFFI0505WQCE](/sequence-files/IGVFFI0505WQCE/), [IGVFFI5997HFUY](/sequence-files/IGVFFI5997HFUY/), [IGVFFI3373KOZN](/sequence-files/IGVFFI3373KOZN/), [IGVFFI3648SBAZ](/sequence-files/IGVFFI3648SBAZ/), [IGVFFI7637WAPF](/sequence-files/IGVFFI7637WAPF/), [IGVFFI1380XBAY](/sequence-files/IGVFFI1380XBAY/), [IGVFFI7847SIPQ](/sequence-files/IGVFFI7847SIPQ/), [IGVFFI3892YYBS](/sequence-files/IGVFFI3892YYBS/), [IGVFFI3983GSVX](/sequence-files/IGVFFI3983GSVX/), [IGVFFI6303CIJR](/sequence-files/IGVFFI6303CIJR/), [IGVFFI2828PORV](/sequence-files/IGVFFI2828PORV/), [IGVFFI4961ENEV](/sequence-files/IGVFFI4961ENEV/), [IGVFFI9480LVQQ](/sequence-files/IGVFFI9480LVQQ/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS3532HUSQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6349GRPM](/in-vitro-systems/IGVFSM6349GRPM/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6349GRPM/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6349GRPM](/in-vitro-systems/IGVFSM6349GRPM/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM6349GRPM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3532HUSQ](/measurement-sets/IGVFDS3532HUSQ/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS3532HUSQ/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"file_set_type": "guide library",
"status": "in progress",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:50:13.806889+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9011JZSP/",
"accession": "IGVFFI9011JZSP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep12_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:20:52.610838+00:00",
"file_format": "fastq",
"file_size": 5587666,
"href": "/sequence-files/IGVFFI9011JZSP/@@download/IGVFFI9011JZSP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/625e0abe-278f-41fb-a5f8-87cc06d7aa91/IGVFFI9011JZSP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep12_S384_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1757ZMTH/",
"accession": "IGVFFI1757ZMTH",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:18:59.882932+00:00",
"file_format": "fastq",
"file_size": 4965861,
"href": "/sequence-files/IGVFFI1757ZMTH/@@download/IGVFFI1757ZMTH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5fabb88d-f6a7-4ec1-9be6-cd3651e91867/IGVFFI1757ZMTH.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep1_S373_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5236DVMS/",
"accession": "IGVFFI5236DVMS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:19:08.998289+00:00",
"file_format": "fastq",
"file_size": 6160542,
"href": "/sequence-files/IGVFFI5236DVMS/@@download/IGVFFI5236DVMS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e0edf250-bc33-44af-b38a-afde72b3002e/IGVFFI5236DVMS.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5093CIBV/",
"accession": "IGVFFI5093CIBV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:21:18.551143+00:00",
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"file_size": 5132904,
"href": "/sequence-files/IGVFFI5093CIBV/@@download/IGVFFI5093CIBV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/97860069-3e18-40a5-a17a-57a583ff9b56/IGVFFI5093CIBV.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep2_S374_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4336OOGL/",
"accession": "IGVFFI4336OOGL",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:22:10.971614+00:00",
"file_format": "fastq",
"file_size": 1616198,
"href": "/sequence-files/IGVFFI4336OOGL/@@download/IGVFFI4336OOGL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c58941c6-3085-4e94-a20d-a7cf197b3871/IGVFFI4336OOGL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep4_S376_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9902DTNW/",
"accession": "IGVFFI9902DTNW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:23:58.589074+00:00",
"file_format": "fastq",
"file_size": 1443054,
"href": "/sequence-files/IGVFFI9902DTNW/@@download/IGVFFI9902DTNW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/70b4ed7c-4694-4241-913d-f3945f974080/IGVFFI9902DTNW.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep7_S379_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9425XFLN/",
"accession": "IGVFFI9425XFLN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep10_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:19:17.710581+00:00",
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"file_size": 1439534,
"href": "/sequence-files/IGVFFI9425XFLN/@@download/IGVFFI9425XFLN.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5937UKNN/",
"accession": "IGVFFI5937UKNN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep11_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:20:18.645106+00:00",
"file_format": "fastq",
"file_size": 6163705,
"href": "/sequence-files/IGVFFI5937UKNN/@@download/IGVFFI5937UKNN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4055c136-cf39-433b-b82b-885eaae3307f/IGVFFI5937UKNN.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2645LXDJ/",
"accession": "IGVFFI2645LXDJ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:23:29.119905+00:00",
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"file_size": 1480117,
"href": "/sequence-files/IGVFFI2645LXDJ/@@download/IGVFFI2645LXDJ.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep6_S378_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7697CPHD/",
"accession": "IGVFFI7697CPHD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep10_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:19:43.699277+00:00",
"file_format": "fastq",
"file_size": 5990829,
"href": "/sequence-files/IGVFFI7697CPHD/@@download/IGVFFI7697CPHD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0bcf7980-dd0a-45e4-8b6a-875e81abb783/IGVFFI7697CPHD.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinD-PCRrep10_S382_R2_001.fastq.gz",
"upload_status": "validated"
},
{
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"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "b04f2097-2568-42fe-8a02-f703247ea289"
}