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"@id": "encode:partitioning_strategy"
},
"perturbation_target": {
"@id": "encode:perturbation_target"
},
"assay_controls": {
"@id": "encode:assay_controls"
},
"resource_contact": {
"@id": "encode:resource_contact"
},
"perturbation_pipeline": {
"@id": "encode:perturbation_pipeline",
"@type": "@id"
},
"biosample_conditions": {
"@id": "encode:biosample_conditions"
},
"Project": "encode:Project",
"ProjectCollection": "encode:ProjectCollection",
"project_type": {
"@id": "encode:project_type"
},
"PublicationData": "encode:PublicationData",
"PublicationDataCollection": "encode:PublicationDataCollection",
"Reference": "encode:Reference",
"ReferenceCollection": "encode:ReferenceCollection",
"reference_type": {
"@id": "encode:reference_type"
},
"ReferenceEpigenome": "encode:ReferenceEpigenome",
"ReferenceEpigenomeCollection": "encode:ReferenceEpigenomeCollection",
"ReplicationTimingSeries": "encode:ReplicationTimingSeries",
"ReplicationTimingSeriesCollection": "encode:ReplicationTimingSeriesCollection",
"TreatmentConcentrationSeries": "encode:TreatmentConcentrationSeries",
"TreatmentConcentrationSeriesCollection": "encode:TreatmentConcentrationSeriesCollection",
"TreatmentTimeSeries": "encode:TreatmentTimeSeries",
"TreatmentTimeSeriesCollection": "encode:TreatmentTimeSeriesCollection",
"UcscBrowserComposite": "encode:UcscBrowserComposite",
"UcscBrowserCompositeCollection": "encode:UcscBrowserCompositeCollection",
"Donor": "encode:Donor",
"FlyDonor": "encode:FlyDonor",
"FlyDonorCollection": "encode:FlyDonorCollection",
"strain_background": {
"@id": "encode:strain_background"
},
"strain_name": {
"@id": "encode:strain_name"
},
"genotype": {
"@id": "encode:genotype"
},
"parent_strains": {
"@id": "encode:parent_strains",
"@type": "@id"
},
"HumanDonor": "encode:HumanDonor",
"HumanDonorCollection": "encode:HumanDonorCollection",
"ethnicity": {
"@id": "encode:ethnicity"
},
"parents": {
"@id": "encode:parents",
"@type": "@id"
},
"siblings": {
"@id": "encode:siblings",
"@type": "@id"
},
"twin": {
"@id": "encode:twin",
"@type": "@id"
},
"twin_type": {
"@id": "encode:twin_type"
},
"children": {
"@id": "encode:children",
"@type": "@id"
},
"MouseDonor": "encode:MouseDonor",
"MouseDonorCollection": "encode:MouseDonorCollection",
"WormDonor": "encode:WormDonor",
"WormDonorCollection": "encode:WormDonorCollection",
"num_times_outcrossed": {
"@id": "encode:num_times_outcrossed"
},
"outcrossed_strain": {
"@id": "encode:outcrossed_strain",
"@type": "@id"
},
"Experiment": "encode:Experiment",
"ExperimentCollection": "encode:ExperimentCollection",
"date_submitted": {
"@id": "encode:date_submitted",
"@type": "xsd:date"
},
"assay_pipeline": {
"@id": "encode:assay_pipeline",
"@type": "@id"
},
"possible_controls": {
"@id": "encode:possible_controls",
"@type": "@id"
},
"internal_status": {
"@id": "encode:internal_status"
},
"pipeline_error_detail": {
"@id": "encode:pipeline_error_detail"
},
"replicates": {
"@id": "encode:replicates",
"@type": "@id"
},
"biosample_summary": {
"@id": "encode:biosample_summary"
},
"assay_slims": {
"@id": "encode:assay_slims"
},
"assay_title": {
"@id": "encode:assay_title"
},
"category_slims": {
"@id": "encode:category_slims"
},
"type_slims": {
"@id": "encode:type_slims"
},
"objective_slims": {
"@id": "encode:objective_slims"
},
"related_series": {
"@id": "encode:related_series",
"@type": "@id"
},
"replication_type": {
"@id": "encode:replication_type"
},
"Replicate": "encode:Replicate",
"ReplicateCollection": "encode:ReplicateCollection",
"antibody": {
"@id": "encode:antibody",
"@type": "@id"
},
"biological_replicate_number": {
"@id": "encode:biological_replicate_number",
"@type": "xsd:integer"
},
"technical_replicate_number": {
"@id": "encode:technical_replicate_number",
"@type": "xsd:integer"
},
"experiment": {
"@id": "encode:experiment",
"@type": "@id"
},
"rbns_protein_concentration": {
"@id": "encode:rbns_protein_concentration",
"@type": "xsd:integer"
},
"rbns_protein_concentration_units": {
"@id": "encode:rbns_protein_concentration_units"
},
"File": "encode:File",
"FileCollection": "encode:FileCollection",
"external_accession": {
"@id": "encode:external_accession"
},
"read_count": {
"@id": "encode:read_count",
"@type": "xsd:integer"
},
"file_format": {
"@id": "encode:file_format"
},
"file_format_type": {
"@id": "encode:file_format_type"
},
"file_format_specifications": {
"@id": "encode:file_format_specifications",
"@type": "@id"
},
"restricted": {
"@id": "encode:restricted",
"@type": "xsd:boolean"
},
"no_file_available": {
"@id": "encode:no_file_available",
"@type": "xsd:boolean"
},
"submitted_file_name": {
"@id": "encode:submitted_file_name"
},
"md5sum": {
"@id": "encode:md5sum"
},
"content_md5sum": {
"@id": "encode:content_md5sum"
},
"fastq_signature": {
"@id": "encode:fastq_signature"
},
"file_size": {
"@id": "encode:file_size",
"@type": "xsd:integer"
},
"platform": {
"@id": "encode:platform",
"@type": "@id"
},
"platforms_multiple_files": {
"@id": "encode:platforms_multiple_files"
},
"read_length": {
"@id": "encode:read_length",
"@type": "xsd:integer"
},
"read_length_zip_files": {
"@id": "encode:read_length_zip_files"
},
"run_type": {
"@id": "encode:run_type"
},
"bed_file_state": {
"@id": "encode:bed_file_state"
},
"bed_file_value": {
"@id": "encode:bed_file_value"
},
"paired_end": {
"@id": "encode:paired_end"
},
"paired_with": {
"@id": "encode:paired_with",
"@type": "@id"
},
"mapped_read_length": {
"@id": "encode:mapped_read_length",
"@type": "xsd:integer"
},
"mapped_run_type": {
"@id": "encode:mapped_run_type"
},
"flowcell_details": {
"@id": "encode:flowcell_details"
},
"output_type": {
"@id": "encode:output_type"
},
"derived_from": {
"@id": "encode:derived_from",
"@type": "@id"
},
"controlled_by": {
"@id": "encode:controlled_by",
"@type": "@id"
},
"dataset": {
"@id": "encode:dataset",
"@type": "@id"
},
"replicate": {
"@id": "encode:replicate",
"@type": "@id"
},
"genome_annotation": {
"@id": "encode:genome_annotation"
},
"step_run": {
"@id": "encode:step_run",
"@type": "@id"
},
"content_error_detail": {
"@id": "encode:content_error_detail"
},
"revoke_detail": {
"@id": "encode:revoke_detail"
},
"href": {
"@id": "encode:href"
},
"upload_credentials": {
"@id": "encode:upload_credentials"
},
"read_length_units": {
"@id": "encode:read_length_units"
},
"biological_replicates": {
"@id": "encode:biological_replicates",
"@type": "xsd:integer"
},
"technical_replicates": {
"@id": "encode:technical_replicates"
},
"analysis_step_version": {
"@id": "encode:analysis_step_version",
"@type": "@id"
},
"output_category": {
"@id": "encode:output_category"
},
"quality_metrics": {
"@id": "encode:quality_metrics",
"@type": "@id"
},
"file_type": {
"@id": "encode:file_type"
},
"GeneticModification": "encode:GeneticModification",
"GeneticModificationCollection": "encode:GeneticModificationCollection",
"category": {
"@id": "encode:category"
},
"zygosity": {
"@id": "encode:zygosity"
},
"modified_site_by_target_id": {
"@id": "encode:modified_site_by_target_id",
"@type": "@id"
},
"modified_site_by_coordinates": {
"@id": "encode:modified_site_by_coordinates"
},
"modified_site_by_sequence": {
"@id": "encode:modified_site_by_sequence"
},
"modified_site_nonspecific": {
"@id": "encode:modified_site_nonspecific"
},
"introduced_tags": {
"@id": "encode:introduced_tags"
},
"introduced_sequence": {
"@id": "encode:introduced_sequence"
},
"method": {
"@id": "encode:method"
},
"rnai_sequences": {
"@id": "encode:rnai_sequences"
},
"guide_rna_sequences": {
"@id": "encode:guide_rna_sequences"
},
"RVD_sequence_pairs": {
"@id": "encode:RVD_sequence_pairs"
},
"reagents": {
"@id": "encode:reagents"
},
"biosamples_modified": {
"@id": "encode:biosamples_modified",
"@type": "@id"
},
"donors_modified": {
"@id": "encode:donors_modified",
"@type": "@id"
},
"Image": "encode:Image",
"ImageCollection": "encode:ImageCollection",
"Page": "encode:Page",
"PageCollection": "encode:PageCollection",
"parent": {
"@id": "encode:parent",
"@type": "@id"
},
"news": {
"@id": "encode:news",
"@type": "xsd:boolean"
},
"news_excerpt": {
"@id": "encode:news_excerpt"
},
"news_keywords": {
"@id": "encode:news_keywords"
},
"layout": {
"@id": "encode:layout"
},
"canonical_uri": {
"@id": "encode:canonical_uri"
},
"year_released": {
"@id": "encode:year_released"
},
"AnalysisStep": "encode:AnalysisStep",
"AnalysisStepCollection": "encode:AnalysisStepCollection",
"step_label": {
"@id": "encode:step_label"
},
"major_version": {
"@id": "encode:major_version",
"@type": "xsd:integer"
},
"analysis_step_types": {
"@id": "encode:analysis_step_types"
},
"input_file_types": {
"@id": "encode:input_file_types"
},
"output_file_types": {
"@id": "encode:output_file_types"
},
"qa_stats_generated": {
"@id": "encode:qa_stats_generated"
},
"pipelines": {
"@id": "encode:pipelines",
