diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..2dbed37 Binary files /dev/null and b/.DS_Store differ diff --git a/.gitignore b/.gitignore index 0abed45..13414f8 100644 --- a/.gitignore +++ b/.gitignore @@ -35,4 +35,6 @@ build/ ## others -run.sh \ No newline at end of file +run.sh +.ipynb_checkpoints/data_generate-checkpoint.ipynb +data_generate.ipynb diff --git a/.gitignore.swp b/.gitignore.swp new file mode 100644 index 0000000..b517bfb Binary files /dev/null and b/.gitignore.swp differ diff --git a/example-data/sequencing_alignment_sample_schema.json b/example-data/sequencing_alignment_sample_schema.json index 19833a5..05e43fd 100644 --- a/example-data/sequencing_alignment_sample_schema.json +++ b/example-data/sequencing_alignment_sample_schema.json @@ -347,7 +347,7 @@ "enum":[ "Accessory sinuses", "Adrenal gland", - "Anus and anal canal", + "Pancreas", "Base of tongue", "Bladder", "Bones, joints and articular cartilage of limbs", diff --git a/example-data/sequencing_experiment_sample_schema.json b/example-data/sequencing_experiment_sample_schema.json index ee28a7c..6524dc0 100644 --- a/example-data/sequencing_experiment_sample_schema.json +++ b/example-data/sequencing_experiment_sample_schema.json @@ -274,7 +274,7 @@ "enum":[ "Accessory sinuses", "Adrenal gland", - "Anus and anal canal", + "Pancreas", "Base of tongue", "Bladder", "Bones, joints and articular cartilage of limbs", diff --git a/example-data/variant_calling_sample_schema.json b/example-data/variant_calling_sample_schema.json index 72a3fbe..8911b74 100644 --- a/example-data/variant_calling_sample_schema.json +++ b/example-data/variant_calling_sample_schema.json @@ -158,7 +158,7 @@ "enum":[ "Accessory sinuses", "Adrenal gland", - "Anus and anal canal", + "Pancreas", "Base of tongue", "Bladder", "Bones, joints and articular cartilage of limbs", diff --git a/playground-data/.DS_Store b/playground-data/.DS_Store new file mode 100644 index 0000000..368cc74 Binary files /dev/null and b/playground-data/.DS_Store differ diff --git a/playground-data/arranger-metadata/aggs-state.json b/playground-data/arranger-metadata/aggs-state.json new file mode 100644 index 0000000..5e3d9af --- /dev/null +++ b/playground-data/arranger-metadata/aggs-state.json @@ -0,0 +1,236 @@ +[ + { + "field": "analysis__first_published_at", + "active": true, + "show": false, + "__typename": "AggState" + }, + { + "field": "analysis__published_at", + "active": true, + "show": false, + "__typename": "AggState" + }, + { + "field": "analysis__updated_at", + "active": true, + "show": false, + "__typename": "AggState" + }, + { + "field": "study_id", + "active": true, + "show": true, + "__typename": "AggState" + }, + { + "field": "analysis__analysis_type", + "active": true, + "show": true, + "__typename": "AggState" + }, + { + "field": "donors__gender", + "active": true, + "show": true, + "__typename": "AggState" + }, + { + "field": "donors__specimens__samples__sample_type", + 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differ diff --git a/playground-data/data_files/anon_chr1_complete.bam.bai b/playground-data/data_files/anon_chr1_complete.bam.bai new file mode 100644 index 0000000..fc82ca1 Binary files /dev/null and b/playground-data/data_files/anon_chr1_complete.bam.bai differ diff --git a/playground-data/example-payloads/.ipynb_checkpoints/alignment_bam-checkpoint.json b/playground-data/example-payloads/.ipynb_checkpoints/alignment_bam-checkpoint.json new file mode 100644 index 0000000..7be8365 --- /dev/null +++ b/playground-data/example-payloads/.ipynb_checkpoints/alignment_bam-checkpoint.json @@ -0,0 +1,174 @@ +{ + "samples": [ + { + "submitterSampleId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", + "sampleType": "Total DNA", + "matchedNormalSubmitterSampleId": null, + "specimen": { + "submitterSpecimenId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", + "specimenType": "Normal - tissue adjacent to primary tumour", + "specimenTissueSource": "Urine", + "tumourNormalDesignation": "Normal" + }, + "donor": { 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b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json @@ -0,0 +1,176 @@ +{ + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", + "samples": [ + { + "submitterSampleId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", + "sampleType": "Total DNA", + "matchedNormalSubmitterSampleId": null, + "specimen": { + "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", + "specimenType": "Pancreas", + "specimenTissueSource": "Sputum", + "tumourNormalDesignation": "Normal" + }, + "donor": { + "submitterDonorId": "TEST_DONOR_hjdxmpeccamrjzybhqrl", + "gender": "Female" + } + } + ], + "donor": { + "submitterDonorId": "TEST_DONOR_hjdxmpeccamrjzybhqrl", + "primarySite": [ + "Pancreas" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ + { + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", + "ageAtDiagnosis": 27, + "cancerTypeCode": "C21.2", + "laterality": "Bilateral", 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a/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json new file mode 100644 index 0000000..464a76e --- /dev/null +++ b/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json @@ -0,0 +1,196 @@ +{ + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", + "samples": [ + { + "submitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_T1", + "sampleType": "Total DNA", + "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimen": { + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_T1", + "specimenType": "Tumour - unknown if derived from primary or metastatic", + "specimenTissueSource": "Blood derived - peripheral