├── osiris2.png ├── notebooks ├── requirements.txt ├── dicom_file.dcm ├── modele_osiris_radiomics.xlsx └── Dicom_API.ipynb ├── pivot ├── OSIRIS_pivot_ResponseEvaluation.csv ├── OSIRIS_pivot_Consent.csv ├── OSIRIS_pivot_Biomarker.csv ├── OSIRIS_pivot_Drug.csv ├── OSIRIS_pivot_TNM.csv ├── OSIRIS_pivot_FamilyCancerHistory.csv ├── OSIRIS_pivot_RelatedPathology.csv ├── OSIRIS_pivot_AdverseEvent.csv ├── OSIRIS_pivot_Expression.csv ├── OSIRIS_pivot_Patient.csv ├── OSIRIS_pivot_Treatment.csv ├── OSIRIS_pivot_Fusion.csv ├── OSIRIS_pivot_BiologicalSample.csv ├── OSIRIS_pivot_TumorPathologyEvent.csv ├── OSIRIS_pivot_CopyNumber.csv ├── OSIRIS_pivot_Variant.csv ├── OSIRIS_pivot_Annotation.csv └── OSIRIS_pivot_Analysis.csv ├── documentation ├── ModeleOmicOSIRIS.pdf ├── ModeleCliniqueOSIRIS.pdf ├── MPD_OSIRIS_model_v1.1.05.png ├── ModeleCliniqueOSIRIS-english_version.pdf ├── OSIRIS_Conventions_alimentation_v1.0_EN.pdf ├── OSIRIS_Conventions_alimentation_v1.0_FR.pdf ├── OSIRIS_Spécifications_Modèle_Données_Cliniques_TC_v1.0_(DRAFT).pdf └── OSIRIS_Spécifications_Modèle_Données_Cliniques_TC_v1.0_(DRAFT).pdf ├── README.md └── data └── DataElementConcept.tsv /osiris2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/osiris2.png -------------------------------------------------------------------------------- /notebooks/requirements.txt: -------------------------------------------------------------------------------- 1 | pandas==1.2.3 2 | numpy==1.20.2 3 | matplotlib==3.4.1 4 | pydicom==2.3.0.dev0 5 | -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_ResponseEvaluation.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Treatment_Ref,Date,Status 2 | L304,1,1,, -------------------------------------------------------------------------------- /notebooks/dicom_file.dcm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/notebooks/dicom_file.dcm -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_Consent.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Consent_Date,Consent_GeneticAnalysisAuthorization 2 | L304,1,2000-11-16,0 -------------------------------------------------------------------------------- /documentation/ModeleOmicOSIRIS.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/documentation/ModeleOmicOSIRIS.pdf -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_Biomarker.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Analysis_Ref,Biomarker_Code,Biomarker_Value,Biomarker_Unit 2 | L304,1,1,cg6548,++, -------------------------------------------------------------------------------- /documentation/ModeleCliniqueOSIRIS.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/documentation/ModeleCliniqueOSIRIS.pdf -------------------------------------------------------------------------------- /notebooks/modele_osiris_radiomics.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/notebooks/modele_osiris_radiomics.xlsx -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_Drug.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Treatment_Ref,Drug_Code,Drug_Name 2 | L304,1,2,c3564,cis-platine 3 | L304,2,2,f456,Imatinib -------------------------------------------------------------------------------- /documentation/MPD_OSIRIS_model_v1.1.05.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/documentation/MPD_OSIRIS_model_v1.1.05.png -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_TNM.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,TumorPathologyEvent_Ref,TNM_Version,TNM_Type,TNM_T,TNM_N,TNM_M 2 | L304,1,1,,,,, 3 | L304,2,2,,,,, -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_FamilyCancerHistory.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,FamilyCancerHistory_TopographyCode,FamilyCancerHistory_Parentage 2 | L304,1,C00.5,C0037047 -------------------------------------------------------------------------------- /documentation/ModeleCliniqueOSIRIS-english_version.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/documentation/ModeleCliniqueOSIRIS-english_version.pdf -------------------------------------------------------------------------------- /documentation/OSIRIS_Conventions_alimentation_v1.0_EN.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/documentation/OSIRIS_Conventions_alimentation_v1.0_EN.pdf -------------------------------------------------------------------------------- /documentation/OSIRIS_Conventions_alimentation_v1.0_FR.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/documentation/OSIRIS_Conventions_alimentation_v1.0_FR.pdf -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_RelatedPathology.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,RelatedPathology_PathologyCode,RelatedPathology_DiagnosisDate,RelatedPathology_PathologyEndDate 2 | L304,1,R60.9,2002-11-14,2003-11-19 -------------------------------------------------------------------------------- /documentation/OSIRIS_Spécifications_Modèle_Données_Cliniques_TC_v1.0_(DRAFT).pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/documentation/OSIRIS_Spécifications_Modèle_Données_Cliniques_TC_v1.0_(DRAFT).pdf -------------------------------------------------------------------------------- /documentation/OSIRIS_Spécifications_Modèle_Données_Cliniques_TC_v1.0_(DRAFT).pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/InstitutNationalduCancer/OSIRIS/HEAD/documentation/OSIRIS_Spécifications_Modèle_Données_Cliniques_TC_v1.0_(DRAFT).pdf -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_AdverseEvent.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Treatment_Ref,TumorPathologyEvent_Ref,AdverseEvent_Code,AdverseEvent_Date,AdverseEvent_EndDate,AdverseEvent_Grade 2 | L304,1,2,1,Mal à la tete,2007-06-13,2007-07-10, 3 | ,,,,,,, 4 | Vincent : Patient_Id est Patient_Ref en deuxième colonne,,,,,,, -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_Expression.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Analysis_Ref,AlterationOnSample_AlterationType,AlterationOnSample_Pathogenicity,AlterationOnSample_Actionability,AlterationOnSample_ProposedForOrientation,GeneExpression_DataType,GeneExpression_Value,Validation_Type,Validation_Method,Validation_Status 2 | L304,,,,,,,,,,, -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_Patient.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Patient_Gender,Patient_Ethnicity,Patient_BirthDate,Patient_DeathDate,Patient_ProviderCenterId,Patient_OriginCenterId,Patient_CauseOfDeath,Patient_LastNewsDate,Patient_LastNewsStatus 2 | L304,1,HL7:M,2043-8,1967-11-08,2017-11-29,IB,IB,UMLS:C0027651,2017-11-29,UMLS:C1546956 3 | L036,2,,,,,,,,, -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_Treatment.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,TumorPathologyEvent_Ref,Treatment_Type,Treatment_LineNumber,Treatment_ActivityCode,Treatment_StartDate,Treatment_EndDate,Treatment_ClinicalTrialContext,Treatment_ClinicalTrialName,Treatment_ClinicalTrialId,Treatment_SurgeryResectionQuality,Treatment_SurgeryNature 2 | L304,1,1,UMLS:C0728940,2,,2006-01-04,2006-11-23,0,,,R0, 3 | L304,2,2,UMLS:C3665472,,,2007-01-12,2008-11-17,1,,,R1, -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_Fusion.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Analysis_Ref,AlterationOnSample_AlterationType,AlterationOnSample_Pathogenicity,AlterationOnSample_Actionability,AlterationOnSample_ProposedForOrientation,Fusion_Type,Fusion_Chromosome5prime,Fusion_Point5prime,Fusion_Chromosome3prime,Fusion_Point3prime,Fusion_NbSpanningPair,Fusion_NbSplitReads,Fusion_InFrame,Validation_Type,Validation_Method,Validation_Status 2 | L304,1,2,OSIRIS:O15-3,,,,LOINC:LA26331-1,,,,,33,5,1,OSIRIS:O16-3,,OSIRIS:O18-2 -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_BiologicalSample.