"@type": "@id"
},
"current_version": {
"@id": "encode:current_version",
"@type": "@id"
},
"AnalysisStepRun": "encode:AnalysisStepRun",
"AnalysisStepRunCollection": "encode:AnalysisStepRunCollection",
"dx_applet_details": {
"@id": "encode:dx_applet_details"
},
"AnalysisStepVersion": "encode:AnalysisStepVersion",
"AnalysisStepVersionCollection": "encode:AnalysisStepVersionCollection",
"minor_version": {
"@id": "encode:minor_version",
"@type": "xsd:integer"
},
"analysis_step": {
"@id": "encode:analysis_step",
"@type": "@id"
},
"software_versions": {
"@id": "encode:software_versions",
"@type": "@id"
},
"Pipeline": "encode:Pipeline",
"PipelineCollection": "encode:PipelineCollection",
"assay_term_names": {
"@id": "encode:assay_term_names"
},
"data_type": {
"@id": "encode:data_type"
},
"analysis_steps": {
"@id": "encode:analysis_steps",
"@type": "@id"
},
"standards_page": {
"@id": "encode:standards_page",
"@type": "@id"
},
"pipeline_type": {
"@id": "encode:pipeline_type"
},
"workflow_language": {
"@id": "encode:workflow_language"
},
"pipeline_output": {
"@id": "encode:pipeline_output"
},
"pipeline_chain": {
"@id": "encode:pipeline_chain",
"@type": "@id"
},
"pipeline_version": {
"@id": "encode:pipeline_version",
"@type": "xsd:integer"
},
"pipeline_newer_version": {
"@id": "encode:pipeline_newer_version",
"@type": "xsd:integer"
},
"QualityMetric": "encode:QualityMetric",
"BismarkQualityMetric": "encode:BismarkQualityMetric",
"BismarkQualityMetricCollection": "encode:BismarkQualityMetricCollection",
"quality_metric_of": {
"@id": "encode:quality_metric_of",
"@type": "@id"
},
"Sequences analysed in total": {
"@id": "encode:Sequences%20analysed%20in%20total",
"@type": "xsd:float"
},
"lambda Sequences analysed in total": {
"@id": "encode:lambda%20Sequences%20analysed%20in%20total",
"@type": "xsd:float"
},
"Mapping efficiency": {
"@id": "encode:Mapping%20efficiency"
},
"lambda Mapping efficiency": {
"@id": "encode:lambda%20Mapping%20efficiency"
},
"lambda C methylated in CpG context": {
"@id": "encode:lambda%20C%20methylated%20in%20CpG%20context"
},
"lambda C methylated in CHG context": {
"@id": "encode:lambda%20C%20methylated%20in%20CHG%20context"
},
"lambda C methylated in CHH context": {
"@id": "encode:lambda%20C%20methylated%20in%20CHH%20context"
},
"C methylated in CHH context": {
"@id": "encode:C%20methylated%20in%20CHH%20context"
},
"C methylated in CHG context": {
"@id": "encode:C%20methylated%20in%20CHG%20context"
},
"C methylated in CpG context": {
"@id": "encode:C%20methylated%20in%20CpG%20context"
},
"ChipSeqFilterQualityMetric": "encode:ChipSeqFilterQualityMetric",
"ChipSeqFilterQualityMetricCollection": "encode:ChipSeqFilterQualityMetricCollection",
"NSC": {
"@id": "encode:NSC",
"@type": "xsd:float"
},
"RSC": {
"@id": "encode:RSC",
"@type": "xsd:float"
},
"PBC1": {
"@id": "encode:PBC1",
"@type": "xsd:float"
},
"PBC2": {
"@id": "encode:PBC2"
},
"fragment length": {
"@id": "encode:fragment%20length",
"@type": "xsd:float"
},
"NRF": {
"@id": "encode:NRF",
"@type": "xsd:float"
},
"cross_correlation_plot": {
"@id": "encode:cross_correlation_plot"
},
"ComplexityXcorrQualityMetric": "encode:ComplexityXcorrQualityMetric",
"ComplexityXcorrQualityMetricCollection": "encode:ComplexityXcorrQualityMetricCollection",
"sample size": {
"@id": "encode:sample%20size",
"@type": "xsd:float"
},
"paired-end": {
"@id": "encode:paired-end",
"@type": "xsd:boolean"
},
"read length": {
"@id": "encode:read%20length",
"@type": "xsd:float"
},
"CorrelationQualityMetric": "encode:CorrelationQualityMetric",
"CorrelationQualityMetricCollection": "encode:CorrelationQualityMetricCollection",
"Pearson correlation": {
"@id": "encode:Pearson%20correlation",
"@type": "xsd:float"
},
"Spearman correlation": {
"@id": "encode:Spearman%20correlation",
"@type": "xsd:float"
},
"Items": {
"@id": "encode:Items",
"@type": "xsd:float"
},
"Standard deviation": {
"@id": "encode:Standard%20deviation",
"@type": "xsd:float"
},
"MAD of log ratios": {
"@id": "encode:MAD%20of%20log%20ratios",
"@type": "xsd:float"
},
"Details": {
"@id": "encode:Details"
},
"CpgCorrelationQualityMetric": "encode:CpgCorrelationQualityMetric",
"CpgCorrelationQualityMetricCollection": "encode:CpgCorrelationQualityMetricCollection",
"CpG pairs": {
"@id": "encode:CpG%20pairs",
"@type": "xsd:float"
},
"CpG pairs with atleast 10 reads each": {
"@id": "encode:CpG%20pairs%20with%20atleast%2010%20reads%20each",
"@type": "xsd:float"
},
"DuplicatesQualityMetric": "encode:DuplicatesQualityMetric",
"DuplicatesQualityMetricCollection": "encode:DuplicatesQualityMetricCollection",
"Reads Examined": {
"@id": "encode:Reads%20Examined",
"@type": "xsd:float"
},
"Read Duplicates": {
"@id": "encode:Read%20Duplicates",
"@type": "xsd:float"
},
"UMI Read Duplicates": {
"@id": "encode:UMI%20Read%20Duplicates",
"@type": "xsd:float"
},
"Percent Duplication": {
"@id": "encode:Percent%20Duplication",
"@type": "xsd:float"
},
"Read Pairs Examined": {
"@id": "encode:Read%20Pairs%20Examined",
"@type": "xsd:float"
},
"Read Pair Duplicates": {
"@id": "encode:Read%20Pair%20Duplicates",
"@type": "xsd:float"
},
"Read Pair Optical Duplicates": {
"@id": "encode:Read%20Pair%20Optical%20Duplicates",
"@type": "xsd:float"
},
"Unmapped Reads": {
"@id": "encode:Unmapped%20Reads",
"@type": "xsd:float"
},
"Unpaired Reads Examined": {
"@id": "encode:Unpaired%20Reads%20Examined",
"@type": "xsd:float"
},
"Unpaired Read Duplicates": {
"@id": "encode:Unpaired%20Read%20Duplicates",
"@type": "xsd:float"
},
"Estimated Library Size": {
"@id": "encode:Estimated%20Library%20Size",
"@type": "xsd:float"
},
"EdwbamstatsQualityMetric": "encode:EdwbamstatsQualityMetric",
"EdwbamstatsQualityMetricCollection": "encode:EdwbamstatsQualityMetricCollection",
"alignedBy": {
"@id": "encode:alignedBy"
},
"isPaired": {
"@id": "encode:isPaired",
"@type": "xsd:float"
},
"isSortedByTarget": {
"@id": "encode:isSortedByTarget",
"@type": "xsd:float"
},
"mappedCount": {
"@id": "encode:mappedCount",
"@type": "xsd:float"
},
"readBaseCount": {
"@id": "encode:readBaseCount",
"@type": "xsd:float"
},
"readCount": {
"@id": "encode:readCount",
"@type": "xsd:float"
},
"readSizeMax": {
"@id": "encode:readSizeMax",
"@type": "xsd:float"
},
"readSizeMean": {
"@id": "encode:readSizeMean",
"@type": "xsd:float"
},
"readSizeMin": {
"@id": "encode:readSizeMin",
"@type": "xsd:float"
},
"readSizeStd": {
"@id": "encode:readSizeStd",
"@type": "xsd:float"
},
"targetBaseCount": {
"@id": "encode:targetBaseCount",
"@type": "xsd:float"
},
"targetSeqCount": {
"@id": "encode:targetSeqCount",
"@type": "xsd:float"
},
"u4mReadCount": {
"@id": "encode:u4mReadCount",
"@type": "xsd:float"
},
"u4mUniquePos": {
"@id": "encode:u4mUniquePos",
"@type": "xsd:float"
},
"u4mUniqueRatio": {
"@id": "encode:u4mUniqueRatio",
"@type": "xsd:float"
},
"uniqueMappedCount": {
"@id": "encode:uniqueMappedCount",
"@type": "xsd:float"
},
"FilteringQualityMetric": "encode:FilteringQualityMetric",
"FilteringQualityMetricCollection": "encode:FilteringQualityMetricCollection",
"pre-filter all reads": {
"@id": "encode:pre-filter%20all%20reads",
"@type": "xsd:float"
},
"pre-filter mapped reads": {
"@id": "encode:pre-filter%20mapped%20reads",
"@type": "xsd:float"
},
"post-filter all reads": {
"@id": "encode:post-filter%20all%20reads",
"@type": "xsd:float"
},
"post-filter mapped reads": {
"@id": "encode:post-filter%20mapped%20reads",
"@type": "xsd:float"
},
"GenericQualityMetric": "encode:GenericQualityMetric",
"GenericQualityMetricCollection": "encode:GenericQualityMetricCollection",
"HistoneChipSeqQualityMetric": "encode:HistoneChipSeqQualityMetric",
"HistoneChipSeqQualityMetricCollection": "encode:HistoneChipSeqQualityMetricCollection",
"nreads": {
"@id": "encode:nreads",
"@type": "xsd:integer"
},
"nreads_in_peaks": {
"@id": "encode:nreads_in_peaks",
"@type": "xsd:integer"
},
"npeak_overlap": {
"@id": "encode:npeak_overlap",
"@type": "xsd:integer"
},
"Fp": {
"@id": "encode:Fp",
"@type": "xsd:float"
},
"Ft": {
"@id": "encode:Ft",
"@type": "xsd:float"
},
"F1": {
"@id": "encode:F1",
"@type": "xsd:float"
},
"F2": {
"@id": "encode:F2",
"@type": "xsd:float"
},
"HotspotQualityMetric": "encode:HotspotQualityMetric",
"HotspotQualityMetricCollection": "encode:HotspotQualityMetricCollection",
"SPOT1 score": {
"@id": "encode:SPOT1%20score",
"@type": "xsd:float"
},
"SPOT2 score": {
"@id": "encode:SPOT2%20score",
"@type": "xsd:float"
},
"hotspot count": {
"@id": "encode:hotspot%20count",
"@type": "xsd:float"
},
"peaks count": {
"@id": "encode:peaks%20count",
"@type": "xsd:float"
},
"total tags": {
"@id": "encode:total%20tags",
"@type": "xsd:float"
},
"hotspot tags": {
"@id": "encode:hotspot%20tags",
"@type": "xsd:float"
},
"IDRQualityMetric": "encode:IDRQualityMetric",
"IDRQualityMetricCollection": "encode:IDRQualityMetricCollection",
"Np": {
"@id": "encode:Np",