blood", + "tumourNormalDesignation": "Tumour" + }, + "donor": { + "submitterDonorId": "TEST_DONOR_zscpyibaevspyxlkyaip", + "gender": "Male" + } + } + ], + "donor": { + "submitterDonorId": 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b/playground-data/jbrowse-config/.ipynb_checkpoints/alignment_bam_hg38-checkpoint.json new file mode 100644 index 0000000..cc2240c --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/alignment_bam_hg38-checkpoint.json @@ -0,0 +1,64 @@ +{ + "type": "AlignmentsTrack", + "trackId": "anon_chr1_complete.bam-1702318669309-sessionTrack", + "name": "anon_chr1_complete.bam", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BamAdapter", + "bamLocation": { + "locationType": "BlobLocation", + "name": "anon_chr1_complete.bam", + "blobId": "b1702318658137-0" + }, + "index": { + "location": { + "locationType": "BlobLocation", + "name": "anon_chr1_complete.bam.bai", + "blobId": "b1702318664524-1" + } + }, + "sequenceAdapter": { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz" + }, + "faiLocation": { + "locationType": "UriLocation", + "uri": 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+} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/alignment_cram.hg38-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/alignment_cram.hg38-checkpoint.json new file mode 100644 index 0000000..6732945 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/alignment_cram.hg38-checkpoint.json @@ -0,0 +1,62 @@ +{ + "type": "AlignmentsTrack", + "trackId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack", + "name": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "CramAdapter", + "cramLocation": { + "locationType": "BlobLocation", + "name": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram", + "blobId": "b1702318762933-2" + }, + "craiLocation": { + "locationType": "BlobLocation", + "name": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram.crai", + "blobId": "b1702318767264-3" + }, + "sequenceAdapter": { + "type": 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+ "bedpeLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF327GBZ/@@download/ENCFF327GBZ.bedpe.gz" + } + }, + "displays": [ + { + "type": "LinearVariantDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-LinearVariantDisplay" + }, + { + "type": "ChordVariantDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-ChordVariantDisplay" + }, + { + "type": "LinearPairedArcDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-LinearPairedArcDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_foldchange_bigwig-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_foldchange_bigwig-checkpoint.json new file mode 100644 index 0000000..ba24707 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_foldchange_bigwig-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff140qly.bigwig-1702320857138-sessionTrack", + "name": "ENCFF140QLY.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF140QLY/@@download/ENCFF140QLY.bigWig" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "encff140qly.bigwig-1702320857138-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_pval_bigwig-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_pval_bigwig-checkpoint.json new file mode 100644 index 0000000..44db553 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_pval_bigwig-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff561sgx.bigwig-1702321270752-sessionTrack", + "name": "ENCFF561SGX.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF561SGX/@@download/ENCFF561SGX.bigWig" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "encff561sgx.bigwig-1702321270752-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/hic_hic-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_hic-checkpoint.json new file mode 100644 index 0000000..1ef9fdc --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_hic-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "HicTrack", + "trackId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.merge.hic-1702319986845-sessionTrack", + "name": "GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.merge.hic", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "HicAdapter", + "hicLocation": { + "locationType": "UriLocation", + "uri": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174533/suppl/GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.merge.hic" + } + }, + "displays": [ + { + "type": "LinearHicDisplay", + "displayId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.merge.hic-1702319986845-sessionTrack-LinearHicDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/hic_insulation_bigwig-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_insulation_bigwig-checkpoint.json new file mode 100644 index 0000000..38c3c1f --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_insulation_bigwig-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.insulationscore.bw-1702320154801-sessionTrack", + "name": "GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.insulationScore.bw", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174533/suppl/GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.insulationScore.bw" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.insulationscore.bw-1702320154801-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/hic_pc1_bigwig-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_pc1_bigwig-checkpoint.json new file mode 100644 index 0000000..e87b2f7 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_pc1_bigwig-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "gse174533%5f11%2dp53%2d15%2dd23.pc1.bw-1702320228955-sessionTrack", + "name": "GSE174533%5F11%2DP53%2D15%2Dd23.PC1.bw", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174533/suppl/GSE174533%5F11%2DP53%2D15%2Dd23.PC1.bw" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "gse174533%5f11%2dp53%2d15%2dd23.pc1.bw-1702320228955-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_coverage_bigWig-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_coverage_bigWig-checkpoint.json new file mode 100644 index 0000000..347361a --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_coverage_bigWig-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff750ori.bigwig-1702321769798-sessionTrack", + "name": "ENCFF750ORI.