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,TumorPathologyEvent_Ref,Consent_Ref,BiologicalSample_ExternalAccession,BiologicalSample_ParentExternalAccession,BiologicalSample_CollectDate,BiologicalSample_TopographyCode,BiologicalSample_Nature,BiologicalSample_Origin,BiologicalSample_StorageTemperature,BiologicalSample_TumorCellularity 2 | L304,1,1,1,ech primary,,2005-12-27,C34,C4039816,OSIRIS:O59-2,MIABIS:Tissue Frozen,30 3 | L304,2,2,1,ech 2,ech primary,2011-02-08,C30,C1519524,OSIRIS:O59-2,FFPE,60 -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_TumorPathologyEvent.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,TumorPathologyEvent_ParentRef,TumorPathologyEvent_Type,TumorPathologyEvent_StartDate,TumorPathologyEvent_PerformanceStatus,TumorPathologyEvent_G8,TumorPathologyEvent_T,TumorPathologyEvent_N,TumorPathologyEvent_M,TumorPathologyEvent_TNMVersion,TumorPathologyEvent_TNMType,TumorPathologyEvent_HistologicalGradeType,TumorPathologyEvent_HistologicalGradeValue,TumorPathologyEvent_StadeType,TumorPathologyEvent_StadeValue,TumorPathologyEvent_DiagnosisDate,TumorPathologyEvent_TopographyCode,TumorPathologyEvent_MorphologyCode,TumorPathologyEvent_Laterality 2 | L304,1,,UMLS:C0677930,2005-11-17,1,6,T0,N1mi,M1,,c,,,,,2005-11-17,C00.8,8002/3,UMLS:C0238767 3 | L304,2,1,UMLS:C0521158,2010-11-18,6,6,T1,N2,M1,,p,,,,,2010-11-18,C11.1,8000-1,UMLS:C0439673 -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ![OSIRIS logo](https://raw.githubusercontent.com/siric-osiris/OSIRIS/master/osiris2.png) 2 | ## Groupe inter-SiRIC sur le partage et l'intégration des données clinico-biologiques en oncologie 3 | ### *Inter-SiRIC task force for clinical and biological data sharing and interoperability in oncology* 4 | 5 | ## Using the OSIRIS data framework 6 | * The framework description is available at [documentation/](documentation/) 7 | * The content of the tables may be found at [data/](data/) 8 | * Alternatively, you can browse the wiki 9 | 10 | ## Extending the OSIRIS data framework 11 | * Please, refer to the guidelines [here](https://github.com/siric-osiris/OSIRIS/wiki/How-to-contribute). 12 | 13 | ## Deploying an i2b2/SHRINE datawarehouse 14 | * You can deploy an i2b2/SHRINE instance using the Docker installation [here](https://github.com/CARPEM/SHRINEDocker) provided by SiRIC CARPEM. 15 | -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_CopyNumber.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Analysis_Ref,AlterationOnSample_AlterationType,AlterationOnSample_Pathogenicity,AlterationOnSample_Actionability,AlterationOnSample_ProposedForOrientation,Alteration_Chromosome,Alteration_GenomicStart,Alteration_GenomicStop,Alteration_GenomeBuild,Alteration_Cytoband,CNV_SegmentIntensity,CNV_SegmentGenomicStatus,CNV_CopyNumber,CNV_LOH,Validation_Type,Validation_Method,Validation_Status 2 | L304,1,3,OSIRIS:O15-4,,,,LA21263-1,87751512,88104391,hg19,10q23.31,33,OSIRIS:O49-2,3,0,OSIRIS:O16-2,Visual check,OSIRIS:O18-2 3 | ,,,,,,,,,,,,,,,,,, 4 | Vincent : Patient_Id est Patient_Ref en deuxième colonne,,,Vincent : Alteration ou Location ?,,,,,,,,,,,,,,, 5 | ,,,,,solution actuelle,,chr1,1,10,,,,,2,,,, 6 | ,,,,,,,chr1,11,30,,,,,5,,,, 7 | ,,,,,,,chr1,1,60,,,,,,1,,, 8 | ,,,,,,,,,,,,,,,,,, 9 | ,,,,,,,,,,,,,,,,,, 10 | ,,,,,,,,,,,,,,,,,, 11 | ,,,,,meilleure solution pour les requetes,,chr1,1,10,,,,,2,1,,, 12 | ,,,,,,,chr1,11,30,,,,,5,1,,, 13 | ,,,,,,,chr1,30,60,,,,,2,1,,, -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_Variant.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Analysis_Ref,AlterationOnSample_AlterationType,AlterationOnSample_Pathogenicity,AlterationOnSample_Actionability,AlterationOnSample_ProposedForOrientation,Alteration_Chromosome,Alteration_GenomicStart,Alteration_GenomicStop,Alteration_GenomeBuild,Alteration_Cytoband,Variant_ReferenceAllele,Variant_AlternativeAllele,Variant_DNASequenceVariationType,VariantInSample_PositionReadDepth,VariantInSample_VariantReadDepth,VariantInSample_StrandBias,VariantInSample_GenomicSourceClass,VariantInSample_AllelicState,Validation_Type,Validation_Method,Validation_Status 2 | L304,1,1,OSIRIS:O15-5,,,,LA21256-5,178916948,178916948,hg19,,T,A,LOINC:LA6690-7,31,6,0,LOINC:LA6684-0,LOINC:LA6706-1,OSIRIS:O16-2,biblio,OSIRIS:O18-1 3 | L304,2,2,OSIRIS:O15-5,,,,LA21263-1,45,896,hg19,,A,T,LOINC:LA6690-7,785,456,0,LOINC:LA6684-0,LOINC:LA6706-1,OSIRIS:O16-1,,OSIRIS:O18-1 4 | ,,,,,,,,,,,,,,,,,,,,,, 5 | Vincent : Patient_Id est Patient_Ref en deuxième colonne,,,,,,,Vincent : Alteration ou Location ?,,,,,,,,,,,,,,, -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_Annotation.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,Alteration_Ref,AlterationOnSample_AlterationType,GenomeEntity_Type,GenomeEntity_Database,GenomeEntity_Id,GenomeEntity_Symbol,Annotation_ReferenceType,Annotation_ReferenceDatabase,Annotation_ReferenceValue,Annotation_MutationPredictionAlgorithm,Annotation_MutationPredictionValue,Annotation_MutationPredictionScore,Annotation_PfamDomain,Annotation_PfamId,Annotation_DNARegionName,Annotation_DNASequenceVariation,Annotation_AminoAcidChange,Annotation_GenomicSequenceVariation,Annotation_RNASequenceVariation,Annotation_AminoAcidChangeType,Annotation_FusionPrimeEnd,Annotation_Strand 2 | L304,1,1,OSIRIS:O15-4,,,,PI3K,OSIRIS:O90-1,COSMIC,COSM760,SIFT,Deleterious,0.35,"PI3K_rbd; PI3-kinase family, ras-binding domain",pfam00794,exon 2,c.1624G>A,p.E542K,,,LA6698-0,, 3 | L304,1,1,Genetic variant,,,,TP53,genome entity,Entrez,123365,,,,,,,,,,,,, 4 | L304,2,1,Genetic variant,,,,TP53,exonic variant transcript,Refseq,NM_001126115,,,,,,exon1,c.73G>T,p.V25F,,,,, 5 | L304,3,1,Genetic variant,,,,TP53,exonic variant transcript,Refseq,NM_001126116,,,,,,exon1,c.73G>T,p.V25F,,,,, 6 | L304,4,1,Genetic variant,,,,TP53,exonic variant transcript,Refseq,NM_001126112,,,,,,exon5,c.469G>T,p.V157F,,,,, 7 | L304,5,1,Genetic variant,,,,TP53,,,,SIFT,Deleterious,0.35,,,,,,,,,, 8 | L304,6,1,Genetic variant,,,,TP53,,,,Polyphen,Deleterious,0.7,,,,,,,,,, -------------------------------------------------------------------------------- /pivot/OSIRIS_pivot_Analysis.csv: -------------------------------------------------------------------------------- 1 | Patient_Id,Instance_Id,TumorPathologyEvent_Ref,BiologicalSample_Ref,Analysis_Code,Analysis_Type,Analysis_Date,Technology_TechnicalProtocol,Technology_PlatformName,Technology_PlatformAccession,Technology_DateOfExperiment,Panel_Name,AnalysisProcess_AnalyticPipelineCode,OmicAnalysis_AlgorithmicCellularity,OmicAnalysis_AlgorithmicPloidy,OmicAnalysis_NumberOfBreakPoints 2 | L304,1,1,ech primary,ATX90U,Genomique,2018-02-07,OSIRIS:O6-4,OSIRIS:O7-66,,2017-09-20,OSIRIS:O10-4,v351,50,OSIRIS:O13-2, 3 | L304,2,2,ech 2,fgh587,NGS,2018-02-07,OSIRIS:O6-12,OSIRIS:O7-46,,2017-09-19,OSIRIS:O10-0,RNAseq pipeline v3.2,50,OSIRIS:O13-2, 4 | L304,3,2,ech 2,rt52485,Genomique,2018-02-09,OSIRIS:O6-3,OSIRIS:O7-25,,2018-02-09,OSIRIS:O10-0,sbd54dsf57s,,,320 5 | ,,,,,,,,,,,,,,, 6 | ,,,Laetitia: !!valeur = instance_id,,,,,,,,,,Vincent : ces deux colonnes sont génériques à toutes les altérations pour être mises ici ?,, 7 | ,,,,Yec'han : j'ai rajouté comme proposition car nous avons un code unique pour chaque analyse que nous faisons et que l'on retrouve dans nos fichiers de résultats => traçabilité facilitée,,,,,,,,,,,"Vincent : spécifique du CNV, déplacer cette colonne dans le fichier CNV ?" 8 | ,,,Vincent : Il faut mettre la reférence de la colonne Instance_Id du fichier BiologicalSample,,,,,,,,,,,,"Laetitia: c'est ici car c'est un annotation qui concerne l'analyse en totalité. Si on la met dans le fichier CNV, il va falloir la répéter sur toutes les lignes" -------------------------------------------------------------------------------- /notebooks/Dicom_API.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "id": "b9f92452-b2df-4fa2-b014-bd95e51ae571", 6 | "metadata": { 7 | "tags": [] 8 | }, 9 | "source": [ 10 | "# Extracting data from DICOM files\n", 11 | "### This notebook extract data from Dicom files using the dicomTags." 