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newstudy/mixed_nfosi_2022 #1736

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newstudy/mixed_nfosi_2022 #1736

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1b06d33
Add mixed_nfosi_2022
anngvu Nov 9, 2022
80eda99
Update citation
anngvu Nov 9, 2022
a51692c
Add LICENSE
anngvu Nov 16, 2022
363e23f
Update meta
anngvu Nov 16, 2022
b6b8b42
Fix cell line sample file manually
anngvu Nov 22, 2022
e23dc9d
Generate case lists
anngvu Nov 22, 2022
635cd21
Update name
anngvu Nov 22, 2022
438ee64
Update validation html report
anngvu Nov 22, 2022
e811deb
Use v3 of mutations data
anngvu Jan 18, 2023
914ea35
Update validation result
anngvu Jan 18, 2023
3cdb88c
Merge branch 'cBioPortal:master' into newstudy/nfosi_2022
anngvu Jan 18, 2023
2f8ea47
Replace bioRxiv citation with better citation
anngvu Jan 19, 2023
d8ad6a4
Update study name per review suggestion
anngvu Jan 30, 2023
bf74461
Use cleaner citation format per review suggestion
anngvu Jan 30, 2023
43c6ca0
Add pmid field to study meta per review suggestion
anngvu Jan 30, 2023
51e8efe
Add reference_genome field per review suggestion
anngvu Jan 30, 2023
cc7f48e
Recategorize type_of_cancer per review suggestion
anngvu Jan 30, 2023
660fd5d
Rename files, no longer use _extended suffix
anngvu Jan 30, 2023
b498f94
Rename all case list file to cases_all.txt per review suggestion
anngvu Jan 30, 2023
97184bf
Use nst in study id per suggestion
anngvu Jan 31, 2023
d929f69
Whoops, propagate study id changes to case list files
anngvu Jan 31, 2023
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150 changes: 150 additions & 0 deletions public/mixed_nfosi_2022/LICENSE
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6 changes: 6 additions & 0 deletions public/mixed_nfosi_2022/case_lists/cases_all.txt
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cancer_study_identifier: nst_nfosi_2022
stable_id: nst_nfosi_2022_all
case_list_name: All samples
case_list_description: All samples (19 samples)
case_list_category: all_cases_in_study
case_list_ids: 2-010_Neurofibroma 2-026_Neurofibroma 2-013_Plexiform_Neurofibroma 2-004_Plexiform_Neurofibroma 2-012_Neurofibroma 2-031_Cell_Line 2-017_Neurofibroma 2-021_Neurofibroma 2-019_Neurofibroma 2-029_Neurofibroma 2-023_Plexiform_Neurofibroma 2-014_Neurofibroma 2-001_Plexiform_Neurofibroma 2-006_Plexiform_Neurofibroma 2-032_Plexiform_Neurofibroma 2-015_Plexiform_Neurofibroma 2-031_Malignant_Peripheral_Nerve_Sheath_Tumor 2-016_Neurofibroma 2-015_Neurofibroma
6 changes: 6 additions & 0 deletions public/mixed_nfosi_2022/case_lists/cases_sequenced.txt
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cancer_study_identifier: nst_nfosi_2022
stable_id: nst_nfosi_2022_sequenced
case_list_name: Samples with mutation data
case_list_description: Samples with mutation data (19 samples)
case_list_category: all_cases_with_mutation_data
case_list_ids: 2-010_Neurofibroma 2-026_Neurofibroma 2-013_Plexiform_Neurofibroma 2-014_Neurofibroma 2-001_Plexiform_Neurofibroma 2-006_Plexiform_Neurofibroma 2-004_Plexiform_Neurofibroma 2-032_Plexiform_Neurofibroma 2-015_Plexiform_Neurofibroma 2-016_Neurofibroma 2-012_Neurofibroma 2-031_Malignant_Peripheral_Nerve_Sheath_Tumor 2-031_Cell_Line 2-017_Neurofibroma 2-015_Neurofibroma 2-021_Neurofibroma 2-019_Neurofibroma 2-029_Neurofibroma 2-023_Plexiform_Neurofibroma