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF750ORI/@@download/ENCFF750ORI.bigWig" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "encff750ori.bigwig-1702321769798-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_methylation_bigBed-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_methylation_bigBed-checkpoint.json new file mode 100644 index 0000000..5df1834 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_methylation_bigBed-checkpoint.json @@ -0,0 +1,25 @@ +{ + "type": "FeatureTrack", + "trackId": "encff256off.bigbed-1702321430813-sessionTrack", + "name": "ENCFF256OFF.bigBed", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigBedAdapter", + "bigBedLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF256OFF/@@download/ENCFF256OFF.bigBed" + } + }, + "displays": [ + { + "type": "LinearBasicDisplay", + "displayId": "encff256off.bigbed-1702321430813-sessionTrack-LinearBasicDisplay" + }, + { + "type": "LinearArcDisplay", + "displayId": "encff256off.bigbed-1702321430813-sessionTrack-LinearArcDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/alignment_bam_hg38.json b/playground-data/jbrowse-config/alignment_bam_hg38.json new file mode 100644 index 0000000..cc2240c --- /dev/null +++ b/playground-data/jbrowse-config/alignment_bam_hg38.json @@ -0,0 +1,64 @@ +{ + "type": "AlignmentsTrack", + "trackId": "anon_chr1_complete.bam-1702318669309-sessionTrack", + "name": "anon_chr1_complete.bam", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BamAdapter", + "bamLocation": { + "locationType": "BlobLocation", + "name": "anon_chr1_complete.bam", + "blobId": "b1702318658137-0" + }, + "index": { + "location": { + "locationType": "BlobLocation", + "name": "anon_chr1_complete.bam.bai", + "blobId": "b1702318664524-1" + } + }, + "sequenceAdapter": { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz" + }, + "faiLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai" + }, + "metadataLocation": { + "locationType": "UriLocation", + "uri": "/path/to/fa.metadata.yaml" + }, + "gziLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi" + } + } + }, + "displays": [ + { + "type": "LinearAlignmentsDisplay", + "displayId": "anon_chr1_complete.bam-1702318669309-sessionTrack-LinearAlignmentsDisplay" + }, + { + "type": "LinearPileupDisplay", + "displayId": "anon_chr1_complete.bam-1702318669309-sessionTrack-LinearPileupDisplay" + }, + { + "type": "LinearSNPCoverageDisplay", + "displayId": "anon_chr1_complete.bam-1702318669309-sessionTrack-LinearSNPCoverageDisplay" + }, + { + "type": "LinearReadArcsDisplay", + "displayId": "anon_chr1_complete.bam-1702318669309-sessionTrack-LinearReadArcsDisplay" + }, + { + "type": "LinearReadCloudDisplay", + "displayId": "anon_chr1_complete.bam-1702318669309-sessionTrack-LinearReadCloudDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/alignment_cram.hg38.json b/playground-data/jbrowse-config/alignment_cram.hg38.json new file mode 100644 index 0000000..6732945 --- /dev/null +++ b/playground-data/jbrowse-config/alignment_cram.hg38.json @@ -0,0 +1,62 @@ +{ + "type": "AlignmentsTrack", + "trackId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack", + "name": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "CramAdapter", + "cramLocation": { + "locationType": "BlobLocation", + "name": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram", + "blobId": "b1702318762933-2" + }, + "craiLocation": { + "locationType": "BlobLocation", + "name": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram.crai", + "blobId": "b1702318767264-3" + }, + "sequenceAdapter": { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz" + }, + "faiLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai" + }, + "metadataLocation": { + "locationType": "UriLocation", + "uri": "/path/to/fa.metadata.yaml" + }, + "gziLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi" + } + } + }, + "displays": [ + { + "type": "LinearAlignmentsDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearAlignmentsDisplay" + }, + { + "type": "LinearPileupDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearPileupDisplay" + }, + { + "type": "LinearSNPCoverageDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearSNPCoverageDisplay" + }, + { + "type": "LinearReadArcsDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearReadArcsDisplay" + }, + { + "type": "LinearReadCloudDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearReadCloudDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/chipseq_IDR_bigBed.json b/playground-data/jbrowse-config/chipseq_IDR_bigBed.json new file mode 100644 index 0000000..cde5021 --- /dev/null +++ b/playground-data/jbrowse-config/chipseq_IDR_bigBed.json @@ -0,0 +1,25 @@ +{ + "type": "FeatureTrack", + "trackId": "encff772oad.bigbed-1702320934124-sessionTrack", + "name": "ENCFF772OAD.bigBed", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigBedAdapter", + "bigBedLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF772OAD/@@download/ENCFF772OAD.bigBed" + } + }, + "displays": [ + { + "type": "LinearBasicDisplay", + "displayId": "encff772oad.bigbed-1702320934124-sessionTrack-LinearBasicDisplay" + }, + { + "type": "LinearArcDisplay", + "displayId": "encff772oad.bigbed-1702320934124-sessionTrack-LinearArcDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/chipseq_bedpe.json b/playground-data/jbrowse-config/chipseq_bedpe.json new file mode 100644 index 0000000..fdb3cdf --- /dev/null +++ b/playground-data/jbrowse-config/chipseq_bedpe.json @@ -0,0 +1,29 @@ +{ + "type": "VariantTrack", + "trackId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack", + "name": "ENCFF327GBZ.bedpe.gz", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BedpeAdapter", + "bedpeLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF327GBZ/@@download/ENCFF327GBZ.bedpe.gz" + } + }, + "displays": [ + { + "type": "LinearVariantDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-LinearVariantDisplay" + }, + { + "type": "ChordVariantDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-ChordVariantDisplay" + }, + { + "type": "LinearPairedArcDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-LinearPairedArcDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/chipseq_foldchange_bigwig.json b/playground-data/jbrowse-config/chipseq_foldchange_bigwig.json new file mode 100644 index 0000000..ba24707 --- /dev/null +++ b/playground-data/jbrowse-config/chipseq_foldchange_bigwig.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff140qly.bigwig-1702320857138-sessionTrack", + "name": "ENCFF140QLY.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF140QLY/@@download/ENCFF140QLY.bigWig" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "encff140qly.bigwig-1702320857138-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/chipseq_pval_bigwig.json b/playground-data/jbrowse-config/chipseq_pval_bigwig.json new file mode 100644 index 0000000..44db553 --- /dev/null +++ b/playground-data/jbrowse-config/chipseq_pval_bigwig.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff561sgx.bigwig-1702321270752-sessionTrack", + "name": "ENCFF561SGX.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF561SGX/@@download/ENCFF561SGX.bigWig" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "encff561sgx.bigwig-1702321270752-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/hic_hic.json b/playground-data/jbrowse-config/hic_hic.json new file mode 100644 index 0000000..1ef9fdc --- /dev/null +++ b/playground-data/jbrowse-config/hic_hic.json @@ -0,0 +1,21 @@ +{ + "type": "HicTrack", + "trackId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.merge.hic-1702319986845-sessionTrack", + "name": "GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.merge.hic", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "HicAdapter", + "hicLocation": { + "locationType": "UriLocation", + "uri": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174533/suppl/GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.merge.hic" + } + }, + "displays": [ + { + "type": "LinearHicDisplay", + "displayId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.merge.hic-1702319986845-sessionTrack-LinearHicDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/hic_insulation_bigwig.json b/playground-data/jbrowse-config/hic_insulation_bigwig.json new file mode 100644 index 0000000..38c3c1f --- /dev/null +++ b/playground-data/jbrowse-config/hic_insulation_bigwig.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.insulationscore.bw-1702320154801-sessionTrack", + "name": "GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.insulationScore.bw", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174533/suppl/GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.insulationScore.bw" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.insulationscore.bw-1702320154801-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/hic_pc1_bigwig.json b/playground-data/jbrowse-config/hic_pc1_bigwig.json new file mode 100644 index 0000000..e87b2f7 --- /dev/null +++ b/playground-data/jbrowse-config/hic_pc1_bigwig.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "gse174533%5f11%2dp53%2d15%2dd23.pc1.bw-1702320228955-sessionTrack", + "name": "GSE174533%5F11%2DP53%2D15%2Dd23.PC1.bw", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174533/suppl/GSE174533%5F11%2DP53%2D15%2Dd23.PC1.bw" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "gse174533%5f11%2dp53%2d15%2dd23.pc1.bw-1702320228955-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/wgbs_cpg_coverage_bigWig.json b/playground-data/jbrowse-config/wgbs_cpg_coverage_bigWig.json new file mode 100644 index 0000000..347361a --- /dev/null +++ b/playground-data/jbrowse-config/wgbs_cpg_coverage_bigWig.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff750ori.bigwig-1702321769798-sessionTrack", + "name": "ENCFF750ORI.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF750ORI/@@download/ENCFF750ORI.bigWig" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "encff750ori.bigwig-1702321769798-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/wgbs_cpg_methylation_bigBed.json b/playground-data/jbrowse-config/wgbs_cpg_methylation_bigBed.json new file mode 100644 index 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IAS", + "Stage IB", + "Stage IB1", + "Stage IB2", + "Stage IBE", + "Stage IBES", + "Stage IBS", + "Stage IC", + "Stage IE", + "Stage IEA", + "Stage IEB", + "Stage IES", + "Stage II", + "Stage II bulky", + "Stage IIA", + "Stage IIA1", + "Stage IIA2", + "Stage IIAE", + "Stage IIAES", + "Stage IIAS", + "Stage IIB", + "Stage IIBE", + "Stage IIBES", + "Stage IIBS", + "Stage IIC", + "Stage IIE", + "Stage IIEA", + "Stage IIEB", + "Stage IIES", + "Stage III", + "Stage IIIA", + "Stage IIIA1", + "Stage IIIA2", + "Stage