12 | ] 13 | }, 14 | { 15 | "cell_type": "markdown", 16 | "id": "2c857a38-eabe-497a-904e-39ad862dad9c", 17 | "metadata": {}, 18 | "source": [ 19 | "#### Installing required packages:\n", 20 | "\n", 21 | "1. Create a new environment (https://docs.python.org/3/library/venv.html)\n", 22 | "\n", 23 | "```python\n", 24 | "python3 -m venv /path/to/new/virtual/environment\n", 25 | "```\n", 26 | "2. Activate the new environment\n", 27 | "\n", 28 | "```python\n", 29 | "source env/bin/activate\n", 30 | "```\n", 31 | "\n", 32 | "3. Install required packages\n", 33 | "\n", 34 | "```python\n", 35 | "pip install -r requirements.txt\n", 36 | "```\n", 37 | "\n", 38 | "4. Run the notebook. :)" 39 | ] 40 | }, 41 | { 42 | "cell_type": "code", 43 | "execution_count": null, 44 | "id": "09335bfd-7719-4c49-ac02-ad28ad21f374", 45 | "metadata": {}, 46 | "outputs": [], 47 | "source": [ 48 | "import pandas as pd\n", 49 | "import numpy as np\n", 50 | "from pydicom import dcmread\n", 51 | "import re\n", 52 | "import glob" 53 | ] 54 | }, 55 | { 56 | "cell_type": "markdown", 57 | "id": "2409bef7-55d0-452b-a562-8903ec428e9b", 58 | "metadata": {}, 59 | "source": [ 60 | "DICOM_file: The path containing the Dicom File.\n", 61 | "tags_file_osiris: the file containing the dicomTags to be extracted.\n", 62 | "For this example the original excel file of Christophe is used." 63 | ] 64 | }, 65 | { 66 | "cell_type": "code", 67 | "execution_count": null, 68 | "id": "085dd51a-7840-4329-a47a-2e5bdc7220f3", 69 | "metadata": {}, 70 | "outputs": [], 71 | "source": [ 72 | "DICOM_file = dcmread(\"dicom_file.dcm\")\n", 73 | "DICOM_file = dcmread(\"files/1-01.dcm\")\n", 74 | "tags_file_osiris = pd.read_excel(\n", 75 | " \"modele_osiris_radiomics.xlsx\", sheet_name=\"Feuil1\", header=0\n", 76 | ")" 77 | ] 78 | }, 79 | { 80 | "cell_type": "markdown", 81 | "id": "3b8b6f69-5c99-46a8-b933-44474b65427a", 82 | "metadata": {}, 83 | "source": [ 84 | "#### Display tags_file_osiris and Dicom File" 85 | ] 86 | }, 87 | { 88 | "cell_type": "code", 89 | "execution_count": null, 90 | "id": "74f1435d-e7e2-4a4c-965c-1028c77f1c26", 91 | "metadata": {}, 92 | "outputs": [], 93 | "source": [ 94 | "tags_file_osiris" 95 | ] 96 | }, 97 | { 98 | "cell_type": "code", 99 | "execution_count": null, 100 | "id": "8ae59cfa-f60b-43e0-a62d-d8d1c0dab5a9", 101 | "metadata": {}, 102 | "outputs": [], 103 | "source": [ 104 | "print(DICOM_file)" 105 | ] 106 | }, 107 | { 108 | "cell_type": "markdown", 109 | "id": "926bd5b8-176f-49d4-9d1e-b26e48af42f3", 110 | "metadata": {}, 111 | "source": [ 112 | "### Extracting the data and building a data frame" 113 | ] 114 | }, 115 | { 116 | "cell_type": "code", 117 | "execution_count": null, 118 | "id": "395c5919-c8c8-430c-9bf0-b2128437e607", 119 | "metadata": {}, 120 | "outputs": [], 121 | "source": [ 122 | "list_tags = []\n", 123 | "dicom_df = pd.DataFrame(columns=[\"tag\", \"name\", \"value\"])\n", 124 | "\n", 125 | "# extraction of dicomTags from the excel file\n", 126 | "for j in range(len(tags_file_osiris)):\n", 127 | " try:\n", 128 | " tag_ext = re.search(r\"\\((.*?)\\)\", tags_file_osiris[\"Source\"][j]).group(1)\n", 129 | " tag_conv = \"0x\" + tag_ext[0:4] + tag_ext[5:]\n", 130 | " list_tags.append(tag_conv)\n", 131 | " except:\n", 132 | " pass\n", 133 | "\n", 134 | "# searching for the tags in the dicom file and building the dataframe\n", 135 | "for i in list_tags:\n", 136 | " try:\n", 137 | " df_tag = str(DICOM_file[i].tag)\n", 138 | " df_name = DICOM_file[i].name\n", 139 | " df_value = DICOM_file[i].value\n", 140 | "\n", 141 | " dicom_df = dicom_df.append(\n", 142 | " {\"tag\": df_tag, \"name\": df_name, \"value\": df_value}, ignore_index=True\n", 143 | " )\n", 144 | "\n", 145 | " except:\n", 146 | " pass\n", 147 | "\n", 148 | "\n", 149 | "dicom_df" 150 | ] 151 | }, 152 | { 153 | "cell_type": "markdown", 154 | "id": "b3a305ee-0a14-424e-8683-92c1ebc1c1ff", 155 | "metadata": {}, 156 | "source": [ 157 | "#### Exporting to CSV" 158 | ] 159 | }, 160 | { 161 | "cell_type": "code", 162 | "execution_count": null, 163 | "id": "180c8dff-aae7-490a-83fb-209e670f5958", 164 | "metadata": {}, 165 | "outputs": [], 166 | "source": [ 167 | "dicom_df.to_csv('dicom_data-osiris.csv')" 168 | ] 169 | }, 170 | { 171 | "cell_type": "markdown", 172 | "id": "f5d14377-3613-4e57-b5c8-8627421bc5b8", 173 | "metadata": {}, 174 | "source": [ 175 | "### Working with file lists and building a transposed dataframe" 176 | ] 177 | }, 178 | { 179 | "cell_type": "code", 180 | "execution_count": null, 181 | "id": "89e65145-147b-40cc-a26d-6ed6d5d3bf40", 182 | "metadata": { 183 | "tags": [] 184 | }, 185 | "outputs": [], 186 | "source": [ 187 | "dcm_files = (glob.glob(\"files/*.dcm\"))" 188 | ] 189 | }, 190 | { 191 | "cell_type": "code", 192 | "execution_count": null, 193 | "id": "d8752cb4-9ace-4798-ade6-a23034b2fa09", 194 | "metadata": {}, 195 | "outputs": [], 196 | "source": [ 197 | "list_tags = []\n", 198 | "\n", 199 | "\n", 200 | "# extraction of dicomTags from the excel file\n", 201 | "for j in range(len(tags_file_osiris)):\n", 202 | " try:\n", 203 | " tag_ext = re.search(r\"\\((.*?)\\)\", tags_file_osiris[\"Source\"][j]).group(1)\n", 204 | " tag_conv = \"0x\" + tag_ext[0:4] + tag_ext[5:]\n", 205 | " list_tags.append(tag_conv)\n", 206 | " except:\n", 207 | " pass\n", 208 | "\n", 209 | "dicom_df = pd.DataFrame(columns=[\"file\",\"tag\", \"value\"])\n", 210 | "dicom_dict = {}\n", 211 | "\n", 212 | "# searching for the tags in the dicom file and building the dataframe\n", 213 | "for i in dcm_files:\n", 214 | " DICOM_file = dcmread(i)\n", 215 | " dicom_dict[i] = {}\n", 216 | " for j in list_tags:\n", 217 | " try:\n", 218 | " tag = str(DICOM_file[j].tag)\n", 219 | " value = DICOM_file[j].value\n", 220 | " dicom_dict[i][tag] = value\n", 221 | " except:\n", 222 | " pass" 223 | ] 224 | }, 225 | { 226 | "cell_type": "code", 227 | "execution_count": null, 228 | "id": "71b5225c-dee9-46f5-920c-2d36ef0828d9", 229 | "metadata": {}, 230 | "outputs": [], 231 | "source": [ 232 | "df_dicom = pd.DataFrame.from_dict(dicom_dict, orient='index')" 233 | ] 234 | }, 235 | { 236 | "cell_type": "code", 237 | "execution_count": null, 238 | "id": "03d3864d-8f63-49d1-96e0-b4b741111a25", 239 | "metadata": {}, 240 | "outputs": [], 241 | "source": [ 242 | "df_dicom.head(10)" 243 | ] 244 | }, 245 | { 246 | "cell_type": "markdown", 247 | "id": "307f6f7f-1b2e-4bd4-a7c4-b30ff5da7a7c", 248 | "metadata": {}, 249 | "source": [ 250 | "#### Just for fun!" 251 | ] 252 | }, 253 | { 254 | "cell_type": "code", 255 | "execution_count": null, 256 | "id": "225ea97e-e261-46f2-ae57-67018c62c828", 257 | "metadata": { 258 | "tags": [] 259 | }, 260 | "outputs": [], 261 | "source": [ 262 | "import matplotlib.pyplot as plt\n", 263 | "\n", 264 | "plt.imshow(DICOM_file.pixel_array, cmap=plt.cm.gray)\n", 265 | "plt.show()" 266 | ] 267 | } 268 | ], 269 | "metadata": { 270 | "kernelspec": { 271 | "display_name": "Python 3", 272 | "language": "python", 273 | "name": "python3" 274 | }, 275 | "language_info": { 276 | "codemirror_mode": { 277 | "name": "ipython", 278 | "version": 3 279 | }, 280 | "file_extension": ".py", 281 | "mimetype": "text/x-python", 282 | "name": "python", 283 | "nbconvert_exporter": "python", 284 | "pygments_lexer": "ipython3", 285 | "version": "3.8.12" 286 | } 287 | }, 288 | "nbformat": 4, 289 | "nbformat_minor": 5 290 | } 291 | -------------------------------------------------------------------------------- /data/DataElementConcept.tsv: -------------------------------------------------------------------------------- 1 | ObjectClass ObjectProperty DataElementConcept ObjectPropertyLabelEN ObjectPropertyLabelFR ConceptualDomain FormatConceptualDomain ConceptualDomainRef Required DataElementConceptDefFR DataElementConceptDefEN