23 changes: 23 additions & 0 deletions public/mixed_nfosi_2022/data_clinical_patient.txt
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#PATIENT_ID SEX NF1_GENOTYPE NF2_GENOTYPE AGE
#Patient ID Sex of the patient NF1 genotype of the patient NF2 genotype of the patient Age of patient
#STRING STRING STRING STRING NUMBER
#1 1 1 1 1
PATIENT_ID SEX NF1_GENOTYPE NF2_GENOTYPE AGE
JH-2-001 Female -/- +/+
JH-2-004 Female -/- +/+
JH-2-006 Female -/- +/+
JH-2-010 Male -/- +/+
JH-2-012 Male -/- +/+
JH-2-013 Female -/- +/+
JH-2-014 Male -/- +/+
JH-2-015 Male -/- +/+
JH-2-016 Female -/- +/+
JH-2-017 Male -/- +/+
JH-2-019 Female -/- +/+
JH-2-021 Male -/- +/+
JH-2-023 Male -/- +/+
JH-2-026 Female -/- +/+
JH-2-031_Cell_Line Male +/+
JH-2-031 Male -/- +/+
JH-2-029 Male -/- +/+
JH-2-032 Female -/- +/+
24 changes: 24 additions & 0 deletions public/mixed_nfosi_2022/data_clinical_sample.txt
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#PATIENT_ID SAMPLE_ID TUMOR TISSUE_SITE
#Patient ID Sample ID Tumor type Site of tissue collection
#STRING STRING STRING STRING
#1 1 1 1
PATIENT_ID SAMPLE_ID TUMOR TISSUE_SITE
JH-2-001 2-001_Plexiform_Neurofibroma Plexiform Neurofibroma Primary Tumor
JH-2-004 2-004_Plexiform_Neurofibroma Plexiform Neurofibroma Primary Tumor
JH-2-006 2-006_Plexiform_Neurofibroma Plexiform Neurofibroma Primary Tumor
JH-2-010 2-010_Neurofibroma Neurofibroma Primary Tumor
JH-2-012 2-012_Neurofibroma Neurofibroma Primary Tumor
JH-2-013 2-013_Plexiform_Neurofibroma Plexiform Neurofibroma Primary Tumor
JH-2-014 2-014_Neurofibroma Neurofibroma Primary Tumor
JH-2-015 2-015_Neurofibroma Neurofibroma Primary Tumor
JH-2-015 2-015_Plexiform_Neurofibroma Plexiform Neurofibroma Primary Tumor
JH-2-016 2-016_Neurofibroma Neurofibroma Primary Tumor
JH-2-017 2-017_Neurofibroma Neurofibroma Primary Tumor
JH-2-019 2-019_Neurofibroma Neurofibroma Primary Tumor
JH-2-021 2-021_Neurofibroma Neurofibroma Primary Tumor
JH-2-023 2-023_Plexiform_Neurofibroma Plexiform Neurofibroma Primary Tumor
JH-2-026 2-026_Neurofibroma Neurofibroma Primary Tumor
JH-2-031_Cell_Line 2-031_Cell_Line Malignant Peripheral Nerve Sheath Tumor
JH-2-031 2-031_Malignant_Peripheral_Nerve_Sheath_Tumor Malignant Peripheral Nerve Sheath Tumor Primary Tumor
JH-2-029 2-029_Neurofibroma Neurofibroma Primary Tumor
JH-2-032 2-032_Plexiform_Neurofibroma Plexiform Neurofibroma Primary Tumor
956 changes: 956 additions & 0 deletions public/mixed_nfosi_2022/data_mutations.txt
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49 changes: 49 additions & 0 deletions public/mixed_nfosi_2022/html_report/log-validate-studies-2022-11-09_16:54.txt
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=== Validation study: /datahub/mixed_nfosi_2022
DEBUG: -: Requesting info from portal at 'http://cbioportal.org'
DEBUG: -: Requesting cancer-types from portal at 'http://cbioportal.org'
DEBUG: -: Requesting genes from portal at 'http://cbioportal.org'
DEBUG: -: Requesting genesets from portal at 'http://cbioportal.org'
DEBUG: -: Requesting genesets_version from portal at 'http://cbioportal.org'
DEBUG: -: Requesting gene-panels from portal at 'http://cbioportal.org'

