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README.md
README.md
 
 
data_clinical_patient.txt
data_clinical_patient.txt
 
 
data_clinical_sample.txt
data_clinical_sample.txt
 
 
data_mutations_extended.txt
data_mutations_extended.txt
 
 
data_timeline_biopsy.txt
data_timeline_biopsy.txt
 
 
data_timeline_ecog.txt
data_timeline_ecog.txt
 
 
data_timeline_labtest.txt
data_timeline_labtest.txt
 
 
data_timeline_spread.txt
data_timeline_spread.txt
 
 
data_timeline_staging.txt
data_timeline_staging.txt
 
 
data_timeline_surgery.txt
data_timeline_surgery.txt
 
 
data_timeline_treatment_medical.txt
data_timeline_treatment_medical.txt
 
 
data_timeline_treatment_radiation.txt
data_timeline_treatment_radiation.txt
 
 
data_timeline_tumorboard.txt
data_timeline_tumorboard.txt
 
 
dates_first_diagnosis.txt
dates_first_diagnosis.txt
 
 

Repository files navigation

Study Files

meta_study.txt

Feld Wert Kommentar
type_of_cancer mixed
cancer_study_identifier e.g. MTB Über alle Meta-Files einer Study hinweg gleich
name e.g. Molekulares Tumorboard Erlangen
description e.g. Molekulares Tumorboard Erlangen
groups e.g. MTB Legt Sichtbarkeit für Keycloak User fest

meta_muations_extended.txt

Feld Wert Kommentar
cancer_study_identifier e.g. MTB
genetic_alteration_type MUTATION_EXTENDED
datatype MAF
stable_id mutations
show_profile_in_analysis_tab true
profile_name e.g. Mutations
profile_description e.g. Mutation data from TSO500
data_filename data_mutations_extended.txt
namesspaces e.g. MTB weitere Spalten können der MAF mit "Namespace.Spaltenname" hinzugefügt werden, hier z.B. "MTB.Klassifikation"

data_muations_extended.txt (MAF-Datei)

Hugo_Symbol Entrez_Gene_Id NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS Tumor_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE BIOTYPE CANONICAL EXON INTRON AF AFR_AF AMR_AF EAS_AF EUR_AF SAS_AF CLIN_SIG SOMATIC PUBMED IMPACT PHENO FILTER flanking_bps vcf_qual gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF vcf_pos t_VF MTB.Klassifikation

meta_sv_fusions.txt

Noch in Arbeit

data_sv_fusions.txt

Noch in Arbeit

meta_clinical_sample.txt

Feld Wert Kommentar
cancer_study_identifier e.g. MTB Über alle Meta-Files einer Study hinweg gleich
genetic_alteration_type CLINICAL
datatype SAMPLE_ATTRIBUTES
data_filename data_clinical_sample.txt

data_clinical_sample.txt

Row 1: The attribute Display Names
Row 2: The attribute Descriptions
Row 3: The attribute Datatype
Row 4: The attribute Priority
Row 5: The attribute name for the database
Row 6: data
#Patient Identifier Sample Identifier Sequenzierung DNA Panel TMB Score MSI DATE
#Patient Identifier Sample Identifier Sequenzierung DNA Panel TMB Score MSI DATE
#STRING STRING STRING STRING STRING STRING
#1 1 1 1 1 1
PATIENT_ID SAMPLE_ID SEQUENCING_DNA_PANEL TMB_SCORE MSI DATE
e.g. 1234567890 e.g. 12345678-1234567890 e.g. TruSight Oncology 500 e.g. 5.0 e.g. 0.85 e.g. 2023-01-01
Pflichtfeld Pflichtfeld

meta_clinical_patient.txt

Feld Wert Kommentar
cancer_study_identifier e.g. MTB
genetic_alteration_type CLINICAL
datatype PATIENT_ATTRIBUTES
data_filename data_clinical_patient.txt

data_clinical_patient.txt

Row 1: The attribute Display Names
Row 2: The attribute Descriptions
Row 3: The attribute Datatype
Row 4: The attribute Priority
Row 5: The attribute name for the database
Row 6: data
#Patient Identifier Birthdate Sex Death Overall survival status Diagnosis date Age when diagnosed ICD10 Code Diagnosis ICD-O3-Localisation ICD-O3-Histology MTB registration date Guideline status Distant metastases Response to last therapy line Tumor site
#Patient Identifier Birthdate Sex Date of death Overall patient survival status Date of diagnosis Age at which a condition or disease was first diagnosed ICD10 Code Diagnosis ICD-O3-Localisation ICD-O3-Histology MTB registration date Leitlinienstatus Description Distant metastases (spread of disease) Response to last therapy line Tumor site
#STRING STRING STRING STRING STRING STRING NUMBER STRING STRING STRING STRING STRING STRING STRING STRING STRING
#1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
PATIENT_ID BIRTHDATE SEX DEATH_DATE OS_STATUS DIAGNOSIS_DATE AGE ICD_10_CODE DIAGNOSIS ICD_03_LOCALISATION ICD_03_Histology DATE_MTB_REGISTRATION GUIDELINE_STATUS_DESC DISTANT_METASTASES RESPONSE TUMOR_SITE
e.g. 1234567890 e.g. 2000-01-01 e.g. w
Pflichtfeld

dates_first_diagnosis.txt

PATIENT_ID DATE
e.g. 1234567890 e.g. 2024-01-01

meta_timeline.txt

Feld Wert Kommentar
cancer_study_identifier e.g. MTB
genetic_alteration_type CLINICAL
datatype TIMELINE
data_filename data_timeline_XXX.txt unterschiedlich, je nach Timeline-Event