IdDataElementConcept Examples 2 | Patient Id Patient_Id Patient Id Id du patient String mandatory Identifiant du patient dans le centre transmetteur de l'information Patient ID in the center providing the information C1 SHIVA_01-001 3 | Patient Gender Patient_Gender Gender Sexe du patient FHIR:AdministrativeGender String mandatory Sexe du patient Gender of the patient C2 4 | Patient Ethnicity Patient_Ethnicity Ethnicity Ethnicité FHIR:Race String optional Origine ethnique du patient Ethnicity of the patient C3 5 | Patient BirthDate Patient_BirthDate Birth Date Date de naissance Date mandatory Date de naissance du patient Date of birth of the patient C4 YYYY-MM-DD 6 | Patient DeathDate Patient_DeathDate Death Date Date de décès Date optional Date de décès du patient Date of death of the patient C5 YYYY-MM-DD 7 | Patient ProviderCenterId Patient_ProviderCenterId Provider Center Id Id du Centre fournisseur de données String mandatory Identifiant du centre transmetteur de l'information (code FINESS) Center ID of the center providing the information C6 8 | Patient OriginCenterId Patient_OriginCenterId Origin Center Id Id du Centre d'origine du patient String mandatory Identifiant du centre d'origine du patient Center ID of the center of origin of the patient C71 9 | Patient CauseOfDeath Patient_CauseOfDeath Cause of death Cause de décès UMLS:C0007465 String mandatory if DeathDate is set Descriptif de la cause de décès du patient Description of the cause of death of the patient C7 10 | Patient LastNewsDate Patient_LastNewsDate Last News Date Date de dernières nouvelles Date mandatory Date de dernières nouvelles du patient (= date de dernière venue du patient si aucune autre information disponible) (le jour est fixé au 15) Date of last news (= date of last patient visit if there is no other information available) (day is set to the 15th) C8 11 | Patient LastNewsStatus Patient_LastNewsStatus Last News Status Etat aux dernières nouvelles OSIRIS:LastNewsStatus String mandatory Indicateur de l'état du patient aux dernières nouvelles (Vivant ou décédé) Indicator of the patient's last known vital status (alive or deceased) C9 12 | Consent Date Consent_Date Date Date de signature du consentement Date mandatory Date de signature du consentement Date of consent signature C72 13 | Consent GeneticAnalysisAuthorization Consent_GeneticAnalysisAuthorization Genetic Analysis Authorization Autorisation pour des analyses génétiques OSIRIS:Boolean String mandatory Autorisation pour des analyses génétiques Consent for genetic analysis C79 14 | RelatedPathology PathologyCode RelatedPathology_PathologyCode Pathology Code Code ICD10 String mandatory if ObjectClass is set Code international de la pathologie associée (hors autre cancer). 3 caractères. International code for the related disease (other than cancer). 3 characters. C13 E11 15 | RelatedPathology DiagnosisDate RelatedPathology_DiagnosisDate Diagnosis Date Date Date mandatory if ObjectClass is set Date du diagnostic de la pathologie associée Date of diagnosis for the related disease. C14 16 | RelatedPathology PathologyEndDate RelatedPathology_PathologyEndDate Pathology End Date Date de fin Date optional Date de fin de la pathologie associée (si elle existe et est connue). Date of the end of the related disease (if occuring and known) C15 17 | FamilyCancerHistory TopographyCode FamilyCancerHistory_TopographyCode Topography Code Code Localisation ICDO3:Topography String mandatory if ObjectClass is set Code international de la localisation de l'antécédent carcinologique International code for the localization of the oncologic primary site C17 18 | FamilyCancerHistory Parentage FamilyCancerHistory_Parentage Parentage Parentage OSIRIS:FamilyCancerHistoryParentage String mandatory if ObjectClass is set Lien de parenté Family relationship C77 19 | TumorPathologyEvent Type TumorPathologyEvent_Type Type Type d'événement OSIRIS:EventType String mandatory Le champ 'Type' permet de décrire à la fois l'événement 'Cancer' en tant que maladie globale que les différents événements constituant cette maladie (Tumeur initiale, Récidive locale, Récidive métastatique). The field 'Type' allows to describe the 'Cancer' event as a global disease, as well as the various events constituting this disease (primary tumor, local relapse, metastatic relapse...) C20 20 | TumorPathologyEvent StartDate TumorPathologyEvent_StartDate Start Date Date de début de l'événement Date mandatory Date de début de l'événement tumoral ou de la maladie Date of start of cancer event or disease C21 21 | TumorPathologyEvent EndDate TumorPathologyEvent_EndDate End Date Date de fin de l'événement Date optional Date de fin de l'événement tumoral ou de la maladie Date of end of cancer event or disease C82 22 | TumorPathologyEvent PerformanceStatus TumorPathologyEvent_PerformanceStatus Performance Status Echelle d'autonomie / Performance status OMS:PerformanceStatus String optional Définition de l'échelle d'autonomie (échelle de Karnofsky ou OMS) Definition of the autonomy scale (Karnofsky scale or OMS) C22 23 | TumorPathologyEvent G8 TumorPathologyEvent_G8 G8 score Outil de dépistage G8 (score) Integer optional Outil d'évaluation de l'état général des patients âgés ayant un cancer Tool for the evaluation of the general condition of the patient C23 24 | TumorPathologyEvent HistologicalGradeType TumorPathologyEvent_HistologicalGradeType Histological Grade Type HistologicalGradeType OSIRIS:HistologicalGradeType String optional, mandatory if HistologicalGradeValue is set Liste des échelles de grading histologique List of histological grading scales C29 25 | TumorPathologyEvent HistologicalGradeValue TumorPathologyEvent_HistologicalGradeValue Histological Grade Value HistologicalGradeValue OSIRIS:HistologicalGradeValue String optional, mandatory if HistologicalGradeType is set Valeur du grade histologique Value of histological grade C30 26 | TumorPathologyEvent StadeType TumorPathologyEvent_StadeType Stade Type StadeType OSIRIS:StadeType String optional, mandatory if StadeValue is set Liste des échelles de stade List of stage scales C31 27 | TumorPathologyEvent StadeValue TumorPathologyEvent_StadeValue Stade Value StadeValue OSIRIS:StadeValue String optional, mandatory if StadeType is set Valeur du stade Stage value C32 28 | TumorPathologyEvent DiagnosisDate TumorPathologyEvent_DiagnosisDate Diagnosis Date Date du diagnostic Date mandatory Date du diagnostic de l'événement tumoral Date of diagnosis of the tumor event C33 29 | TumorPathologyEvent TopographyCode TumorPathologyEvent_TopographyCode Topography Code Code Localisation ICDO3:Topography String mandatory Localisation de la tumeur primaire Localisation of the primary tumor C34 30 | TumorPathologyEvent MorphologyCode TumorPathologyEvent_MorphologyCode Morphology Code Code Morphologie / Lésion ICDO3:Morphology String mandatory Code international de la lésion / type histologique / morphologie de l'événement tumoral International code of lesion / histological type / tumor morphology of the tumoral event C35 31 | TumorPathologyEvent Laterality TumorPathologyEvent_Laterality Laterality Latéralité OSIRIS:Laterality String optional Latéralité de la localisation (si elle existe) Laterality of location (if it exists) C36 32 | TNM T TNM_T T T OSIRIS:T_TNM String optional, mandatory if either N, M or TNMType is set Taille de la tumeur, propagation sur le site de la tumeur primitive Size of the tumor, propagation the site of the primary tumor C83 33 | TNM N TNM_N N N OSIRIS:N_TNM String optional, mandatory if either T, M or TNMType is set Propagation au niveau ganglionnaire Propagation at the ganglion level C84 34 | TNM M TNM_M M M OSIRIS:M_TNM String optional, mandatory if either T, N or TNMType is set Propagation à distance, présence de