IIIAE", + "Stage IIIAES", + "Stage IIIAS", + "Stage IIIB", + "Stage IIIBE", + "Stage IIIBES", + "Stage IIIBS", + "Stage IIIC", + "Stage IIIC1", + "Stage IIIC2", + "Stage IIID", + "Stage IIIE", + "Stage IIIES", + "Stage IIIS", + "Stage IIS", + "Stage IS", + "Stage IV", + "Stage IVA", + "Stage IVA1", + "Stage IVA2", + "Stage IVAE", + "Stage IVAES", + "Stage IVAS", + "Stage IVB", + "Stage IVBE", + "Stage IVBES", + "Stage IVBS", + "Stage IVC", + "Stage IVE", + "Stage IVES", + "Stage IVS", + "Cannot be assessed" + ] + }, + "tumour_grading_system": { + "type": "string", + "enum": [ + "FNCLCC grading system", + "Four-tier grading system", + "Gleason grade group system", + "Grading system for GISTs", + "Grading system for GNETs", + "ISUP grading system", + "Nuclear grading system for DCIS", + "Scarff-Bloom-Richardson grading system", + "Three-tier grading system", + "Two-tier grading system", + "WHO grading system for CNS tumours" + ] + }, + "tumour_grade": { + "type": "string", + "enum": [ + "Low grade", + "High grade", + "GX", + "G1", + "G2", + "G3", + "G4", + "Low", + "High", + "Grade I", + "Grade II", + "Grade III", + "Grade IV", + "Grade Group 1", + "Grade Group 2", + "Grade Group 3", + "Grade Group 4", + "Grade Group 5" + ] + }, + "percent_tumour_cells": { + "type": "integer", + "minimum": 0 + }, + "reference_pathology_confirmed": { + "type": "string", + "enum": [ + "Yes", + "No", + "Unknown" + ] + }, + "cell_line": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "cell_line_name", + "cellosaurus_id", + "treatment" + ] + }, + "required": [ + "cell_line_name" + ], + "properties": { + "cell_line_name": { + "type": "string" + }, + "cellosaurus_id": { + "type": ["string","null"] + }, + "treatment": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum":[ + "treatment_type", + "compound_name", + "duration", + "time_point", + "dosage", + "dosage_units" + ] + }, + "properties":{ + "treatment_typed": { + "type": ["string","null"] + }, + "compound_name": { + "type": ["string","null"] + }, + "duration": { + "type": ["string","null"] + }, + "time_point": { + "type": ["integer","null"] + }, + "dosage": { + "type": ["integer","null"] + }, + "dosage_units": { + "type": ["string"] + } + } + } + } + } + } + } + } + }, + "qualityControl" : { + "type":"array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "test_name", + "test_value", + "expected_value", + "test_measurement_method", + "test_pass" + ] + }, + "properties": { + "test_name": { + "type": "string" + }, + "test_value": { + "type": "string" + }, + "expected_value": { + "type": "string" + }, + "test_measurement_method": { + "type": "string" + }, + "test_pass": { + "type": "string", + "enum":[ + "PASS", + "FAIL", + "WARN" + ] + } + } + } + }, + "publication" : { + "type":"object", + "propertyNames": { + "enum": [ + "title", + "doi" + ] + }, + "properties": { + "title": { + "type": ["string","null"] + }, + "doi": { + "type": ["string","null"] + } + } + }, + "archive" : { + "type":"object", + "propertyNames": { + "enum": [ + "ega", + "sra", + "icgc_argo" + ] + }, + "properties":{ + "EGA": { + "type": "array", + "items": { + "type": "object", + "properties": { + "EGAF": { + "type": "string" + } + } + } + }, + "SRA": { + "type": "array", + "items": { + "type": "object", + "properties": { + "GSE": { + "type": "string" + } + } + } + }, + "icgc_argo": { + "type": "array", + "items": { + "type": "object", + "properties": { + "fileID": { + "type": "string" + } + } + } + } + } + }, + "collaborator" : { + "type":"array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "name", + "contact_email", + "affiliation" + ] + }, + "properties": { + "name": { + "type": "string" + }, + "contact_email": { + "type": ["string","null"], + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "affiliation": { + "type": ["string","null"] + } + } + } + } + } + } + } \ No newline at end of file diff --git a/playground-data/song-schemas/VariantCall.json b/playground-data/song-schemas/VariantCall.json new file mode 100644 index 0000000..c658fd6 --- /dev/null +++ b/playground-data/song-schemas/VariantCall.json @@ -0,0 +1,81 @@ +{ + "studyId" : "ABC123", + "analysisType" : { + "name" : "variantCall" + }, + "experiment": { + "variantCallingTool": "silver bullet", + "matchedNormalSampleSubmitterId": "sample-x24-11a", + "randomField14" : "we can define any EXPERIMENT field. For example, randomField14", + "randomField15" : "as a second example, we can define another random EXPERIMENT field called randomField15", + "info" : { + "randomField16" : "alternatively, put some extra EXPERIMENT fields here" + } + }, + "samples": [ + { + "submitterSampleId": "internal_sample_1", + "sampleType": "Total RNA", + "matchedNormalSubmitterSampleId": "sample-x24-11a", + "specimen": { + "submitterSpecimenId": "internal_specimen_1", + "specimenType": "Primary tumour", + "specimenTissueSource": "Solid tissue", + "tumourNormalDesignation": "Tumour", + "randomField1" : "we can define any SPECIMEN field. For example, randomField1", + "randomField2" : "as a second example, we can define another random SPECIMEN field called randomField2", + "info" : { + "randomField3" : "alternatively, put some extra SPECIMEN fields here" + } + }, + "donor": { + "submitterDonorId": "internal_donor_123456789-00", + "gender": "Female", + "age": 30, + "randomField4" : "we can define any DONOR field. For example, randomField4", + "randomField5" : "as a second example, we can define another random DONOR field called randomField5", + "info" : { + "randomField6" : "alternatively, put some extra DONOR fields here" + } + }, + "randomField7" : "we can define any SAMPLE field. For example, randomField7", + "randomField8" : "as