"@type": "xsd:float"
},
"Nt": {
"@id": "encode:Nt",
"@type": "xsd:float"
},
"N1": {
"@id": "encode:N1",
"@type": "xsd:float"
},
"N2": {
"@id": "encode:N2",
"@type": "xsd:float"
},
"IDR_cutoff": {
"@id": "encode:IDR_cutoff",
"@type": "xsd:float"
},
"self_consistency_ratio": {
"@id": "encode:self_consistency_ratio",
"@type": "xsd:float"
},
"rescue_ratio": {
"@id": "encode:rescue_ratio",
"@type": "xsd:float"
},
"reproducibility_test": {
"@id": "encode:reproducibility_test"
},
"N_optimal": {
"@id": "encode:N_optimal",
"@type": "xsd:float"
},
"N_conservative": {
"@id": "encode:N_conservative",
"@type": "xsd:float"
},
"IDR_plot_true": {
"@id": "encode:IDR_plot_true"
},
"IDR_plot_rep1_pr": {
"@id": "encode:IDR_plot_rep1_pr"
},
"IDR_plot_rep2_pr": {
"@id": "encode:IDR_plot_rep2_pr"
},
"IDR_plot_pool_pr": {
"@id": "encode:IDR_plot_pool_pr"
},
"IDR_parameters_true": {
"@id": "encode:IDR_parameters_true"
},
"IDR_parameters_rep1_pr": {
"@id": "encode:IDR_parameters_rep1_pr"
},
"IDR_parameters_rep2_pr": {
"@id": "encode:IDR_parameters_rep2_pr"
},
"IDR_parameters_pool_pr": {
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"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/Software",
"/policy/SoftwareVersion",
"/policy/Source",
"/policy/StarQualityMetric",
"/policy/Target",
"/policy/Treatment",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/TrimmingQualityMetric",
"/policy/UcscBrowserComposite",
"/policy/User",
"/policy/WormDonor"
]
},
"rdfs:label": "Schema Version",
"rdfs:comment": "The version of the JSON schema that the server uses to validate the object."
},
"title": {
"@id": "/policy/title",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStep",
"/policy/AntibodyLot",
"/policy/Award",
"/policy/Consortium",
"/policy/File",
"/policy/Lab",
"/policy/Page",
"/policy/Pipeline",
"/policy/Platform",
"/policy/Publication",
"/policy/Software",
"/policy/Source",
"/policy/Target",
"/policy/User"
]
},
"rdfs:subPropertyOf": [
"dc:title"
],
"rdfs:label": [
"Name",
"Name of lab or vendor",
"Title"
],
"rdfs:comment": [
"A unique name for affiliation identification, current convention is comma separated PI's first & last name and institute label. (e.g. John Doe, UNI).",
"The complete name of the originating lab or vendor. ",
"The grant name from the NIH database, if applicable.",
"The name shown in the browser's title bar and tabs.",
"The preferred viewable name of the analysis step, likely the same as the name.",
"The preferred viewable name of the pipeline.",
"The preferred viewable name of the software.",
"The title of the file either the accession or the external_accession.",
"Title of the Consortium.",
"Title of the publication or communication."
]
},
"name": {
"@id": "/policy/name",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStep",
"/policy/AnalysisStepVersion",
"/policy/Award",
"/policy/Consortium",
"/policy/GenericQualityMetric",
"/policy/Lab",
"/policy/Organism",
"/policy/Page",
"/policy/Software",
"/policy/Source",
"/policy/Target"
]
},
"rdfs:label": [
"Auto-generated name",
"Common name",
"Name",
"Number",
"URL Name"
],
"rdfs:comment": [
"A short unique name for the lab, current convention is lower cased and hyphen delimited ",
"A short unique name for the lab, current convention is lower cased and hyphen delimited of PI's first and last name (e.g. john-doe).",
"A short unique name for the organism (e.g. 'mouse' or 'human').",
"Full name of the analysis step with major version number.",
"The name of the quality metric",
"The name shown in this page's URL.",
"The official grant number from the NIH database, if applicable",
"Unique name of the software package, lower cased version of title."
]
},
"description": {
"@id": "/policy/description",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AccessKey",
"/policy/Annotation",
"/policy/Award",
"/policy/Biosample",
"/policy/Consortium",
"/policy/Document",
"/policy/Embedding",
"/policy/Experiment",
"/policy/GeneticModification",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Project",
"/policy/PublicationData",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/Software",
"/policy/Source",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/UcscBrowserComposite"
]
},
"rdfs:subPropertyOf": [
"dc:description"
],
"rdfs:label": "Description",
"rdfs:comment": [
"A place to provide a curated discription of the pipeline. Only wranglers can post",
"A plain text description of the biosample. Do not include experiment details, genetic modifications or treatments.",
"A plain text description of the dataset.",
"A plain text description of the document.",
"A plain text description of the genetic modification.",
"A plain text description of the software.",
"A plain text description of the source.",
"Brief description of consortium."
]
},
"milestones": {
"@id": "/policy/milestones",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Award",
"rdfs:label": "Milestone"
},
"start_date": {
"@id": "/policy/start_date",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Award",
"/policy/Consortium"
]
},
"rdfs:label": "Start date"
},
"end_date": {
"@id": "/policy/end_date",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Award",
"/policy/Consortium"
]
},
"rdfs:label": "End date"
},
"pi": {
"@id": "/policy/pi",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Award",
"/policy/Lab"
]
},
"rdfs:label": "P.I.",
"rdfs:comment": [
"Principle Investigator of the grant.",
"Principle Investigator of the lab."
],
"rdfs:range": "/policy/User"
},
"rfa": {
"@id": "/policy/rfa",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Award",
"/policy/Consortium"
]
},
"rdfs:label": "Phase",
"rdfs:comment": "The name of the bioproject phase."
},
"project": {
"@id": "/policy/project",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Award",
"/policy/Consortium"
]
},
"rdfs:label": "BioProject",
"rdfs:comment": "The collection of biological data related to a single initiative, originating from a consortium."
},
"viewing_group": {
"@id": "/policy/viewing_group",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Award",
"rdfs:label": "View access group",
"rdfs:comment": "The group that determines which set of data the user has permission to view."
},
"Consortium": {
"@id": "/policy/Consortium",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/consortium.json"
},
"ConsortiumCollection": {
"@id": "/policy/ConsortiumCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"labs": {
"@id": "/policy/labs",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Consortium",
"rdfs:label": "Labs",
"rdfs:comment": "Consortium Labs.",
"rdfs:range": "/policy/Lab"
},
"grants": {
"@id": "/policy/grants",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Consortium",
"rdfs:label": "Grants",
"rdfs:comment": "Consortium Grants.",
"rdfs:range": "/policy/Award"
},
"publications": {
"@id": "/policy/publications",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Consortium",
"rdfs:label": "Publication",
"rdfs:comment": "Consortium Publication.",
"rdfs:range": "/policy/Publication"
},
"datasets": {
"@id": "/policy/datasets",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Consortium",
"/policy/Perturbation",
"/policy/Publication"
]
},
"rdfs:label": "Datasets",
"rdfs:comment": [
"A datasets generated by consortium members.",
"A datasets referred to by the publication."
],
"rdfs:range": "/policy/Dataset"
},
"consortium_tools": {
"@id": "/policy/consortium_tools",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Consortium",
"rdfs:label": "Consortium Tools"
},
"Document": {
"@id": "/policy/Document",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/document.json"
},
"DocumentCollection": {
"@id": "/policy/DocumentCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"notes": {
"@id": "/policy/notes",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStep",
"/policy/AnalysisStepRun",
"/policy/AnalysisStepVersion",
"/policy/Annotation",
"/policy/AntibodyCharacterization",
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/BiosampleCharacterization",
"/policy/ConstructCharacterization",
"/policy/Document",
"/policy/DonorCharacterization",
"/policy/Embedding",
"/policy/Experiment",
"/policy/File",
"/policy/FlyDonor",
"/policy/GeneticModification",
"/policy/GeneticModificationCharacterization",
"/policy/HumanDonor",
"/policy/Image",
"/policy/Library",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Platform",
"/policy/Project",
"/policy/PublicationData",
"/policy/RNAiCharacterization",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/Replicate",
"/policy/ReplicationTimingSeries",
"/policy/Software",
"/policy/SoftwareVersion",
"/policy/Source",
"/policy/Target",
"/policy/Treatment",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:label": "Notes",
"rdfs:comment": "DCC internal notes."