métastases Remote propagation, presence of metastases C85 35 | TNM Version TNM_Version TNM Version Version du TNM OSIRIS:TNMVersion String optional Version de la classification TNM TNM classification version C86 36 | TNM Type TNM_Type TNM Type Type de TNM OSIRIS:TNMType String optional, mandatory if either T, N or M is set c, p, r,... c, p, r,... C87 37 | Analysis Code Analysis_Code Code Code unique de l'analyse String optional Code de l'analyse Code of analysis C70 38 | Analysis Type Analysis_Type Type Type d'analyse OSIRIS:AnalysisType String mandatory if ObjectClass is set Type d'analyse Type of analysis C37 39 | Analysis Date Analysis_Date Date Date d'analyse Date mandatory if ObjectClass is set Date d'analyse Date of analysis C38 40 | ResponseEvaluation Date ResponseEvaluation_Date Date Date de l'évaluation de la réponse Date mandatory if ObjectClass is set Date de l'évaluation de la réponse au traitement Date of assessment of treatment response C78 41 | ResponseEvaluation Status ResponseEvaluation_Status Status Statut de l'évaluation de la réponse OSIRIS:RECIST String mandatory if ObjectClass is set Evaluation de la réponse au traitement Assessment of treatment response C73 42 | Biomarker Code Biomarker_Code Code Code du marqueur OSIRIS:BiomarkerCode String mandatory if ObjectClass is set Nom du biomarqueur Biomarker name C39 43 | Biomarker Value Biomarker_Value Value Valeur du marqueur String mandatory if ObjectClass is set Valeur du biomarqueur Biomarker value C40 44 | Biomarker Unit Biomarker_Unit Unit Unité d'expression du marqueur String optional Unité d'expression du biomarqueur Biomarker unit C81 45 | Treatment Type Treatment_Type Type Type de traitement OSIRIS:TreatmentType String mandatory if ObjectClass is set Type de traitement Type of treatment C41 46 | Treatment LineNumber Treatment_LineNumber Line Number Numéro de ligne String optional Ligne de traitement Line of treatment C74 47 | Treatment ActivityCode Treatment_ActivityCode Activity Code Codification de l'acte CCAM String optional Code CCAM de l'acte CCAM code of the medical act C42 48 | Treatment StartDate Treatment_StartDate Start Date Date de début Date mandatory if ObjectClass is set Date de début du traitement Date of treatment start C43 49 | Treatment EndDate Treatment_EndDate End Date Date de fin Date mandatory if ObjectClass is set Date de fin du traitement Date of treatment end C44 50 | Treatment ClinicalTrialContext Treatment_ClinicalTrialContext Clinical Trial Context Clinical trial (Yes | No) OSIRIS:Boolean String optional Traitement effectué dans un contexte d'étude clinique Treatment performed in a clinical study setting C45 51 | Treatment ClinicalTrialName Treatment_ClinicalTrialName Clinical Trial Name Nom de l'essai clinique String optional, mandatory if ClinicalTrialContext is 'Yes' Nom de l'étude clinique Name of the clinical study C75 52 | Treatment ClinicalTrialId Treatment_ClinicalTrialId Clinical Trial Id Identifiant de l'essai clinique String optional, mandatory if ClinicalTrialContext is 'Yes' Identifiant NCT de l'étude clinique NCT identifier of the clinical study C76 53 | Treatment SurgeryResectionQuality Treatment_SurgeryResectionQuality Surgery Resection Quality Qualité de la résection (anapath) OSIRIS:SurgeryResectionQuality String optional Qualité de la résection (anapath) Quality of resection (anapath) C46 54 | Treatment SurgeryNature Treatment_SurgeryNature Surgery Nature Nature de la chirurgie String optional Nature de la chirurgie Nature of the surgery C47 55 | AdverseEvent Code AdverseEvent_Code Code Code de l'événement indésirable MedDRA_CTCAE-v5.0 String mandatory if ObjectClass is set Code international de l'événement indésirable survenu en cours de traitement (hors autre cancer), seulement les 4 premières lettres. International code of the adverse event occurring during treatment (excluding other cancer), only the first 4 letters. C48 56 | AdverseEvent Date AdverseEvent_Date Date Date de l'événement indésirable Date mandatory if ObjectClass is set Date du diagnostic de l'événement indésirable Date of the diagnosis of the adverse event C49 57 | AdverseEvent EndDate AdverseEvent_EndDate End Date Date de fin Date optional Date de fin de l'événement indésirable (si elle est connue) End date of the adverse event (if known) C50 58 | AdverseEvent Grade AdverseEvent_Grade Grade Grade String mandatory if ObjectClass is set Grade de l'évenement indésirable Grade of the adverse event C80 59 | Drug Code Drug_Code Code Code molécule ATC String mandatory if ObjectClass is set Code de la classification thérapeutique (5ème niveau si possible) Therapeutic classification code (5th level if possible) C51 60 | Drug Name Drug_Name Name Nom de la molécule String mandatory if ObjectClass is set Nom de la molécule Name of the molecule C52 61 | BiologicalSample ExternalAccession BiologicalSample_ExternalAccession Sample External Accession Id unique de l'échantillon String mandatory if ObjectClass is set Identifiant unique de l'échantillon Unique identifier of the sample C53 62 | BiologicalSample ParentExternalAccession BiologicalSample_ParentExternalAccession Parent sample External Accession Identifiant unique de l'échantillon parent String optional Identifiant unique de l'échantillon parent (s'il en existe un, exemple N°histo) Unique identifier of the parent sample (if there is one, example histo#) C54 63 | BiologicalSample CollectDate BiologicalSample_CollectDate Collect Date Date du prélèvement Date mandatory if ObjectClass is set Date du prélèvement Date of sampling C56 64 | BiologicalSample TopographyCode BiologicalSample_TopographyCode Topography Code Code Localisation ICDO3:Topography String mandatory if ObjectClass is set Code de la localisation tumorale Code of tumor localization C57 65 | BiologicalSample Nature BiologicalSample_Nature Nature Nature de l'échantillon OSIRIS:SampleNature String mandatory if ObjectClass is set Nature de l'échantillon Nature of the sample C58 66 | BiologicalSample Origin BiologicalSample_Origin Origin Nature du prélèvement (tumoral / sain) OSIRIS:SampleOrigin String mandatory if ObjectClass is set Nature du prélèvement d'origine (Sain ou Tumoral) Nature of the original sample (Healthy or Tumoral) C59 67 | BiologicalSample StorageTemperature BiologicalSample_StorageTemperature Storage Temperature Mode de conservation OSIRIS:StorageTemperature String optional Mode de conservation Mode of preservation C60 68 | BiologicalSample TumorCellularity BiologicalSample_TumorCellularity Tumor Cellularity % de cellules tumorales Integer optional Pourcentage de cellules tumorales quantifié dans l'échantillon Percentage of tumor cells quantified in the sample C61 69 | Technology TechnicalProtocol Technology_TechnicalProtocol Technical Protocol Technical Protocol OSIRIS:TechnicalProtocol String mandatory Protocole de l'expérience Protocol used for the experiment O6 70 | Technology PlatformName Technology_PlatformName Platform Name Platform Name OSIRIS:PlatformName String mandatory Nom de la plateforme technologique (fournisseur suivi du nom de la plateforme) Technological platform name (provider followed by the platform name) O7 Agilent Human CGH 1x1M 71 | Technology PlatformAccession Technology_PlatformAccession Platform Accession Platform Accession String optional Identifiant GEO de la plateforme GEO Identifier of the platform O8 GPL21026 72 | Technology DateOfExperiment Technology_DateOfExperiment Date Of Experiment Date Of Experiment Date optional Date de l'expérience Date when the experiment was performed O9 2018-20-03 73 | Panel Name Panel_Name Name Name OSIRIS:PanelName String optional Nom du panel ciblé utilisé (fournisseur suivi du nom du panel) Name of the panel targeted by the experimental analysis (provider followed by the panel name) O10 Ion