data_timeline_biopsy.txt

PATIENT_ID START_DATE STOP_DATE EVENT_TYPE STYLE_COLOR SAMPLE DATE
e.g. 1234567890 e.g. 0 BIOPSY #0000ff e.g. Fernmetastase e.g. 2023-01-01
Pflichtspalte;
Tage seit der Erstdiagnose		 Pflichtspalte;
Bei Zeitpunkt-Events leer		 Pflichtspalte

data_timeline_ecog.txt

PATIENT_ID START_DATE STOP_DATE EVENT_TYPE STYLE_COLOR ECOG DISEASE DATE
e.g. 1234567890 e.g. 0 ECOG #0000ff e.g. 1 e.g. Bösartige Neubildung der Schilddrüse e.g. 2023-01-01
Pflichtspalte;
Tage seit der Erstdiagnose		 Pflichtspalte;
Bei Zeitpunkt-Events leer		 Pflichtspalte

data_timeline_labtest.txt

PATIENT_ID START_DATE STOP_DATE EVENT_TYPE STYLE_COLOR TEST RESULT UNIT DATE
e.g. 1234567890 e.g. 0 LAB_TEST #0000ff e.g. PSA e.g. 5,66 e.g. ng/ml e.g. 2023-01-01
Pflichtspalte;
Tage seit der Erstdiagnose		 Pflichtspalte;
Bei Zeitpunkt-Events leer		 Pflichtspalte

data_timeline_spread.txt

PATIENT_ID START_DATE STOP_DATE EVENT_TYPE STYLE_COLOR DESCRIPTION DISEASE DATE
e.g. 1234567890 e.g. 0 SPREAD OF DISEASE #0000ff e.g. Metastasiert e.g. Bösartige Neubildung der Schilddrüse e.g. 2023-01-01
Pflichtspalte;
Tage seit der Erstdiagnose		 Pflichtspalte;
Bei Zeitpunkt-Events leer		 Pflichtspalte

data_timeline_staging.txt

PATIENT_ID START_DATE STOP_DATE EVENT_TYPE STYLE_COLOR TNM_ORG CTNM DTNM GESAMT_R STADIUM FIGO_STADIUM GLEASON_SCORE ANN_ARBOR DISEASE DATE
e.g. 1234567890 e.g. 0 STAGING #0000ff e.g. UICC e.g. cM1 e.g. cM1 e.g. R0 e.g. IV e.g. 7b e.g. Bösartige Neubildung der Schilddrüse e.g. 2023-01-01
Pflichtspalte;
Tage seit der Erstdiagnose		 Pflichtspalte;
Bei Zeitpunkt-Events leer		 Pflichtspalte

data_timeline_surgery.txt

PATIENT_ID START_DATE STOP_DATE EVENT_TYPE STYLE_COLOR STATUS INTENTION TUMOR_SECTION METASTASIS_RESECTION METASTASIS_LOCATION R_CLASSIFICATION R_DEFINITELY NOTE DISEASE DATE
e.g. 1234567890 e.g. 0 e.g. 120 SURGERY #0000ff e.g. durchgeführt e.g. Diagnostisch e.g. Nein e.g. Ja e.g. Knochen e.g. RX e.g. 1 e.g. Teilresektion e.g. Bösartige Neubildung der Schilddrüse e.g. 2023-01-01
Pflichtspalte;
Tage seit der Erstdiagnose		 Pflichtspalte;
Bei Zeitpunkt-Events leer		 Pflichtspalte

data_timeline_tumorboard.txt

PATIENT_ID START_DATE STOP_DATE EVENT_TYPE STYLE_COLOR TUMORBOARD TYPE QUESTION RECOMMENDATION NOTE DATE
e.g. 1234567890 e.g. 0 e.g. 120 TUMORBOARD #0000ff e.g. TB Molekulares Tumorboard e.g. Prätherapeutisch e.g. 2023-01-01
Pflichtspalte;
Tage seit der Erstdiagnose		 Pflichtspalte;
Bei Zeitpunkt-Events leer		 Pflichtspalte

data_timeline_treatment_medical.txt

PATIENT_ID START_DATE STOP_DATE EVENT_TYPE STYLE_COLOR TREATMENT_TYPE SUBTYPE AGENT AGENT_CLASS SUBSTANCE_ATC ENDING_STATUS RESULT REASON_FOR_TERMINATION STARTED ENDED
e.g. 1234567890 e.g. 0 e.g. 120 TREATMENT #0000ff Medical Therapy e.g. Chemotherapie, Immuntherapie e.g. Docetaxel e.g. L02AE02 e.g. Reguläres Ende e.g. Progression e.g. Progression e.g. 2023-01-01 e.g. 2023-01-02
Pflichtspalte;
Tage seit der Erstdiagnose		 Pflichtspalte;
Bei Zeitpunkt-Events leer		 Pflichtspalte

data_timeline_treatment_radiation.txt

PATIENT_ID START_DATE STOP_DATE EVENT_TYPE STYLE_COLOR TREATMENT_TYPE SUBTYPE ENDING_STATUS STATUS STARTED ENDED
e.g. 1234567890 e.g. 0 e.g. 120 TREATMENT #0000ff Radiation Therapy e.g. Radio-/Chemotherapie  e.g. Reguläres Ende e.g. durchgeführt e.g. 2023-01-01 e.g. 2023-01-02
Pflichtspalte;
Tage seit der Erstdiagnose		 Pflichtspalte;
Bei Zeitpunkt-Events leer		 Pflichtspalte

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Study Files für den Import nach cBioPortal

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