},
"references": {
"@id": "/policy/references",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/AntibodyCharacterization",
"/policy/Biosample",
"/policy/BiosampleCharacterization",
"/policy/Document",
"/policy/DonorCharacterization",
"/policy/Embedding",
"/policy/Experiment",
"/policy/FlyDonor",
"/policy/HumanDonor",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Project",
"/policy/PublicationData",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/Software",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:label": "Reference",
"rdfs:comment": "A publication that provide smore information about the object.",
"rdfs:range": "/policy/Publication"
},
"date_created": {
"@id": "/policy/date_created",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStep",
"/policy/AnalysisStepRun",
"/policy/AnalysisStepVersion",
"/policy/Annotation",
"/policy/AntibodyCharacterization",
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/BiosampleCharacterization",
"/policy/BismarkQualityMetric",
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric",
"/policy/ConstructCharacterization",
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/Document",
"/policy/DonorCharacterization",
"/policy/DuplicatesQualityMetric",
"/policy/EdwbamstatsQualityMetric",
"/policy/Embedding",
"/policy/Experiment",
"/policy/File",
"/policy/FilteringQualityMetric",
"/policy/FlyDonor",
"/policy/GenericQualityMetric",
"/policy/GeneticModification",
"/policy/GeneticModificationCharacterization",
"/policy/HistoneChipSeqQualityMetric",
"/policy/HotspotQualityMetric",
"/policy/HumanDonor",
"/policy/IDRQualityMetric",
"/policy/IdrSummaryQualityMetric",
"/policy/Image",
"/policy/Library",
"/policy/MadQualityMetric",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Page",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Platform",
"/policy/Project",
"/policy/Publication",
"/policy/PublicationData",
"/policy/RNAiCharacterization",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/Replicate",
"/policy/ReplicationTimingSeries",
"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/Software",
"/policy/SoftwareVersion",
"/policy/StarQualityMetric",
"/policy/Treatment",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/TrimmingQualityMetric",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:subPropertyOf": [
"dc:created"
],
"rdfs:label": "Date created",
"rdfs:comment": "The date the object was created."
},
"submitted_by": {
"@id": "/policy/submitted_by",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStep",
"/policy/AnalysisStepRun",
"/policy/AnalysisStepVersion",
"/policy/Annotation",
"/policy/AntibodyCharacterization",
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/BiosampleCharacterization",
"/policy/BismarkQualityMetric",
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric",
"/policy/ConstructCharacterization",
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/Document",
"/policy/DonorCharacterization",
"/policy/DuplicatesQualityMetric",
"/policy/EdwbamstatsQualityMetric",
"/policy/Embedding",
"/policy/Experiment",
"/policy/File",
"/policy/FilteringQualityMetric",
"/policy/FlyDonor",
"/policy/GenericQualityMetric",
"/policy/GeneticModification",
"/policy/GeneticModificationCharacterization",
"/policy/HistoneChipSeqQualityMetric",
"/policy/HotspotQualityMetric",
"/policy/HumanDonor",
"/policy/IDRQualityMetric",
"/policy/IdrSummaryQualityMetric",
"/policy/Image",
"/policy/Library",
"/policy/MadQualityMetric",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Page",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Platform",
"/policy/Project",
"/policy/Publication",
"/policy/PublicationData",
"/policy/RNAiCharacterization",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/Replicate",
"/policy/ReplicationTimingSeries",
"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/Software",
"/policy/SoftwareVersion",
"/policy/StarQualityMetric",
"/policy/Treatment",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/TrimmingQualityMetric",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:subPropertyOf": [
"dc:creator"
],
"rdfs:label": "Submitted by",
"rdfs:range": "/policy/User"
},
"lab": {
"@id": "/policy/lab",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/AntibodyCharacterization",
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/BiosampleCharacterization",
"/policy/BismarkQualityMetric",
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric",
"/policy/ConstructCharacterization",
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/Document",
"/policy/DonorCharacterization",
"/policy/DuplicatesQualityMetric",
"/policy/EdwbamstatsQualityMetric",
"/policy/Embedding",
"/policy/Experiment",
"/policy/File",
"/policy/FilteringQualityMetric",
"/policy/FlyDonor",
"/policy/GenericQualityMetric",
"/policy/GeneticModification",
"/policy/GeneticModificationCharacterization",
"/policy/HistoneChipSeqQualityMetric",
"/policy/HotspotQualityMetric",
"/policy/HumanDonor",
"/policy/IDRQualityMetric",
"/policy/IdrSummaryQualityMetric",
"/policy/Library",
"/policy/MadQualityMetric",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Page",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Project",
"/policy/Publication",
"/policy/PublicationData",
"/policy/RNAiCharacterization",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/Software",
"/policy/StarQualityMetric",
"/policy/Treatment",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/TrimmingQualityMetric",
"/policy/UcscBrowserComposite",
"/policy/User",
"/policy/WormDonor"
]
},
"rdfs:label": [
"Affiliation",
"Lab"
],
"rdfs:comment": [
"Lab associated with the submission.",
"Lab user is primarily associated with."
],
"rdfs:range": "/policy/Lab"
},
"award": {
"@id": "/policy/award",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/AntibodyCharacterization",
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/BiosampleCharacterization",
"/policy/BismarkQualityMetric",
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric",
"/policy/ConstructCharacterization",
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/Document",
"/policy/DonorCharacterization",
"/policy/DuplicatesQualityMetric",
"/policy/EdwbamstatsQualityMetric",
"/policy/Embedding",
"/policy/Experiment",
"/policy/File",
"/policy/FilteringQualityMetric",
"/policy/FlyDonor",
"/policy/GenericQualityMetric",
"/policy/GeneticModification",
"/policy/GeneticModificationCharacterization",
"/policy/HistoneChipSeqQualityMetric",
"/policy/HotspotQualityMetric",
"/policy/HumanDonor",
"/policy/IDRQualityMetric",
"/policy/IdrSummaryQualityMetric",
"/policy/Library",
"/policy/MadQualityMetric",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Page",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Project",
"/policy/Publication",
"/policy/PublicationData",
"/policy/RNAiCharacterization",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/Software",
"/policy/StarQualityMetric",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/TrimmingQualityMetric",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:label": "Grant",
"rdfs:comment": "Grant associated with the submission.",
"rdfs:range": "/policy/Award"
},
"aliases": {
"@id": "/policy/aliases",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStep",
"/policy/AnalysisStepRun",
"/policy/AnalysisStepVersion",
"/policy/Annotation",
"/policy/AntibodyCharacterization",
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/BiosampleCharacterization",
"/policy/BismarkQualityMetric",
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric",
"/policy/ConstructCharacterization",
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/Document",
"/policy/DonorCharacterization",
"/policy/DuplicatesQualityMetric",
"/policy/EdwbamstatsQualityMetric",
"/policy/Embedding",
"/policy/Experiment",
"/policy/File",
"/policy/FilteringQualityMetric",
"/policy/FlyDonor",
"/policy/GenericQualityMetric",
"/policy/GeneticModification",
"/policy/GeneticModificationCharacterization",
"/policy/HistoneChipSeqQualityMetric",
"/policy/HotspotQualityMetric",
"/policy/HumanDonor",
"/policy/IDRQualityMetric",
"/policy/IdrSummaryQualityMetric",
"/policy/Library",
"/policy/MadQualityMetric",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Platform",
"/policy/Project",
"/policy/PublicationData",
"/policy/RNAiCharacterization",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/Replicate",
"/policy/ReplicationTimingSeries",
"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/Software",
"/policy/SoftwareVersion",
"/policy/Source",
"/policy/StarQualityMetric",
"/policy/Target",
"/policy/Treatment",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/TrimmingQualityMetric",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:label": "Lab alias",
"rdfs:comment": "A lab specific identifier to reference an object."
},
"attachment": {
"@id": "/policy/attachment",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AntibodyCharacterization",
"/policy/BiosampleCharacterization",
"/policy/BismarkQualityMetric",
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric",
"/policy/ConstructCharacterization",
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/Document",
"/policy/DonorCharacterization",
"/policy/DuplicatesQualityMetric",
"/policy/EdwbamstatsQualityMetric",
"/policy/FilteringQualityMetric",
"/policy/GenericQualityMetric",
"/policy/GeneticModificationCharacterization",
"/policy/HistoneChipSeqQualityMetric",
"/policy/HotspotQualityMetric",
"/policy/IDRQualityMetric",
"/policy/IdrSummaryQualityMetric",
"/policy/Image",
"/policy/MadQualityMetric",
"/policy/Perturbation",
"/policy/RNAiCharacterization",
"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/StarQualityMetric",
"/policy/TrimmingQualityMetric"
]
},
"rdfs:label": [
"Document file metadata",
"Genetic modification characterization document metadata",
"QC metric document metadata"
]
},
"document_type": {
"@id": "/policy/document_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Document",
"rdfs:label": "Type",
"rdfs:comment": "The category that best describes the document."
},
"urls": {
"@id": "/policy/urls",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Document",
"rdfs:subPropertyOf": [
"rdfs:seeAlso"
],
"rdfs:label": "URL",
"rdfs:comment": "An external resource with additional information to the document."
},
"Lab": {
"@id": "/policy/Lab",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/lab.json"
},
"LabCollection": {
"@id": "/policy/LabCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"awards": {
"@id": "/policy/awards",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "Grant",
"rdfs:comment": "A grant associated with the lab.",
"rdfs:range": "/policy/Award"
},
"institute_label": {
"@id": "/policy/institute_label",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "Institute label",
"rdfs:comment": "An abbreviation for the institute the lab is associated with."
},
"institute_name": {
"@id": "/policy/institute_name",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "Institute",
"rdfs:comment": "The name for the institute the lab is associated with."
},
"address1": {
"@id": "/policy/address1",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "Address line 1"
},
"address2": {
"@id": "/policy/address2",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "Address line 2"
},
"city": {
"@id": "/policy/city",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "City"
},
"state": {
"@id": "/policy/state",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "State/Province/Region"
},
"country": {
"@id": "/policy/country",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "Country"
},
"postal_code": {
"@id": "/policy/postal_code",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "ZIP/Postal code"
},
"fax": {
"@id": "/policy/fax",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "Fax number",
"rdfs:comment": "A fax number for the lab (with country code)."
},
"phone1": {
"@id": "/policy/phone1",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "Primary phone number",
"rdfs:comment": "The lab's primary phone number (with country code)."
},
"phone2": {
"@id": "/policy/phone2",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Lab",
"rdfs:label": "Alternate phone number",
"rdfs:comment": "The lab's alternative phone number (with country code)."