AmpliSeq Cancer Hotspot Panel v2 74 | AnalysisProcess AnalyticPipelineCode AnalysisProcess_AnalyticPipelineCode Analytic Pipeline Code Analytic Pipeline Code String mandatory Identifiant du pipeline utilisé pour l'analyse (unique dans le centre) Identifier of the pipeline used into the analysis (unique in the center) O11 sbd54dsf57s 75 | OmicAnalysis AlgorithmicCellularity OmicAnalysis_AlgorithmicCellularity Algorithmic Cellularity Algorithmic Cellularity Integer optional Pourcentage de cellules tumorales calculé pour l'échantillon Calculated percentage of tumor cells in sample O12 50 76 | OmicAnalysis AlgorithmicPloidy OmicAnalysis_AlgorithmicPloidy Algorithmic Ploidy Algorithmic Ploidy OSIRIS:AlgorithmicPloidy String optional Nombre de sets de chromosomes calculé pour une cellules de l'échantillon Calculated number of sets of chromosomes in a cell of the sample O13 O13-2 77 | OmicAnalysis NumberOfBreakPoints OmicAnalysis_NumberOfBreakPoints Number Of Break Points Number Of Break Points Integer optional Nombre de cassures calculé pour un profile génomique Calculated number of break points in genomic profile O14 320 78 | AlterationOnSample AlterationType AlterationOnSample_AlterationType Alteration Type Alteration Type OSIRIS:AlterationType String mandatory Type général de l'altération génétique (type de haut niveau) General type of the detected genetic alteration (high level type) O15 Copy number variation 79 | AlterationOnSample Pathogenicity AlterationOnSample_Pathogenicity Pathogenicity Pathogenicity OSIRIS:AlterationOnSample_Pathogenicity String optional Conclusion du biologiste sur la pathogénicité du variant avant la rcpm Conclusion of the biologist on the pathogenicity of the variant before the Molecular Tumor Board O81 80 | AlterationOnSample Actionability AlterationOnSample_Actionability Actionability Actionability OSIRIS:AlterationOnSample_Actionability String optional Conclusion du clinicien sur l'actionabilité du variant lors de la rcpm Conclusion of the clinicians wether the variant is actionable or not during the Molecular Tumor Board O82 81 | AlterationOnSample ProposedForOrientation AlterationOnSample_ProposedForOrientation Proposed For Orientation Proposed For Orientation OSIRIS:Boolean String optional La conclusion de la RCPM a-t-elle été utilisée pour l'orientation thérapeutique du patient? Is the ClinicalTumorBoardConclusion used to orient the treatment decision ? O83 82 | Validation Type Validation_Type Type Type OSIRIS:ValidationType String mandatory if ObjectClass is set Type de validation de l'altération détectée Type of validation of the detected alteration O16 Experimental, by biologist 83 | Validation Method Validation_Method Method Method String mandatory if ObjectClass is set Méthode de validation en fonction du type de validation Validation method depending on the type of validation O17 84 | Validation Status Validation_Status Status Status OSIRIS:ValidationStatus String mandatory if ObjectClass is set Status de validation de l'altération détectée Validation status of the detected alteration O18 Validated 85 | Alteration Chromosome Alteration_Chromosome Chromosome Chromosome OSIRIS:Chromosome String mandatory Chromosome contenant l'altération détectée Chromosome containing the genetic finding O19 86 | Alteration GenomicStart Alteration_GenomicStart Genomic Start Genomic Start Integer mandatory Localisation du nucléotide de début de l'altération détectée Nucleotide location for start of genomic finding on the positive (+) genomics strand, 1-based O20 87 | Alteration GenomicStop Alteration_GenomicStop Genomic Stop Genomic Stop Integer mandatory Localisation des nucléotides pour la fin de l'altération génomique sur le brin génomique positif (+), basé sur 1 Nucleotide location for end of genomic finding on the positive (+) genomic strand, 1-based O21 88 | Alteration GenomeBuild Alteration_GenomeBuild Genome Build Genome Build FHIR:Sequence String mandatory Version du génome utilisée comme référence Genome Build used for reference O22 89 | Alteration Cytoband Alteration_Cytoband Cytoband Cytoband String optional Localisation cytogénétique Cytogenetic location O23 90 | GenomeEntity Type GenomeEntity_Type Type Type OSIRIS:GenomeEntityType String mandatory Type de l'entité du génome. Par exemple: gène, ARNm, ARNnc .. Type of the genome entity. For eg: gene, mRNA, ncRNA... O24 91 | GenomeEntity Database GenomeEntity_Database Database Database OSIRIS:GenomeEntityDatabase String mandatory Base de données de l'entité génomique Database of the genome entity O25 92 | GenomeEntity Id GenomeEntity_Id Id Id String mandatory Identifiant de l'entité génomique dans la base de données d'entités génomiques Identifier of the genome entity in the genome entity database O26 93 | GenomeEntity Symbol GenomeEntity_Symbol Symbol Symbol String mandatory if Gene Symbole Hugo du gène Hugo gene symbol O27 94 | Fusion Type Fusion_Type Type Type OSIRIS:FusionType String optional Type de l'événement de fusion. Par exemple: translocation, readthrough Type of the fusion event. For eg: translocation, readthrough O28 95 | Fusion Point5prime Fusion_Point5prime Point 5 prime Point 5 prime Integer mandatory Position du point de fusion sur le partenaire en 5 prime Position of the fusion point on the 5 prime partner O35 96 | Fusion Chromosome5prime Fusion_Chromosome5prime Chromosome 5 prime Chromosome 5 prime OSIRIS:Chromosome String mandatory Chromosome du point de fusion sur le partenaire en 5 prime O97 97 | Fusion Point3prime Fusion_Point3prime Point 3 prime Point 3 prime Integer mandatory Position du point de fusion sur le partenaire en 3 prime Position of the fusion point on the 3 prime partner O40 98 | Fusion Chromosome3prime Fusion_Chromosome3prime Chromosome 3 prime Chromosome 3 prime OSIRIS:Chromosome String mandatory Chromosome du point de fusion sur le partenaire en 3 prime O98 99 | Fusion InFrame Fusion_InFrame In Frame In Frame OSIRIS:Boolean String optional Indiquez si la fusion est dans le cadre de lecture Specify whether the fusion is in frame O41 100 | Fusion NbSpanningPair Fusion_NbSpanningPair Nb Spanning Pair Nb Spanning Pair Integer mandatory Nombre de paires de reads couvrant la fusion Number of reads pairs spanning the fusion O44 101 | Fusion NbSplitReads Fusion_NbSplitReads Nb Split Reads Nb Split Reads Integer optional Nombre de reads contenant le point de fusion Number of reads containing the fusion point O46 102 | CNV SegmentIntensity CNV_SegmentIntensity Segment Intensity Segment Intensity Float mandatory Intensité du signal mesuré Intensity of the measured signal O47 103 | CNV SegmentGenomicStatus CNV_SegmentGenomicStatus Segment Genomic Status Segment Genomic Status OSIRIS:SegmentGenomicStatus String mandatory Status du nombre de copies Copy number status O49 104 | CNV CopyNumber CNV_CopyNumber Copy Number Copy Number Integer optional Nombre estimé de copies d'ADN Estimated DNA copy number O50 105 | CNV LOH CNV_LOH LOH LOH OSIRIS:Boolean String optional Le segment est-il situé dans une région de perte d'hétérozygotie? (peut être indépendant des informations du numéro de copie Is the segment located in a region of loss of heterozygosity ? (can be independant from copy number information O51 106 | CNV SegmentSize CNV_SegmentSize SegmentSize Taille du segment Integer optional Taille du segment comportant le CNV 107 | Variant ReferenceAllele Variant_ReferenceAllele Reference Allele Reference Allele String mandatory Allèle de référence du brin plus à cette position. Incluez la séquence délétée pour une délétion, ou '-' pour une insertion. Plus strand reference allele at this position. Include the sequence deleted for a deletion, or '-' for an insertion. O53 108 | Variant AlternativeAllele Variant_AlternativeAllele Alternative Allele Alternative Allele