a second example, we can define another random SAMPLE field called randomField8", + "info" : { + "randomField9" : "alternatively, put some extra SAMPLE fields here" + } + } + ], + "files": [ + { + "dataType": "Variant Calling Data", + "fileName": "example.vcf.gz", + "fileSize": 52, + "fileMd5sum": "9a793e90d0d1e11301ea8da996446e59", + "fileAccess" : "open", + "fileType": "VCF", + "randomField10" : "we can define any FILE field. For example, randomField10", + "randomField11" : "as a second example, we can define another random FILE field called randomField11", + "info" : { + "randomField12" : "alternatively, put some extra FILE fields here" + } + }, + { + "dataType": "Variant Calling Index", + "fileName": "example.vcf.gz.idx", + "fileSize": 24, + "fileMd5sum": "c03274816eb4907a92b8e5632cd6eb81", + "fileAccess" : "open", + "fileType": "IDX", + "randomField10" : "we can define any FILE field. For example, randomField10", + "randomField13" : "as a second example, we can define another random FILE field called randomField13", + "info" : { + "randomField12" : "alternatively, put some extra FILE fields here" + } + } + ], + "randomField17" : "we can define any ANALYSIS field. For example, randomField17", + "randomField18" : "as a second example, we can define another random ANALYSIS field called randomField18", + "info" : { + "randomField19" : "alternatively, put some extra ANALYSIS fields here" + } +} diff --git a/playground-data/song-schemas/general.json b/playground-data/song-schemas/general.json new file mode 100644 index 0000000..7390e20 --- /dev/null +++ b/playground-data/song-schemas/general.json @@ -0,0 +1,1461 @@ +{ + "name": "general", + "schema": { + "type": "object", + "required": [ + "workflow", + "experiment", + "donor", + "specimen" + ], + "properties": { + "workflow": { + "propertyNames": { + "enum": [ + "workflow_name", + "workflow_short_name", + "workflow_version", + "genome_build", + "inputs", + "workflow_tools" + ] + }, + "required": [ + "workflow_name", + "genome_build", + "inputs" + ], + "type": "object", + "properties": { + "workflow_name": { + "type": "string", + "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$" + }, + "workflow_short_name": { + "type": "string", + "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+[a-zA-Z0-9]+$" + }, + "workflow_version": { + "type": "string" + }, + "genome_build": { + "type": "string", + "enum": [ + "GRCh37", + "GRCh38_hla_decoy_ebv", + "GRCh38_Verily_v1" + ] + }, + "inputs": { + "type": "array", + "items": { + "type": "object", + "properties": { + "tumour_analysis_id": { + "type": "string", + "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$" + }, + "normal_analysis_id": { + "type": "string", + "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$" + }, + "analysis_type": { + "type": "string", + "const": "sequencing_alignment" + } + } + }, + "minItems": 1, + "maxItems": 2 + }, + "run_id": { + "type": "string" + }, + "session_id": { + "type": "string", + "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$" + } + } + }, + "experiment": { + "propertyNames": { + "enum": [ + "platform", + "experimental_strategy", + "platform_model", + "sequencing_center", + "experimental_protocol", + "library_isolation_protocol", + "submitter_sequencing_experiment_id", + "library_strandedness", + "chip_target", + "target_capture_kit", + "primary_target_regions", + "capture_target_regions" + ] + }, + "required": [ + "platform", + "experimental_strategy", + "submitter_sequencing_experiment_id" + ], + "type": "object", + "properties": { + "platform": { + "type": [ + "string", + "null" + ] + }, + "experimental_strategy": { + "type": [ + "string", + "null" + ] + }, + "experimental_protocol": { + "type": [ + "string", + "null" + ] + }, + "library_isolation_protocol": { + "enum": [ + "TRIzol Reagent (Thermo Fisher)", + "RNeasy kits (QIAGEN)", + "RNase free DNase I (Thermo Fisher)", + "Pico Pure RNA isolation kit (Thermo Fisher)", + "mirVANA microRNA isolation kit (Thermo Fisher)", + "Absolutely Total RNA, miRNA & mRNA Purification Kits (Stratagene, Agilent technologies)", + "SV total RNA isolation kit (Promega)", + "RNAqueous Kit (Thermo Fisher)", + "AllPrep DNA/RNA Micro Kit (QIAGEN)", + "GenElute Mammalian Total RNA Miniprep kit (MilliporeSigma)", + "Spectrum Plant Total RNA kit (MilliporeSigma)", + "peqGOLD Total RNA kits (PeqLab Biotechnologie)", + "RNAlater (Thermo Fisher)", + null + ] + }, + "submitter_sequencing_experiment_id": { + "type": [ + "string", + "null" + ] + }, + "library_strandedness": { + "enum": [ + "UNSTRANDED", + "FIRST_READ_SENSE_STRAND", + "FIRST_READ_ANTISENSE_STRAND", + null + ] + }, + "chip_target": { + "type": [ + "string", + "null" + ] + }, + "platform_model": { + "type": [ + "string", + "null" + ] + }, + "sequencing_center": { + "type": [ + "string", + "null" + ] + }, + "target_capture_kit": { + "enum": [ + "xGen Exome Research Panel V1 (IDT)", + "SeqCap EZ MedExome (Roche)", + "SureSelect Human All Exon V6 (Agilent)", + "Human Core Exome Kit + RefSeq V1 (Twist)", + null + ] + }, + "primary_target_regions": { + "type": [ + "string", + "null" + ] + }, + "capture_target_regions": { + "type": [ + "string", + "null" + ] + } + }, + "allOf": [ + { + "if": { + "properties": { + "experimental_strategy": { + "const": "RNA-Seq" + } + } + }, + "then": { + "properties": { + "library_strandedness": { + "enum": [ + "UNSTRANDED", + "FIRST_READ_SENSE_STRAND", + "FIRST_READ_ANTISENSE_STRAND" + ] + } + }, + "required": [ + "library_strandedness" + ] + } + }, + { + "if": { + "properties": { + "experimental_strategy": { + "enum": [ + "WXS", + "Targeted-Seq" + ] + } + } + }, + "then": { + "properties": { + "target_capture_kit": { + "type": "string", + "pattern": "^[a-zA-Z0-9]{1}[a-zA-Z0-9\\-_\\.:']{0,98}[a-zA-Z0-9]{1}$" + }, + "primary_target_regions": { + "type": "string", + "pattern": "^[a-zA-Z0-9]{1}[a-zA-Z0-9\\-_\\.:']{0,98}[a-zA-Z0-9]{1}$" + }, + "capture_target_regions": { + "type": "string", + "pattern": "^[a-zA-Z0-9]{1}[a-zA-Z0-9\\-_\\.:']{0,98}[a-zA-Z0-9]{1}$" + } + }, + "required": [ + "target_capture_kit", + "primary_target_regions", + "capture_target_regions" + ] + } + }, + { + "if": { + "properties": { + "experimental_strategy": { + "const": "ChIP-Seq" + } + } + }, + "then": { + "properties": { + "chip_target": { + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "chip_target" + ] + } + } + ] + }, + "donor": { + "type": "object", + "propertyNames": { + "enum": [ + "submitter_donor_id", + "primary_site", + "vital_status", + "survival_time", + "cause_of_death", + "primary_diagnosis", + "comorbidity" + ] + }, + "required": [ + "submitter_donor_id", + "primary_site", + "vital_status", + "primary_diagnosis" + ], + "properties": { + "submitter_donor_id": { + "type": "string" + }, + "primary_site": { + "type": "array", + "minItems": 1, + "items": { + "type": "string", + "enum": [ + "Accessory sinuses", + "Adrenal gland", + "Base of tongue", + "Bladder", + "Bones, joints and articular cartilage of limbs", + "Bones, joints and articular cartilage of other and unspecified sites", + "Brain", + "Breast", + "Bronchus and lung", + "Cervix uteri", + "Colon", + "Connective, subcutaneous and other soft tissues", + "Corpus uteri", + "Esophagus", + "Eye and adnexa", + "Floor of mouth", + "Gallbladder", + "Gum", + "Heart, mediastinum, and pleura", + "Hematopoietic and reticuloendothelial systems", + "Hypopharynx", + "Kidney", + "Larynx", + "Lip", + "Liver and intrahepatic bile ducts", + "Lymph nodes", + "Meninges", + "Nasal cavity and middle ear", + "Nasopharynx", + "Oropharynx", + "Other and ill-defined digestive organs", + "Other and ill-defined sites", + "Other and ill-defined sites in lip, oral cavity and pharynx", + "Other and ill-defined sites within respiratory system and intrathoracic organs", + "Other and unspecified female genital organs", + "Other and unspecified major salivary glands", + "Other and unspecified male genital organs", + "Other and unspecified parts of biliary tract", + "Other and unspecified parts of mouth", + "Other and unspecified parts of tongue", + "Other and unspecified urinary organs", + "Other endocrine glands and related structures", + "Ovary", + "Palate", + "Pancreas", + "Parotid gland", + "Penis", + "Peripheral nerves and autonomic nervous system", + "Placenta", + "Prostate gland", + "Pyriform sinus", + "Rectosigmoid junction", + "Rectum", + "Renal pelvis", + "Retroperitoneum and peritoneum", + "Skin", + "Small intestine", + "Spinal cord, cranial nerves, and other parts of central nervous system", + "Stomach", + "Testis", + "Thymus", + "Thyroid gland", + "Tonsil", + "Trachea", + "Ureter", + "Uterus, NOS", + "Vagina", + "Vulva" + ] + } + } + , + "vital_status": { + "type": "string", + "enum": [ + "Alive", + "Deceased" + ] + }, + "survival_time": { + "type": ["null","integer"], + "minimum": 0 + }, + "cause_of_death": { + "type": ["null","string"], + "enum": [ + "Died of cancer", + "Died of other reasons", + "Unknown", + null + ] + }, + "primary_diagnosis": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "submitter_primary_diagnosis_id", + "age_at_diagnosis", + "cancer_type_code", + "clinical_tumour_staging_system", + "clinical_stage_group", + "lymph_nodes_examined_status", + "performance_status", + "laterality", + "treatment", + "follow_up" + ] + }, + "required": [ + "submitter_primary_diagnosis_id", + "age_at_diagnosis", + "cancer_type_code", + "lymph_nodes_examined_status" + ], + "properties": { + "submitter_primary_diagnosis_id": { + "type": "string" + }, + "age_at_diagnosis": { + "type": "integer", + "minimum": 0 + }, + "cancer_type_code": { + "type": "string", + "pattern": "^[C|D][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$" + }, + "clinical_tumour_staging_system": { + "type": "string", + "enum": [ + "AJCC 8th edition", + "AJCC 7th edition", + "AJCC 6th edition", + "Ann Arbor staging system", + "Binet staging system", + "Durie-Salmon staging system", + "FIGO staging system", + "Lugano staging system", + "Rai staging system", + "Revised International staging system (RISS)", + "St Jude staging system" + ] + }, + "clinical_stage_group": { + "type": "string", + "enum": [ + "Occult Carcinoma", + "Stage 0", + "Stage 0a", + "Stage 0is", + "Stage 1", + "Stage 1A", + "Stage 1B", + "Stage A", + "Stage B", + "Stage C", + "Stage I", + "Stage IA", + "Stage IA1", + "Stage IA2", + "Stage IA3", + "Stage IAB", + "Stage IAE", + "Stage IAES", + "Stage IAS", + "Stage IB", + "Stage IB1", + "Stage IB2", + "Stage IBE", + "Stage IBES", + "Stage IBS", + "Stage IC", + "Stage IE", + "Stage IEA", + "Stage IEB", + "Stage IES", + "Stage II", + "Stage II bulky", + "Stage IIA", + "Stage IIA1", + "Stage IIA2", + "Stage IIAE", + "Stage IIAES", + "Stage IIAS", + "Stage IIB", + "Stage IIBE", + "Stage IIBES", + "Stage IIBS", + "Stage IIC", + "Stage IIE", + "Stage IIEA", + "Stage IIEB", + "Stage IIES", + "Stage III", + "Stage IIIA", + "Stage IIIA1", + "Stage IIIA2", + "Stage IIIAE", + "Stage IIIAES", + "Stage IIIAS", + "Stage IIIB", + "Stage IIIBE", + "Stage IIIBES", + "Stage IIIBS", + "Stage IIIC", + "Stage IIIC1", + "Stage IIIC2", + "Stage IIID", + "Stage IIIE", + "Stage IIIES", + "Stage IIIS", + "Stage IIS", + "Stage IS", + "Stage IV", + "Stage IVA", + "Stage IVA1", + "Stage IVA2", + "Stage IVAE", + "Stage IVAES", + "Stage IVAS", + "Stage