},
"Library": {
"@id": "/policy/Library",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/library.json"
},
"LibraryCollection": {
"@id": "/policy/LibraryCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"documents": {
"@id": "/policy/documents",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStep",
"/policy/Annotation",
"/policy/AntibodyCharacterization",
"/policy/Biosample",
"/policy/BiosampleCharacterization",
"/policy/ConstructCharacterization",
"/policy/DonorCharacterization",
"/policy/Embedding",
"/policy/Experiment",
"/policy/FlyDonor",
"/policy/GeneticModification",
"/policy/GeneticModificationCharacterization",
"/policy/HumanDonor",
"/policy/Library",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Project",
"/policy/PublicationData",
"/policy/RNAiCharacterization",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/Treatment",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:label": "Document",
"rdfs:comment": [
"A document that provides additional information (not data file).",
"Supporting document describing how the genetic modification(s) was/were produced."
],
"rdfs:range": "/policy/Document"
},
"lot_id": {
"@id": "/policy/lot_id",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/Library"
]
},
"rdfs:label": "Lot ID",
"rdfs:comment": [
"The lot identifier provided by the originating lab or vendor.",
"The lot identifier provided by the vendor, for nucleic acids or proteins purchased directly from a vendor (e.g. total RNA)."
]
},
"product_id": {
"@id": "/policy/product_id",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/Library"
]
},
"rdfs:label": "Product ID",
"rdfs:comment": [
"The product identifier provided by the originating lab or vendor.",
"The product identifier provided by the vendor, for nucleic acids or proteins purchased directly from a vendor (e.g. total RNA)."
]
},
"source": {
"@id": "/policy/source",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/FlyDonor",
"/policy/Library",
"/policy/MouseDonor",
"/policy/WormDonor"
]
},
"rdfs:label": "Source",
"rdfs:comment": [
"The originating lab or vendor.",
"The vendor, for nucleic acids or proteins purchased directly from a vendor (e.g. total RNA)."
],
"rdfs:range": "/policy/Source"
},
"accession": {
"@id": "/policy/accession",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/File",
"/policy/FlyDonor",
"/policy/GeneticModification",
"/policy/HumanDonor",
"/policy/Library",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Project",
"/policy/PublicationData",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:label": "Accession",
"rdfs:comment": "A unique identifier to be used to reference the object prefixed with ENC."
},
"alternate_accessions": {
"@id": "/policy/alternate_accessions",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/File",
"/policy/FlyDonor",
"/policy/GeneticModification",
"/policy/HumanDonor",
"/policy/Library",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Project",
"/policy/PublicationData",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:label": [
"Alternate Accession",
"Alternate accession"
],
"rdfs:comment": "An accession previously assigned to an object that has been merged with this object."
},
"spikeins_used": {
"@id": "/policy/spikeins_used",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "A spike-ins dataset.",
"rdfs:comment": "A specific spike-ins type dataset",
"rdfs:range": "/policy/Reference"
},
"biosample": {
"@id": "/policy/biosample",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Biosample",
"rdfs:comment": "The biosample that nucleic acid was isolated from to generate the library.",
"rdfs:range": "/policy/Biosample"
},
"nucleic_acid_term_name": {
"@id": "/policy/nucleic_acid_term_name",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Molecule term",
"rdfs:comment": "SO (Sequence Ontology) term best matching the molecule isolated to generate the library (e.g. 'RNA' for a total RNA library, even if that library is subsequently reverse transcribed for DNA sequencing.)"
},
"dbxrefs": {
"@id": "/policy/dbxrefs",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/File",
"/policy/FlyDonor",
"/policy/HumanDonor",
"/policy/Library",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Platform",
"/policy/Project",
"/policy/PublicationData",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/Treatment",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:subPropertyOf": [
"rdfs:seeAlso"
],
"rdfs:label": [
"Database external identifier",
"External identifier"
],
"rdfs:comment": [
"A unique identifier from external resource from an external resource that may have 1-to-1 or 1-to-many relationships with DGA objects.",
"A unique identifier from external resource.",
"An identifier from an external resource that may have 1-to-1 or 1-to-many relationships with ENCODE objects.",
"An identifier from external resource.",
"Identifier an from external resource that may have 1-to-1 or 1-to-many relationships with ENCODE objects.",
"Identifier from an external resource that may have 1-to-1 or 1-to-many relationships with DGA objects.",
"Identifier from an external resource that may have 1-to-1 or 1-to-many relationships with ENCODE objects.",
"Identifier from external resource that may have 1-to-1 or 1-to-many relationships with ENCODE objects."
]
},
"nucleic_acid_starting_quantity": {
"@id": "/policy/nucleic_acid_starting_quantity",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Nucleic acid starting quantity",
"rdfs:comment": "The starting amount of nucleic acid before selection and purification."
},
"nucleic_acid_starting_quantity_units": {
"@id": "/policy/nucleic_acid_starting_quantity_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Nucleic acid starting quantity units",
"rdfs:comment": "The units used for starting amount of nucleic acid."
},
"extraction_method": {
"@id": "/policy/extraction_method",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Extraction method",
"rdfs:comment": "A short description or reference of the nucleic acid extraction protocol used in library preparation, if applicable."
},
"fragmentation_method": {
"@id": "/policy/fragmentation_method",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Fragmentation method",
"rdfs:comment": "A short description or reference of the nucleic acid fragmentation protocol used in library preparation, if applicable."
},
"fragmentation_date": {
"@id": "/policy/fragmentation_date",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Fragmentation date",
"rdfs:comment": "The date that the nucleic acid was fragmented."
},
"library_size_selection_method": {
"@id": "/policy/library_size_selection_method",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Size selection method",
"rdfs:comment": "A short description or reference of the size selection protocol used in library preparation, if applicable."
},
"lysis_method": {
"@id": "/policy/lysis_method",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Lysis method",
"rdfs:comment": "A short description or reference of the cell lysis protocol used in library preparation, if applicable"
},
"crosslinking_method": {
"@id": "/policy/crosslinking_method",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Crosslinking method",
"rdfs:comment": "A short description or reference of the crosslinking protocol used in library preparation, if applicable."
},
"size_range": {
"@id": "/policy/size_range",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Size range",
"rdfs:comment": "The measured size range of the purified nucleic acid, in bp."
},
"strand_specificity": {
"@id": "/policy/strand_specificity",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "Strand specific",
"rdfs:comment": "The preparation of the library uses a strand-specific protocol."
},
"treatments": {
"@id": "/policy/treatments",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Biosample",
"/policy/GeneticModification",
"/policy/Library"
]
},
"rdfs:label": "Treatment",
"rdfs:range": "/policy/Treatment",
"rdfs:comment": "Relevant mutagenesis treatment applied to result in the modification."
},
"depleted_in_term_name": {
"@id": "/policy/depleted_in_term_name",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Biosample",
"/policy/Library"
]
}
},
"nucleic_acid_term_id": {
"@id": "/policy/nucleic_acid_term_id",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Library",
"rdfs:label": "nucleic_acid_term_id"
},
"depleted_in_term_id": {
"@id": "/policy/depleted_in_term_id",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Biosample",
"/policy/Library"
]
},
"rdfs:label": "depleted_in_term_id"
},
"Organism": {
"@id": "/policy/Organism",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/organism.json"
},
"OrganismCollection": {
"@id": "/policy/OrganismCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"scientific_name": {
"@id": "/policy/scientific_name",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Organism",
"rdfs:label": "Binomial name",
"rdfs:comment": "The genus species for the organism (e.g. 'Mus musculus')."
},
"taxon_id": {
"@id": "/policy/taxon_id",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Organism",
"rdfs:label": "Taxon ID",
"rdfs:comment": "The NCBI taxon ID for the organism (e.g. 10090)."
},
"Platform": {
"@id": "/policy/Platform",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/platform.json"
},
"PlatformCollection": {
"@id": "/policy/PlatformCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"term_id": {
"@id": "/policy/term_id",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Platform",
"rdfs:label": "Platform ID",
"rdfs:comment": "OBI (Ontology for Biomedical Investigations) ontology identifier for the measurement device."
},
"term_name": {
"@id": "/policy/term_name",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Platform",
"rdfs:label": "Platform name",
"rdfs:comment": "OBI (Ontology for Biomedical Investigations) ontology term for the measurement device."
},
"Publication": {
"@id": "/policy/Publication",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/publication.json"
},
"PublicationCollection": {
"@id": "/policy/PublicationCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"abstract": {
"@id": "/policy/abstract",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:subPropertyOf": [
"dc:abstract"
],
"rdfs:label": "Abstract",
"rdfs:comment": "Abstract of the publication or communication."
},
"authors": {
"@id": "/policy/authors",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Authors"
},
"date_published": {
"@id": "/policy/date_published",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Date published"
},
"date_revised": {
"@id": "/policy/date_revised",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Date revised"
},
"issue": {
"@id": "/policy/issue",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Issue",
"rdfs:comment": "The issue of the publication."
},
"page": {
"@id": "/policy/page",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Page",
"rdfs:comment": "Pagination of the reference"
},
"volume": {
"@id": "/policy/volume",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Volume",
"rdfs:comment": "The volume of the publication."
},
"journal": {
"@id": "/policy/journal",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Journal",
"rdfs:comment": "The journal of the publication."
},
"identifiers": {
"@id": "/policy/identifiers",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Identifier",
"rdfs:comment": "An identifier that references data found in the object."
},
"supplementary_data": {
"@id": "/policy/supplementary_data",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Supplementary data details"
},
"categories": {
"@id": "/policy/categories",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Category"
},
"published_by": {
"@id": "/policy/published_by",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Published by"
},
"data_used": {
"@id": "/policy/data_used",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Data used"
},
"publication_year": {
"@id": "/policy/publication_year",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Publication",
"rdfs:label": "Publication year"
},
"Software": {
"@id": "/policy/Software",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/software.json"
},
"SoftwareCollection": {
"@id": "/policy/SoftwareCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"software_type": {
"@id": "/policy/software_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Software",
"rdfs:label": "Type"
},
"bug_tracker_url": {
"@id": "/policy/bug_tracker_url",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Software",
"rdfs:label": "Bug tracker URL",
"rdfs:comment": "An external resource to track bugs for the software."
},
"source_url": {
"@id": "/policy/source_url",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Pipeline",
"/policy/Software"
]
},
"rdfs:label": "Source URL",
"rdfs:comment": "An external resource to the code base."
},
"purpose": {
"@id": "/policy/purpose",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/GeneticModification",
"/policy/Software"
]
},
"rdfs:label": "Purpose",
"rdfs:comment": "The purpose of the genetic modification."