String mandatory Allèle alternatif observé du brin plus à cette position. Incluez la séquence délétée pour une délétion, ou '-' pour une insertion. Plus strand observed alternative allele at this position. Include the sequence inserted for a insertion, or '-' for a deletion. O54 109 | Variant DNASequenceVariationType Variant_DNASequenceVariationType DNA Sequence Variation Type DNA Sequence Variation Type LOINC:48019-4 String mandatory Type codifié de la variation de la séquence d'ADN Codified type of the DNA sequence variation O55 110 | Annotation ReferenceType Annotation_ReferenceType Reference Type Reference Type OSIRIS:Annotation_ReferenceType String mandatory if DNASequenceVariation is set O90 111 | Annotation ReferenceDatabase Annotation_ReferenceDatabase Reference Database Reference Database OSIRIS:Annotation_ReferenceDatabase String mandatory if DNASequenceVariation is set O91 112 | Annotation ReferenceValue Annotation_ReferenceValue Reference Value Reference Value String optional O92 113 | Annotation MutationPredictionAlgorithm Annotation_MutationPredictionAlgorithm Mutation Prediction Algorithm Mutation Prediction Algorithm OSIRIS:MutationPredictionAlgorithm String optional Algorithme pour prédire l'effet de variation sur la protéine Algorithm to predict the variation effect over the protein O63 114 | Annotation MutationPredictionValue Annotation_MutationPredictionValue Mutation Prediction Value Mutation Prediction Value String optional Prédiction de l'effet de variation sur la protéine Prediction of the variation effect over the protein O64 115 | Annotation MutationPredictionScore Annotation_MutationPredictionScore Mutation Prediction Score Mutation Prediction Score Float optional Niveau de confiance de la prédiction de l'effet de variation sur la protéine Level of confidence of the prediction of the variation effect over the protein O65 116 | Annotation PfamDomain Annotation_PfamDomain Pfam Domain Pfam Domain String optional Domaines Pfams liés à la position d'altération Pfams domains related to alteration position O58 117 | Annotation PfamId Annotation_PfamId Pfam Id Pfam Id String optional Identifiant des domaines Pfams liés à la position d'altération Identifier of Pfams domains related to alteration position O59 118 | Annotation DNARegionName Annotation_DNARegionName DNA Region Name DNA Region Name String optional Nom lisible par l'homme de la région d'intérêt liée au transcript (ex: exon1, intron1, UTR3 ') Human readable name for the region of interest related to the transcript (eg: exon1, intron1, UTR3') O66 119 | Annotation DNASequenceVariation Annotation_DNASequenceVariation DNA Sequence Variation DNA Sequence Variation String mandatory Nomenclature HGVS sur le transcript choisi HGVS nomenclature on the chosen transcript O71 c.6964C>T 120 | Annotation AminoAcidChange Annotation_AminoAcidChange Amino Acid Change Amino Acid Change String optional Nomenclature HGVS sur le transcript de protéine choisi HGVS nomenclature on the chosen protein transcript O72 p.Arg2322Cys 121 | Annotation GenomicSequenceVariation Annotation_GenomicSequenceVariation Genomic Sequence Variation Genomic Sequence Variation String optional Nomenclature HGVS sur le GenomeReferenceSequenceId choisi HGVS nomenclature on the given GenomeReferenceSequenceId. O73 g.1567234_1567235insTG 122 | Annotation RNASequenceVariation Annotation_RNASequenceVariation RNA Sequence Variation RNA Sequence Variation String optional HGVS nomenclature sur le TranscriptReferenceSequenceId choisi et expérimentalement observé sur l'ARN. HGVS nomenclature on the given TranscriptReferenceSequenceId and experimentely observed on RNA. O74 r.67g>u 123 | Annotation AminoAcidChangeType Annotation_AminoAcidChangeType Amino Acid Change Type Amino Acid Change Type OSIRIS:AminoAcidChangeType String optional Nomenclature des changements au niveau des protéines nomenclature of changes at protein-level O75 124 | Annotation FusionPrimeEnd Annotation_FusionPrimeEnd Fusion Prime End Fusion Prime End OSIRIS:Annotation_FusionPrimeEnd String optional Indication du prime end du partenaire de fusion Prime end of the fusion partner O93 5prime 125 | Annotation Strand Annotation_Strand Strand Strand OSIRIS:Strand String optional Brin Strand O94 + 126 | Annotation OnSplicingSite Annotation_OnSplicingSite OnSplicingSite Sur site d'épissage OSIRIS:Boolean String optional Indication que la variation est sur un site de splicing Indicate wether the variant is on a splicing site O95 127 | VariantInSample PositionReadDepth VariantInSample_PositionReadDepth Position Read Depth Position Read Depth Integer mandatory Profondeur totale de séquençage à la position du variant observée dans l'échantillon Total sequencing depth at the variant position observed in the specimen O76 128 | VariantInSample VariantReadDepth VariantInSample_VariantReadDepth Variant Read Depth Variant Read Depth Integer mandatory Profondeur de séquençage de l'allèle alternatif à la position variant observée dans l'échantillon Sequencing depth of the alternative allele at the variant position observed in the specimen O77 129 | VariantInSample StrandBias VariantInSample_StrandBias Strand Bias Strand Bias OSIRIS:Boolean String optional Indication de l'existence d'un biais de brin à la position du variant Indication of the existence of strand bias at the variant position O78 130 | VariantInSample GenomicSourceClass VariantInSample_GenomicSourceClass Genomic Source Class Genomic Source Class LOINC:LL378-1 String mandatory Classe génomique du variant (par exemple: constitutionel, somatique et prénatal) Genomic class of the variant (eg: germline, somatic, and prenatal) O79 Somatic 131 | VariantInSample AllelicState VariantInSample_AllelicState Allelic State Allelic State LOINC:LL381-5 String optional Niveau d'occurrence allélique d'une variation de séquence d'ADN Level of allelic occurrence of a DNA Sequence Variation O80 132 | GeneExpression DataType GeneExpression_DataType Data Type Data Type OSIRIS:ExpressionDataType String mandatory Type de la valeur d'expression correspondant au niveau de traitement des données Type of the expression value corresponding to the level of data processing O84 133 | GeneExpression Value GeneExpression_Value Value Value Float mandatory Valeur numérique de l'expression Numerical value for expression O85 134 | Equipment ModelName Equipment_ModelName Manufacturer's model name DICOM dicomTag (0008,1090) I1 135 | Equipment Manufacturer Equipment_Manufacturer Manufacturer's name DICOM dicomTag (0008,0070) I2 136 | Study StudyInstanceUID Study_StudyInstanceUID Study Instance UID DICOM dicomTag (0020,000D) I3 137 | Study StudyDescription Study_StudyDescription Study description DICOM dicomTag (0008,1030) I4 138 | Study AcquisitionDate Study_AcquisitionDate Acquisition date DICOM dicomTag (0008, 0032), (0008, 0022) or dicomTag (0008, 0021), (0008, 0023) or dicomTag (0008, 0031), (0008, 0033) I5 139 | Study Location Study_Location Location AE title etc ? IP adress port ? PACS CLB ou web server? ou ID Patient? I6 140 | Study InstitutionName Study_InstitutionName Institution's name DICOM dicomTag (0008,0080) I7 141 | Study ModalitiesInStudy Study_ModalitiesInStudy Modalities in study DICOM dicomTag (0008,0061) I8 142 | Study NbStudyRelatedSeries Study_NbStudyRelatedSeries Number of Study Related Series DICOM dicomtag(0020,1206) I9 143 | Series SeriesNumber Series_SeriesNumber Series Number DICOM dicomTag(0020,0011) I10 144 | Series SeriesInstanceUID Series_SeriesInstanceUID Series Instance UID DICOM dicomTag (0020,000E) I11 145 | Series Modality Series_Modality Modality DICOM dicomTag (0008, 0060) I12 146 | Series Description Series_Description Description DICOM dicomTag (00e1, 1040), (0008, 103e), (0008, 1030) I13 147 | Series BodyPartExamined