IVB", + "Stage IVBE", + "Stage IVBES", + "Stage IVBS", + "Stage IVC", + "Stage IVE", + "Stage IVES", + "Stage IVS", + "Cannot be assessed" + ] + }, + "lymph_nodes_examined_status": { + "type": "string", + "enum": [ + "Cannot be determined", + "No", + "No lymph nodes found in resected specimen", + "Not applicable", + "Yes" + ] + }, + "performance_status": { + "type": "string", + "enum": [ + "Grade 0", + "Grade 1", + "Grade 2", + "Grade 3", + "Grade 4", + "Unknown" + ] + }, + "laterality": { + "type": "string", + "enum": [ + "Bilateral", + "Left", + "Midline", + "Not a paired site", + "Right", + "Unilateral, side not specified", + "Unknown" + ] + }, + "follow_up": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "submitter_follow_up_id", + "interval_of_followup", + "disease_status_at_followup", + "relapse_type", + "submitter_treatment_id" + ] + }, + "required": [ + "submitter_follow_up_id", + "interval_of_followup", + "disease_status_at_followup" + ], + "properties": { + "submitter_follow_up_id": { + "type": "string" + }, + "submitter_treatment_id": { + "type": "string" + }, + "interval_of_followup": { + "type": "integer", + "minimum": 0 + }, + "disease_status_at_followup": { + "type": "string", + "enum": [ + "Complete remission", + "Distant progression", + "Loco-regional progression", + "No evidence of disease", + "Partial remission", + "Progression NOS", + "Relapse or recurrence", + "Stable" + ] + }, + "relapse_type": { + "type": "string", + "enum": [ + "Distant recurrence/metastasis", + "Local recurrence", + "Local recurrence and distant metastasis", + "Progression (liquid tumours)" + ] + } + } + } + }, + "treatment": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "submitter_treatment_id", + "treatment_type", + "treatment_intent", + "treatment_start_interval", + "treatment_duration", + "response_to_treatment", + "chemotherapy", + "hormone_therapy", + "radiation", + "immunotherapy", + "surgery" + ] + }, + "required": [ + "submitter_treatment_id", + "treatment_type" + ], + "properties": { + "submitter_treatment_id": { + "type": "string" + }, + "treatment_type": { + "type": "array", + "items": { + "type": "string", + "enum": [ + "Ablation", + "Bone marrow transplant", + "Chemotherapy", + "Endoscopic therapy", + "Hormonal therapy", + "Immunotherapy", + "No treatment", + "Other targeting molecular therapy", + "Photodynamic therapy", + "Radiation therapy", + "Stem cell transplant", + "Surgery" + ] + } + }, + "treatment_intent": { + "type": "string", + "enum": [ + "Curative", + "Palliative", + "Unknown" + ] + }, + "treatment_start_interval": { + "type": "integer", + "minimum": 0 + }, + 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"enum": [ + "radiationTherapyModality", + "radiationTherapyType", + "anatomicalSiteIrradiated", + "radiationTherapyDosage", + "radiationTherapyFractions" + ] + }, + "required": [ + "radiationTherapyModality", + "radiationTherapyType", + "anatomicalSiteIrradiated", + "radiationTherapyDosage", + "radiationTherapyFractions" + ], + "properties": { + "radiationTherapyModality": { + "type": "string", + "enum": [ + "Electron", + "Heavy Ions", + "Photon", + "Proton" + ] + }, + "radiationTherapyType": { + "type": "string", + "enum": [ + "External", + "Internal" + ] + }, + "anatomicalSiteIrradiated": { + "type": "string", + "enum": [ + "Abdomen", + "Body", + "Brain", + "Chest", + "Head", + "Liver", + "Lower Limb", + "Lung", + "Neck", + "Pelvis", + "Skin", + "Spine", + "Thorax", + "Upper Limb" + ] + }, + "radiationTherapyDosage": { + "type": "number" + }, + "radiationTherapyFractions": { + "type": "integer" + } + } + } + }, + "immunotherapy": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "drugName", + "drugRxnormcui", + "immunotherapyType" + ] + }, + "required": [ + "drugName", + "drugRxnormcui", + "immunotherapyType" + ], + "properties": { + "immunotherapyType": { + "type": "string", + "enum": [ + "Cell-based", + "Immune checkpoint inhibitors", + "Monoclonal antibodies other than immune checkpoint inhibitors", + "Other immunomodulatory substances" + ] + }, + "drugName": { + "type": "string" + }, + "drugRxnormcui": { + "type": "string" + } + } + } + }, + "surgery": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "surgeryType", + "surgerySite", + "surgeryLocation", + "residualTumourClassification" + ] + }, + "required": [ + "surgeryType" + ], + "properties": { + "surgeryType": { + "type": "string" + }, + "surgerySite": { + "type": "string" + }, + "surgeryLocation": { + "type": "string", + "enum": [ + "Local recurrence", + "Metastatic", + "Primary" + ] + }, + "residualTumourClassification": { + 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"null" + ] + } + } + }, + "archive": { + "type": "object", + "propertyNames": { + "enum": [ + "ega", + "sra", + "icgcargo", + "encode" + ] + }, + "properties": { + "ega": { + "type": "array", + "items": { + "type": "object", + "properties": { + "egaf": { + "type": "string" + } + } + } + }, + "sra": { + "type": "array", + "items": { + "type": "object", + "properties": { + "gse": { + "type": "string" + } + } + } + }, + "icgcargo": { + "type": "array", + "items": { + "type": "object", + "properties": { + "fileId": { + "type": "string" + } + } + } + }, + "encode": { + "type": "array", + "items": { + "type": "object", + "properties": { + "fileId": { + "type": "string" + } + } + } + } + } + }, + "collaborators": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "name", + "contactEmail", + "affiliation" + ] + }, + "properties": { + "name": { + "type": "string" + }, + "contactEmail": { + "type": [ + "string", + "null" + ], + "pattern": 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