},
"used_by": {
"@id": "/policy/used_by",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Software",
"rdfs:label": "Used by"
},
"versions": {
"@id": "/policy/versions",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStep",
"/policy/Software"
]
},
"rdfs:range": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStepVersion",
"/policy/SoftwareVersion"
]
}
},
"SoftwareVersion": {
"@id": "/policy/SoftwareVersion",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/software_version.json"
},
"SoftwareVersionCollection": {
"@id": "/policy/SoftwareVersionCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"software": {
"@id": "/policy/software",
"@type": "rdf:Property",
"rdfs:domain": "/policy/SoftwareVersion",
"rdfs:label": "Software",
"rdfs:comment": "Unique name of the software package.",
"rdfs:range": "/policy/Software"
},
"version": {
"@id": "/policy/version",
"@type": "rdf:Property",
"rdfs:domain": "/policy/SoftwareVersion",
"rdfs:label": "Version",
"rdfs:comment": "The version of a particular software."
},
"download_checksum": {
"@id": "/policy/download_checksum",
"@type": "rdf:Property",
"rdfs:domain": "/policy/SoftwareVersion",
"rdfs:label": "Download checksum",
"rdfs:comment": "The checksum of the particular version of software used."
},
"downloaded_url": {
"@id": "/policy/downloaded_url",
"@type": "rdf:Property",
"rdfs:domain": "/policy/SoftwareVersion",
"rdfs:label": "Download URL",
"rdfs:comment": "An external resource to track version for the software downloaded."
},
"Source": {
"@id": "/policy/Source",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/source.json"
},
"SourceCollection": {
"@id": "/policy/SourceCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"Treatment": {
"@id": "/policy/Treatment",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/treatment.json"
},
"TreatmentCollection": {
"@id": "/policy/TreatmentCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"treatment_type": {
"@id": "/policy/treatment_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Treatment",
"rdfs:label": "Type",
"rdfs:comment": "The classification of the treatment."
},
"treatment_term_id": {
"@id": "/policy/treatment_term_id",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Treatment",
"rdfs:label": "Term ID",
"rdfs:comment": "Ontology identifier describing a component in the treatment."
},
"treatment_term_name": {
"@id": "/policy/treatment_term_name",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/MatchedSet",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/Treatment",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries"
]
},
"rdfs:label": "Term name",
"rdfs:comment": "Ontology term describing a component in the treatment."
},
"amount": {
"@id": "/policy/amount",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Treatment",
"rdfs:label": "Amount of treatment applied"
},
"amount_units": {
"@id": "/policy/amount_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Treatment",
"rdfs:label": "Amount units"
},
"duration": {
"@id": "/policy/duration",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Treatment",
"rdfs:label": "Duration"
},
"duration_units": {
"@id": "/policy/duration_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Treatment",
"rdfs:label": "Duration units"
},
"temperature": {
"@id": "/policy/temperature",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Treatment",
"rdfs:label": "Temperature"
},
"temperature_units": {
"@id": "/policy/temperature_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Treatment",
"rdfs:label": "Temperature units"
},
"biosamples_used": {
"@id": "/policy/biosamples_used",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Treatment",
"rdfs:label": "Treatment biosample",
"rdfs:comment": "Biosample used in this treatment.",
"rdfs:range": "/policy/Biosample"
},
"antibodies_used": {
"@id": "/policy/antibodies_used",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Treatment",
"rdfs:label": "Treatment antibody",
"rdfs:comment": "Antibody used in this treatment.",
"rdfs:range": "/policy/AntibodyLot"
},
"AccessKey": {
"@id": "/policy/AccessKey",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/access_key.json"
},
"AccessKeyCollection": {
"@id": "/policy/AccessKeyCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"user": {
"@id": "/policy/user",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AccessKey",
"rdfs:label": "User",
"rdfs:range": "/policy/User"
},
"access_key_id": {
"@id": "/policy/access_key_id",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AccessKey",
"rdfs:label": "Access key ID"
},
"secret_access_key_hash": {
"@id": "/policy/secret_access_key_hash",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AccessKey",
"rdfs:label": "Secret access key Hash"
},
"AntibodyLot": {
"@id": "/policy/AntibodyLot",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/antibody_lot.json"
},
"AntibodyLotCollection": {
"@id": "/policy/AntibodyLotCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"lot_id_alias": {
"@id": "/policy/lot_id_alias",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AntibodyLot",
"rdfs:label": "Lot ID Alias",
"rdfs:comment": "The lot identifier for this lot deemed to be exactly the same by the vendor. "
},
"antigen_description": {
"@id": "/policy/antigen_description",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AntibodyLot",
"rdfs:label": "Antigen description",
"rdfs:comment": "The plain text description of the antigen used in raising the antibody (e.g. amino acid residue locations of the antigen)."
},
"antigen_sequence": {
"@id": "/policy/antigen_sequence",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AntibodyLot",
"rdfs:label": "Antigen sequence",
"rdfs:comment": "The amino acid sequence of the antigen."
},
"clonality": {
"@id": "/policy/clonality",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AntibodyLot",
"rdfs:label": "Antibody clonality",
"rdfs:comment": "The diversification of the immune cell lineage to make the antibody."
},
"host_organism": {
"@id": "/policy/host_organism",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AntibodyLot",
"rdfs:label": "Host",
"rdfs:comment": "The organism the antibody was grown in.",
"rdfs:range": "/policy/Organism"
},
"isotype": {
"@id": "/policy/isotype",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AntibodyLot",
"rdfs:label": "Isotype",
"rdfs:comment": "The class of antibody ( e.g. IgA, IgD, IgE, IgG or IgM)"
},
"purifications": {
"@id": "/policy/purifications",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AntibodyLot",
"rdfs:label": "Purification method",
"rdfs:comment": "A purification protocol used to isolate the antibody."
},
"targets": {
"@id": "/policy/targets",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/AntibodyLot",
"/policy/Embedding",
"/policy/Model",
"/policy/Perturbation"
]
},
"rdfs:comment": [
"For predictions of particular features (e.g. distribution of a histone mark), specify the predicted feature(s).",
"The name of the gene whose expression or product is the intended goal of the antibody."
],
"rdfs:range": "/policy/Target",
"rdfs:label": "Targets"
},
"characterizations": {
"@id": "/policy/characterizations",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AntibodyLot",
"/policy/Biosample",
"/policy/FlyDonor",
"/policy/GeneticModification",
"/policy/HumanDonor",
"/policy/MouseDonor",
"/policy/WormDonor"
]
},
"rdfs:range": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AntibodyCharacterization",
"/policy/BiosampleCharacterization",
"/policy/DonorCharacterization",
"/policy/GeneticModificationCharacterization"
]
}
},
"lot_reviews": {
"@id": "/policy/lot_reviews",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AntibodyLot",
"rdfs:label": "Antibody lot review"
},
"Biosample": {
"@id": "/policy/Biosample",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/biosample.json"
},
"BiosampleCollection": {
"@id": "/policy/BiosampleCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"submitter_comment": {
"@id": "/policy/submitter_comment",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AntibodyCharacterization",
"/policy/Biosample",
"/policy/BiosampleCharacterization",
"/policy/ConstructCharacterization",
"/policy/DonorCharacterization",
"/policy/Experiment",
"/policy/File",
"/policy/FlyDonor",
"/policy/GeneticModification",
"/policy/GeneticModificationCharacterization",
"/policy/HumanDonor",
"/policy/MatchedSet",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Pipeline",
"/policy/RNAiCharacterization",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/WormDonor"
]
},
"rdfs:label": "Submitter comment",
"rdfs:comment": "Additional information specified by the submitter to be displayed as a comment on the portal."
},
"biosample_term_id": {
"@id": "/policy/biosample_term_id",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Project",
"/policy/PublicationData",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries"
]
},
"rdfs:label": "Ontology ID",
"rdfs:comment": [
"Ontology identifier describing biosample.",
"Ontology term describing biosample."
]
},
"tissue_term_id": {
"@id": "/policy/tissue_term_id",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/Model",
"/policy/Perturbation"
]
},
"rdfs:label": "Tissue Ontology ID",
"rdfs:comment": "Ontology identifier describing tissue."
},
"disease_term_id": {
"@id": "/policy/disease_term_id",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Experiment",
"/policy/HumanDonor"
]
},
"rdfs:label": "Disease Ontology ID",
"rdfs:comment": "Ontology identifier describing disease(ICD10)"
},
"biosample_term_name": {
"@id": "/policy/biosample_term_name",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Project",
"/policy/PublicationData",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries"
]
},
"rdfs:label": "Ontology term",
"rdfs:comment": "Ontology term describing biosample."
},
"disease_term_name": {
"@id": "/policy/disease_term_name",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Experiment",
"/policy/HumanDonor"
]
},
"rdfs:label": [
"Disease term name",
"Ontology Disease term"
],
"rdfs:comment": [
"Ontology term describing disease(ICD10CM)",
"Ontology term describing disease."
]
},
"biosample_type": {
"@id": "/policy/biosample_type",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Project",
"/policy/PublicationData",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries"
]
},
"rdfs:label": "Biosample type",
"rdfs:comment": [
"The categorization of the biosample.",
"The general category of the biosample."
]
},
"genetic_modifications": {
"@id": "/policy/genetic_modifications",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Biosample",
"/policy/FlyDonor",
"/policy/MouseDonor",
"/policy/WormDonor"
]
},
"rdfs:label": "Genetic modification",
"rdfs:comment": "Genetic modification(s).",
"rdfs:range": "/policy/GeneticModification"
},
"donor": {
"@id": "/policy/donor",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Donor",
"rdfs:comment": "The donor or strain the biosample was originated from.",
"rdfs:range": "/policy/Donor"
},
"organism": {
"@id": "/policy/organism",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Embedding",
"/policy/FlyDonor",
"/policy/HumanDonor",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MouseDonor",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Project",
"/policy/PublicationData",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/Target",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/UcscBrowserComposite",
"/policy/WormDonor"
]
},
"rdfs:label": "Organism",
"rdfs:comment": [
"Organism bearing the target.",
"Organism of the donor.",
"The organism the biosample was originated from."
],
"rdfs:range": "/policy/Organism"
},
"passage_number": {
"@id": "/policy/passage_number",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Passage number",
"rdfs:comment": "Number of passages including the passages from the source."