Series_BodyPartExamined Body Part Examined DICOM dicomTag (0018,0015) I14 148 | Series NbSeriesRelatedInstances Series_NbSeriesRelatedInstances Number of Series Related Instances DICOM dicomtag (0020,1209) I15 149 | Series SoftwareVersion Series_SoftwareVersion Software's version DICOM dicomTag (0018,1020) I16 150 | Injection Radiopharmaceutical Injection_Radiopharmaceutical Radiopharmaceutical DICOM dicomTag (0018,0031) I17 151 | Injection ContrastBolusAgent Injection_ContrastBolusAgent Contrast/bolus agent DICOM dicomTag (0018,0010) I18 152 | Injection ContrastBolusStartTime Injection_ContrastBolusStartTime Contrast/bolus start time DICOM dicomTag (0018,1042) I19 153 | Injection ContrastBolusStopTime Injection_ContrastBolusStopTime Contrast/bolus stop time DICOM dicomTag (0018,1043) I20 154 | Injection RadiopharmaceuticalStartTime Injection_RadiopharmaceuticalStartTime Radiopharmaceutical start time DICOM dicomTag (0018,1072) I21 155 | Injection RadionuclideTotalDose Injection_RadionuclideTotalDose Radionuclide total dose DICOM dicomTag (0018,1074) I22 156 | CommonImage SOPInstanceUID CommonImage_SOPInstanceUID SOP Instance UID DICOM dicomtag (0008,0018) I23 157 | CommonImage SliceThickness CommonImage_SliceThickness Slice thickness DICOM dicomTag (0018,0050) I24 158 | CommonImage PixelSpacing CommonImage_PixelSpacing Pixel spacing DICOM dicomTag (0028,0030) I25 159 | CommonImage FieldOfView CommonImage_FieldOfView Field of view I26 160 | CommonImage Rows CommonImage_Rows rows DICOM dicomTag (0028,0010) I27 161 | CommonImage Columns CommonImage_Columns columns DICOM dicomTag (0028,0011) I28 162 | MRImage SequenceName MRImage_SequenceName Sequence's name DICOM dicomTag (0018,0024) I29 163 | MRImage MagneticFieldStrength MRImage_MagneticFieldStrength Magnetic field strength DICOM dicomTag (0018,0087) I30 164 | MRImage MRAcquisitionType MRImage_MRAcquisitionType MR acquisition type DICOM dicomTag (0018,0023) I31 165 | MRImage RepetitionTime MRImage_RepetitionTime Repetition time DICOM dicomTag (0018,0080) I32 166 | MRImage EchoTime MRImage_EchoTime EchoTime DICOM dicomTag (0018,0081) I33 167 | MRImage ImagingFrequency MRImage_ImagingFrequency ImagingFrequency DICOM dicomTag (0018,0084) I34 168 | MRImage FlipAngle MRImage_FlipAngle FlipAngle DICOM dicomTag (0018,0024) I35 169 | MRImage InversionTime MRImage_InversionTime InversionTime DICOM dicomTag (0018,0082) I36 170 | MRImage ReceiveCoilName MRImage_ReceiveCoilName ReceiveCoilName DICOM dicomTag (0018,1250) I37 171 | CTImage KVp CTImage_KVp KVp DICOM dicomTag (0018,0060) I38 172 | CTImage XRayTubeCurrent CTImage_XRayTubeCurrent XRayTubeCurrent DICOM dicomTag (0018,1151) I39 173 | CTImage ExposureTime CTImage_ExposureTime ExposureTime DICOM dicomTag (0018,1150) I40 174 | CTImage SpiralPitchFactor CTImage_SpiralPitchFactor SpiralPitchFactor DICOM dicomTag (0018,9311) I41 175 | CTImage FilterType CTImage_FilterType FilterType DICOM dicomTag (0018,1160) I42 176 | CTImage ConvolutionKernel CTImage_ConvolutionKernel ConvolutionKernel DICOM dicomTag (0018,1210) I43 177 | PTImage AttenuationCorrectionMethod PTImage_AttenuationCorrectionMethod AttenuationCorrectionMethod DICOM dicomTag (0054,1101) I44 178 | PTImage ReconstructionMethod PTImage_ReconstructionMethod ReconstructionMethod DICOM dicomTag (0054,1103) I45 179 | PTImage ScatterCorrectionMethod PTImage_ScatterCorrectionMethod ScatterCorrectionMethod DICOM dicomTag (0054,1105) I46 180 | NMImage AttenuationCorrectionMethod NMImage_AttenuationCorrectionMethod AttenuationCorrectionMethod DICOM dicomTag (0054,1101) I47 181 | NMImage ReconstructionMethod NMImage_ReconstructionMethod ReconstructionMethod DICOM dicomTag (0054,1103) I48 182 | NMImage ScatterCorrectionMethod NMImage_ScatterCorrectionMethod ScatterCorrectionMethod DICOM dicomTag (0054,1105) I49 183 | DXImage ImageLaterality DXImage_ImageLaterality ImageLaterality DICOM dicomTag (0020,0062) I50 184 | DXImage PatientOrientation DXImage_PatientOrientation PatientOrientation DICOM dicomTag (0020,0020) I51 185 | DXImage AnatomicRegionSequenceCodeMeaning DXImage_AnatomicRegionSequenceCodeMeaning AnatomicRegionSequenceCodeMeaning DICOM dicomTag (0008,0104) I52 186 | DXImage Anatomic Region SequenceCodeValue DXImage_Anatomic Region SequenceCodeValue Anatomic Region SequenceCodeValue DICOM dicomTag (0008,0100) I53 187 | DXImage KVP DXImage_KVP KVP DICOM dicomTag (0008,0060) I54 188 | DXImage Exposure DXImage_Exposure Exposure DICOM dicomTag (0018,1152) I55 189 | DXImage ExposureTime DXImage_ExposureTime ExposureTime DICOM dicomTag (0018,1150) I56 190 | DXImage ContrastBolusAgent DXImage_ContrastBolusAgent ContrastBolusAgent DICOM dicomTag(0018,0010) I57 191 | ROISegmentation ReferencedSOPInstanceUID ROISegmentation_ReferencedSOPInstanceUID ReferencedSOPInstanceUID DICOM dicomtag (0008,1150) I58 192 | ROISegmentation ROINumber ROISegmentation_ROINumber ROINumber DICOM dicomtag (3006,0084) I59 193 | ROISegmentation ROIName ROISegmentation_ROIName ROIName DICOM dicomtag (3006,0026) I60 194 | ROISegmentation ROIDescription ROISegmentation_ROIDescription ROIDescription DICOM dicomtag (3006,0028) I61 195 | ROISegmentation ROIType ROISegmentation_ROIType ROIType I62 196 | ROISegmentation ROIFilename ROISegmentation_ROIFilename ROIFilename I63 197 | RadiomicsCriteria SoftwareName RadiomicsCriteria_SoftwareName SoftwareName IBSI? I64 198 | RadiomicsCriteria SoftwareVersion RadiomicsCriteria_SoftwareVersion SoftwareVersion IBSI? I65 199 | RadiomicsCriteria Method RadiomicsCriteria_Method Method IBSI? I66 200 | RadiomicsCriteria UsedImageFilter RadiomicsCriteria_UsedImageFilter UsedImageFilter IBSI? I67 201 | RadiomicsCriteria DistanceWeighting RadiomicsCriteria_DistanceWeighting DistanceWeighting IBSI? I68 202 | RadiomicsCriteria NumberOfGreyLevels RadiomicsCriteria_NumberOfGreyLevels NumberOfGreyLevels IBSI? I69 203 | RadiomicsCriteria BinSize RadiomicsCriteria_BinSize BinSize IBSI? I70 204 | RadiomicsCriteria IntensityResampling RadiomicsCriteria_IntensityResampling IntensityResampling IBSI? I71 205 | RadiomicsCriteria LowestIntensity RadiomicsCriteria_LowestIntensity LowestIntensity IBSI? I72 206 | RadiomicsCriteria BoundsRangeOfValueAfterDiscretisation RadiomicsCriteria_BoundsRangeOfValueAfterDiscretisation BoundsRangeOfValueAfterDiscretisation IBSI? I73 Uniquely identifies the referenced id or filename 207 | RadiomicsCriteria SpatialResamplingMethod RadiomicsCriteria_SpatialResamplingMethod SpatialResamplingMethod IBSI? I74 208 | RadiomicsCriteria SpatialResamplingValues RadiomicsCriteria_SpatialResamplingValues SpatialResamplingValues IBSI? I75 209 | RadiomicsCriteria TextureMatrixAggregation RadiomicsCriteria_TextureMatrixAggregation TextureMatrixAggregation IBSI? I76 210 | RadiomicsImageFilter SoftwareName RadiomicsImageFilter_SoftwareName SoftwareName IBSI? I77 211 | RadiomicsImageFilter SoftwareVersion RadiomicsImageFilter_SoftwareVersion SoftwareVersion IBSI? I78 212 | RadiomicsImageFilter FilterName RadiomicsImageFilter_FilterName FilterName IBSI? I79 213 | RadiomicsImageFilter FilterType RadiomicsImageFilter_FilterType FilterType IBSI? I80 214 | RadiomicsImageFilter FilterInterpolation RadiomicsImageFilter_FilterInterpolation FilterInterpolation IBSI? I81 215 | RadiomicsImageFilter IntensityRounding RadiomicsImageFilter_IntensityRounding IntensityRounding IBSI? I82 216 | RadiomicsImageFilter BoundaryCondition RadiomicsImageFilter_BoundaryCondition BoundaryCondition IBSI? I83 217 | RadiomicsFeature Id RadiomicsFeature_Id Id IBSI? I84 218 | RadiomicsFeature Name RadiomicsFeature_Name Name IBSI? I85 219 | RadiomicsFeature Value RadiomicsFeature_Value Value IBSI? I86 220 | 221 | 222 | 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | --------------------------------------------------------------------------------