DEBUG: meta_clinical_patient.txt: Starting validation of meta file
INFO: meta_clinical_patient.txt: Validation of meta file complete

DEBUG: meta_clinical_sample.txt: Starting validation of meta file
INFO: meta_clinical_sample.txt: Validation of meta file complete

DEBUG: meta_mutations_extended.txt: Starting validation of meta file
INFO: meta_mutations_extended.txt: Validation of meta file complete

DEBUG: meta_study.txt: Starting validation of meta file
INFO: meta_study.txt: Validation of meta file complete
INFO: meta_study.txt: No reference genome specified -- using default (hg19)

DEBUG: data_clinical_sample.txt: Starting validation of file
INFO: data_clinical_sample.txt: Validation of file complete
INFO: data_clinical_sample.txt: Read 24 lines. Lines with warning: 0. Lines with error: 0

INFO: -: No directory named 'case_lists' found, so assuming no custom case lists.
ERROR: -: No case list found with stable_id 'mixed_nfosi_2022_sequenced', please add this case list to specify which samples are profiled for mutations. This is required for calculation of samples with mutations in OncoPrint and Study Summary.

DEBUG: data_clinical_patient.txt: Starting validation of file
WARNING: data_clinical_patient.txt: Columns OS_MONTHS and/or OS_STATUS not found. Overall survival analysis feature will not be available for this study.
WARNING: data_clinical_patient.txt: Columns DFS_MONTHS and/or DFS_STATUS not found. Disease free analysis feature will not be available for this study.
ERROR: data_clinical_patient.txt: line 21: column 1: Patient defined multiple times in file; value encountered: 'JH-2-031 (already defined on line 20)'
INFO: data_clinical_patient.txt: Validation of file complete
INFO: data_clinical_patient.txt: Read 23 lines. Lines with warning: 0. Lines with error: 1

DEBUG: data_mutations_extended.txt: Starting validation of file
WARNING: data_mutations_extended.txt: column 68: A SWISSPROT column was found in datafile without specifying associated 'swissprot_identifier' in metafile, assuming 'swissprot_identifier: name'.
INFO: data_mutations_extended.txt: lines [2, 3, 5, (28808 more)]: Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA]; values encountered: ['3'Flank', 'Intron', '3'UTR', '(5 more)']
ERROR: data_mutations_extended.txt: lines [4, 7, 22, (9291 more)]: column 4: The reference genome in column NCBI_Build does not correspond with the reference genome specified for this study (GRCh37); value encountered: 'GRCh38'
WARNING: data_mutations_extended.txt: lines [4, 7, 22, (8345 more)]: SWISSPROT value is not a (single) UniProtKB/Swiss-Prot name. Loader will try to find UniProtKB accession using Entrez gene id or gene symbol.; values encountered: ['Q9UKB5.139', 'Q13029.214', 'Q8N1P7.139', '(2190 more)']
INFO: data_mutations_extended.txt: lines [27, 52, 53, (2992 more)]: This variant (Gene symbol 'Unknown', Entrez gene ID 0) will be filtered out; value encountered: 'IGR'
WARNING: data_mutations_extended.txt: lines [44, 162, 163, (936 more)]: Missing value in SWISSPROT column; this column is recommended to make sure that the UniProt canonical isoform is used when drawing Pfam domains in the mutations view.; value encountered: ''
WARNING: data_mutations_extended.txt: lines [93, 97, 167, (650 more)]: No Amino_Acid_Change or HGVSp_Short value. This mutation record will get a generic "MUTATED" flag
WARNING: data_mutations_extended.txt: lines [181, 11042, 18159, (4 more)]: SWISSPROT value is not a single UniProtKB/Swiss-Prot name. Found multiple separated by a `,`. Loader will try to find UniProtKB accession using Entrez gene id or gene symbol.; values encountered: ['A0A0B4J2D9.43,P0DP09.24', 'P62861.147,P35544.162', 'P01768.117,P0DP03.21']
WARNING: data_mutations_extended.txt: lines [977, 1142, 1143, (7 more)]: Gene symbol not known to the cBioPortal instance. This record will not be loaded.; values encountered: ['ENST00000529081', 'LMLN2', 'ENST00000634254', '(6 more)']
INFO: data_mutations_extended.txt: Validation of file complete
INFO: data_mutations_extended.txt: Read 41101 lines. Lines with warning: 9294. Lines with error: 9294

INFO: -: Validation complete
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