},
"model_organism_mating_status": {
"@id": "/policy/model_organism_mating_status",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Mating status",
"rdfs:comment": "The mating status of the animal."
},
"internal_tags": {
"@id": "/policy/internal_tags",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/HumanDonor",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Pipeline",
"/policy/Project",
"/policy/PublicationData",
"/policy/Reference",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/UcscBrowserComposite"
]
}
},
"originated_from": {
"@id": "/policy/originated_from",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Originated from",
"rdfs:comment": "A biosample that the sample was orginated from.",
"rdfs:range": "/policy/Biosample"
},
"pooled_from": {
"@id": "/policy/pooled_from",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:comment": "A biosample from which an aliquot was taken to form the biosample.",
"rdfs:range": "/policy/Biosample"
},
"part_of": {
"@id": "/policy/part_of",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Separated from",
"rdfs:comment": "A biosample from which a discrete component was taken. That component is this biosample.",
"rdfs:range": "/policy/Biosample"
},
"host": {
"@id": "/policy/host",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Host biosample",
"rdfs:comment": "A biosample that was hosting this biosample.",
"rdfs:range": "/policy/Biosample"
},
"subcellular_fraction_term_name": {
"@id": "/policy/subcellular_fraction_term_name",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Subcellular fraction name",
"rdfs:comment": "The GO (Gene Ontology) term name for cellular component that constitutes the biosample."
},
"phase": {
"@id": "/policy/phase",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Cell-cycle phase",
"rdfs:comment": "Specification of cell cycle phase of the biosample."
},
"culture_harvest_date": {
"@id": "/policy/culture_harvest_date",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Culture harvest date",
"rdfs:comment": "For cultured samples, the date the biosample was taken."
},
"culture_start_date": {
"@id": "/policy/culture_start_date",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Culture start date",
"rdfs:comment": "For cultured samples, the date the culture was started. For cell lines, the date this particular growth was started, not the date the line was established."
},
"date_obtained": {
"@id": "/policy/date_obtained",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Date obtained",
"rdfs:comment": "For tissue samples, the date the biosample was taken."
},
"starting_amount": {
"@id": "/policy/starting_amount",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Starting amount",
"rdfs:comment": "The initial quantity of cells, tissue or animals obtained."
},
"starting_amount_units": {
"@id": "/policy/starting_amount_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Starting amount units",
"rdfs:comment": "The units used to quantify the amount of cells or tissue obtained."
},
"PMI": {
"@id": "/policy/PMI",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Post-mortem interval",
"rdfs:comment": "The amount of time elapsed since death."
},
"PMI_units": {
"@id": "/policy/PMI_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Post-mortem interval units",
"rdfs:comment": "The unit in which the PMI time was reported."
},
"preservation_method": {
"@id": "/policy/preservation_method",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Preservation method",
"rdfs:comment": "The method by which the sample was preserved: cryopreservation (slow-freeze) or flash-freezing."
},
"model_organism_sex": {
"@id": "/policy/model_organism_sex",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Model organism sex",
"rdfs:comment": "The sex of the organism the biosample comes from."
},
"mouse_life_stage": {
"@id": "/policy/mouse_life_stage",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Mouse life stage",
"rdfs:comment": "The life stage of the mouse biosample."
},
"fly_life_stage": {
"@id": "/policy/fly_life_stage",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Fly life stage",
"rdfs:comment": "Fly development stage of the animals used to prepare the biosample."
},
"fly_synchronization_stage": {
"@id": "/policy/fly_synchronization_stage",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Fly synchronization stage",
"rdfs:comment": "Fly development stage at which flies were synchronized."
},
"post_synchronization_time": {
"@id": "/policy/post_synchronization_time",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Post-synchronization time",
"rdfs:comment": "The time that elapsed past the point when animals were synchronized."
},
"post_synchronization_time_units": {
"@id": "/policy/post_synchronization_time_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Post-synchronization time units",
"rdfs:comment": "The units of time that elapsed past the point when animals were synchronized."
},
"post_treatment_time": {
"@id": "/policy/post_treatment_time",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Post-treatment time",
"rdfs:comment": "The time that elapsed past the point when biosamples were treated."
},
"post_treatment_time_units": {
"@id": "/policy/post_treatment_time_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Post-treatment time units",
"rdfs:comment": "The units of time that elapsed past the point when biosamples were treated."
},
"worm_life_stage": {
"@id": "/policy/worm_life_stage",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Worm life stage",
"rdfs:comment": "Worm development stage of the animals used to prepare the biosample."
},
"worm_synchronization_stage": {
"@id": "/policy/worm_synchronization_stage",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Worm synchronization stage",
"rdfs:comment": "Worm development stage at which the animals were synchronized."
},
"model_organism_age": {
"@id": "/policy/model_organism_age",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Model organism donor age",
"rdfs:comment": " The age or age range of the model donor organism when biological material was sampled."
},
"model_organism_age_units": {
"@id": "/policy/model_organism_age_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Model organism donor age units",
"rdfs:comment": "Age units of the model organism."
},
"model_organism_health_status": {
"@id": "/policy/model_organism_health_status",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "Model organism donor health status",
"rdfs:comment": "Health status of the model organism."
},
"nih_institutional_certification": {
"@id": "/policy/nih_institutional_certification",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Biosample",
"rdfs:label": "NIH institutional certification",
"rdfs:comment": "Institutional certification given by the NIH for human biosamples."
},
"biosample_synonyms": {
"@id": "/policy/biosample_synonyms",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Project",
"/policy/PublicationData",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries"
]
}
},
"organ_slims": {
"@id": "/policy/organ_slims",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Project",
"/policy/PublicationData",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries"
]
}
},
"system_slims": {
"@id": "/policy/system_slims",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Project",
"/policy/PublicationData",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries"
]
}
},
"developmental_slims": {
"@id": "/policy/developmental_slims",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Biosample",
"/policy/Embedding",
"/policy/Experiment",
"/policy/MatchedSet",
"/policy/Model",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Perturbation",
"/policy/Project",
"/policy/PublicationData",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries"
]
}
},
"sex": {
"@id": "/policy/sex",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Biosample",
"/policy/HumanDonor"
]
},
"rdfs:label": "Sex"
},
"age": {
"@id": "/policy/age",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Biosample",
"/policy/HumanDonor"
]
},
"rdfs:label": [
"Age",
"Donor age"
],
"rdfs:comment": "The age or age range of the donor when biological material was sampled."
},
"age_units": {
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},
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"Health status"
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},
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},
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},
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},
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},
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},
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"Meta-data field in model record with type"
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},
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"encyclopedia version"
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" The version of the ENCODE encyclopeida to which this annotation belongs.",
" The version of the encyclopeida to which this embeddings belongs.",
" The version of the encyclopeida to which this gene perturbation belongs.",
" The version of the encyclopeida to which this model belongs."
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},
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"The collection tags such as dataset resource and disease type for annotation.",
"The collection tags such as dataset resource and disease type for embedding.",
"The collection tags such as dataset resource and disease type for model.",
"The collection tags such as dataset resource and disease type for perturbation."
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},
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},
"rdfs:label": "Knowledge Portal Disease Area",
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" The timepoint for which the embedding is relevant.",
" The timepoint for which the model is relevant.",
" The timepoint for which the perturbation is relevant."
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},
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"The life_stage for which the embedding is relevant.",
"The life_stage for which the model is relevant.",
"The life_stage for which the perturbation is relevant."
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},
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},
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"Version of software used to derived the annotation calls.",
"Version of software used to derived the embedding calls.",
"Version of software used to derived the model calls.",
"Version of software used to derived the reference file set."
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},
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},
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},
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},
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},
"rdfs:label": [
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},
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},
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"/policy/File",
"/policy/Model",
"/policy/MultiomicsSeries",
"/policy/Perturbation"
]
}
},
"Embedding": {
"@id": "/policy/Embedding",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/FileSet",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/embedding.json"
},
"EmbeddingCollection": {
"@id": "/policy/EmbeddingCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"embeddings_type": {
"@id": "/policy/embeddings_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Embedding",
"rdfs:label": "Type",
"rdfs:comment": "The category that best describes the embeddings set."
},
"embeddings_category": {
"@id": "/policy/embeddings_category",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Embedding",
"rdfs:label": "Embeddings Category",
"rdfs:comment": "The name of the cell embedding that will be used as default for display on cellxgene, which should correspond to a key in ‘obsm’.."
},
"embeddings_unit": {
"@id": "/policy/embeddings_unit",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Embedding",
"rdfs:label": "Embedding Unit",
"rdfs:comment": "Unit used to create embedding"
},
"embeddings_cells": {
"@id": "/policy/embeddings_cells",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Embedding",
"rdfs:label": "Embeddings Cells",
"rdfs:comment": "Number of cells/nuclei in embedding"
},
"embeddings_pipeline": {
"@id": "/policy/embeddings_pipeline",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Embedding",
"rdfs:label": "Embedding Pipeline",
"rdfs:range": "/policy/Pipeline"
},
"embeddings_source": {
"@id": "/policy/embeddings_source",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Embedding",
"rdfs:label": "Embeddings Source",
"rdfs:comment": "The name of the cell embedding that will be used as default for use on cellxgene, which should correspond to obsm"
},
"embeddings_underlying_assay": {
"@id": "/policy/embeddings_underlying_assay",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Embedding"
},
"datasets_annotation": {
"@id": "/policy/datasets_annotation",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Embedding",
"/policy/Model",
"/policy/Pipeline"
]
},
"rdfs:label": "Annotation",
"rdfs:comment": [
"A Annotation referred to by the publication.",
"Annotations referred to by the embeding."
],
"rdfs:range": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Annotation",
"/policy/Dataset"
]
}
},
"datasets_experiment": {
"@id": "/policy/datasets_experiment",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Embedding",
"/policy/Model",
"/policy/Pipeline"
]
},
"rdfs:label": "Assay",
"rdfs:comment": [
"A Experiment referred to by model.",
"Assays referred to by the embeddings."
],
"rdfs:range": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Dataset",
"/policy/Experiment"
]
}
},
"tissue_term_name": {
"@id": "/policy/tissue_term_name",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Embedding",
"/policy/Model",
"/policy/Perturbation"
]
},
"rdfs:label": "Tissue Term",
"rdfs:comment": "Ontology Term describing tissue"
},
"MatchedSet": {
"@id": "/policy/MatchedSet",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Series",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/matched_set.json"
},
"Series": {
"@id": "/policy/Series",
"@type": "rdfs:Class",
"rdfs:subClassOf": "/policy/Item"
},
"MatchedSetCollection": {
"@id": "/policy/MatchedSetCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"related_datasets": {
"@id": "/policy/related_datasets",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/MatchedSet",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries"
]
},
"rdfs:label": "Dataset",
"rdfs:range": "/policy/Experiment"
},
"assay_synonyms": {
"@id": "/policy/assay_synonyms",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Experiment",
"/policy/MatchedSet",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Project",
"/policy/PublicationData",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/UcscBrowserComposite"
]
}
},
"assay_term_name": {
"@id": "/policy/assay_term_name",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/BismarkQualityMetric",
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric",
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/DuplicatesQualityMetric",
"/policy/EdwbamstatsQualityMetric",
"/policy/Experiment",
"/policy/FilteringQualityMetric",
"/policy/GenericQualityMetric",
"/policy/HistoneChipSeqQualityMetric",
"/policy/HotspotQualityMetric",
"/policy/IDRQualityMetric",
"/policy/IdrSummaryQualityMetric",
"/policy/MadQualityMetric",
"/policy/MatchedSet",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Project",
"/policy/PublicationData",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/StarQualityMetric",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/TrimmingQualityMetric",
"/policy/UcscBrowserComposite"
]
},
"rdfs:label": "Assay name",
"rdfs:comment": "OBI (Ontology for Biomedical Investigations) ontology term for the assay."
},
"assay_term_id": {
"@id": "/policy/assay_term_id",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/BismarkQualityMetric",
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric",
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/DuplicatesQualityMetric",
"/policy/EdwbamstatsQualityMetric",
"/policy/Experiment",
"/policy/FilteringQualityMetric",
"/policy/GenericQualityMetric",
"/policy/HistoneChipSeqQualityMetric",
"/policy/HotspotQualityMetric",
"/policy/IDRQualityMetric",
"/policy/IdrSummaryQualityMetric",
"/policy/MadQualityMetric",
"/policy/MatchedSet",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/Project",
"/policy/PublicationData",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/StarQualityMetric",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries",
"/policy/TrimmingQualityMetric",
"/policy/UcscBrowserComposite"
]
},
"rdfs:label": "Assay ID",
"rdfs:comment": "OBI (Ontology for Biomedical Investigations) ontology identifier for the assay."
},
"revoked_datasets": {
"@id": "/policy/revoked_datasets",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/MatchedSet",
"/policy/MultiomicsSeries",
"/policy/OrganismDevelopmentSeries",
"/policy/ReferenceEpigenome",
"/policy/ReplicationTimingSeries",
"/policy/TreatmentConcentrationSeries",
"/policy/TreatmentTimeSeries"
]
},
"rdfs:range": "/policy/File"
},
"Model": {
"@id": "/policy/Model",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/FileSet",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/model.json"
},
"ModelCollection": {
"@id": "/policy/ModelCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"model_name": {
"@id": "/policy/model_name",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Model",
"rdfs:label": "Model Name",
"rdfs:comment": "Model name."
},
"model_type": {
"@id": "/policy/model_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Model",
"rdfs:label": "Model Type",
"rdfs:comment": "Model type."
},
"model_input": {
"@id": "/policy/model_input",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Model",
"rdfs:label": "Model Input",
"rdfs:comment": "Model Input."
},
"model_output": {
"@id": "/policy/model_output",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Model",
"rdfs:label": "Model Output",
"rdfs:comment": "Model Output."
},
"model_format": {
"@id": "/policy/model_format",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Model",
"rdfs:label": "Model Format",
"rdfs:comment": "Model Format."
},
"model_training": {
"@id": "/policy/model_training",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Model",
"rdfs:label": "Model Training",
"rdfs:comment": "Description of model training."
},
"model_validation": {
"@id": "/policy/model_validation",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Model",
"rdfs:label": "Model Validation",
"rdfs:comment": "Description of model validation."
},
"model_biosamples": {
"@id": "/policy/model_biosamples",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Model",
"rdfs:label": "Model Biosamples",
"rdfs:comment": "Multiple Model Biosamples, attach list."
},
"model_underlying_assay": {
"@id": "/policy/model_underlying_assay",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Model",
"rdfs:label": "Underlying Assay",
"rdfs:comment": "Assay used to generate data"
},
"MultiomicsSeries": {
"@id": "/policy/MultiomicsSeries",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Series",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/multiomics_series.json"
},
"MultiomicsSeriesCollection": {
"@id": "/policy/MultiomicsSeriesCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"OrganismDevelopmentSeries": {
"@id": "/policy/OrganismDevelopmentSeries",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Series",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/organism_development_series.json"
},
"OrganismDevelopmentSeriesCollection": {
"@id": "/policy/OrganismDevelopmentSeriesCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"Perturbation": {
"@id": "/policy/Perturbation",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/FileSet",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/perturbation.json"
},
"PerturbationCollection": {
"@id": "/policy/PerturbationCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"perturbation_type": {
"@id": "/policy/perturbation_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Modification type",
"rdfs:comment": "Type of gene modification performed"
},
"assay_design": {
"@id": "/policy/assay_design",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Assay Design",
"rdfs:comment": "Design of the gene modification assay"
},
"assay_readout": {
"@id": "/policy/assay_readout",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Assay Readout",
"rdfs:comment": "Readout of the perturbation assay"
},
"phenotypes_measured": {
"@id": "/policy/phenotypes_measured",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Phenotypes Measured",
"rdfs:comment": "Phenotypes being measured directly or indirectly in assay"
},
"library": {
"@id": "/policy/library",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/Perturbation",
"/policy/Replicate"
]
},
"rdfs:label": "Library",
"rdfs:comment": [
"Guide library used, if a known library then reference that otherwise 'custom' and then provide guide sequences in separate PDF file",
"The nucleic acid library used in this replicate."
],
"rdfs:range": "/policy/Library"
},
"pooled_design": {
"@id": "/policy/pooled_design",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Pooled Design",
"rdfs:comment": "Phenotypes being measured directly or indirectly in assay"
},
"source_rna": {
"@id": "/policy/source_rna",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Source of siRNA/shRNA",
"rdfs:comment": "Details of source of siRNA reagents and their sequence"
},
"commerical_assay": {
"@id": "/policy/commerical_assay",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Details of any commerically available assays used",
"rdfs:comment": "Details of any commerically available assays used"
},
"gating_strategy": {
"@id": "/policy/gating_strategy",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Gating Strategy",
"rdfs:comment": "For cell sorting experiments, description of the gating strategy used (full details in experimental protocol)"
},
"partitioning_strategy": {
"@id": "/policy/partitioning_strategy",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Partitioning Strategy",
"rdfs:comment": "For cell partitioning, description of how the cells were partitioned (full details in experimental protocol)"
},
"perturbation_target": {
"@id": "/policy/perturbation_target",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Perturbation Target",
"rdfs:comment": "Target of perurbation"
},
"assay_controls": {
"@id": "/policy/assay_controls",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Assay Controls",
"rdfs:comment": "Assay Controls"
},
"resource_contact": {
"@id": "/policy/resource_contact",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Resource Contact",
"rdfs:comment": "Contact"
},
"perturbation_pipeline": {
"@id": "/policy/perturbation_pipeline",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Pipeline",
"rdfs:comment": "Pipeline referred to by the perturbation.",
"rdfs:range": "/policy/Pipeline"
},
"biosample_conditions": {
"@id": "/policy/biosample_conditions",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Perturbation",
"rdfs:label": "Biosample Conditions",
"rdfs:comment": "Any specalized conditions the cells/tissues were subjected to"
},
"Project": {
"@id": "/policy/Project",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/FileSet",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/project.json"
},
"ProjectCollection": {
"@id": "/policy/ProjectCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"project_type": {
"@id": "/policy/project_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Project",
"rdfs:label": "Type",
"rdfs:comment": "The category that best describes the project."
},
"PublicationData": {
"@id": "/policy/PublicationData",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/FileSet",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/publication_data.json"
},
"PublicationDataCollection": {
"@id": "/policy/PublicationDataCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"Reference": {
"@id": "/policy/Reference",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/FileSet",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/reference.json"
},
"ReferenceCollection": {
"@id": "/policy/ReferenceCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"reference_type": {
"@id": "/policy/reference_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Reference",
"rdfs:label": "Type",
"rdfs:comment": "The category that best describes the reference set."
},
"ReferenceEpigenome": {
"@id": "/policy/ReferenceEpigenome",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Series",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/reference_epigenome.json"
},
"ReferenceEpigenomeCollection": {
"@id": "/policy/ReferenceEpigenomeCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"ReplicationTimingSeries": {
"@id": "/policy/ReplicationTimingSeries",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Series",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/replication_timing_series.json"
},
"ReplicationTimingSeriesCollection": {
"@id": "/policy/ReplicationTimingSeriesCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"TreatmentConcentrationSeries": {
"@id": "/policy/TreatmentConcentrationSeries",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Series",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/treatment_concentration_series.json"
},
"TreatmentConcentrationSeriesCollection": {
"@id": "/policy/TreatmentConcentrationSeriesCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"TreatmentTimeSeries": {
"@id": "/policy/TreatmentTimeSeries",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Series",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/treatment_time_series.json"
},
"TreatmentTimeSeriesCollection": {
"@id": "/policy/TreatmentTimeSeriesCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"UcscBrowserComposite": {
"@id": "/policy/UcscBrowserComposite",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/FileSet",
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/ucsc_browser_composite.json"
},
"UcscBrowserCompositeCollection": {
"@id": "/policy/UcscBrowserCompositeCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"FlyDonor": {
"@id": "/policy/FlyDonor",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Donor",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/fly_donor.json"
},
"Donor": {
"@id": "/policy/Donor",
"@type": "rdfs:Class",
"rdfs:subClassOf": "/policy/Item"
},
"FlyDonorCollection": {
"@id": "/policy/FlyDonorCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"strain_background": {
"@id": "/policy/strain_background",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/FlyDonor",
"/policy/MouseDonor",
"/policy/WormDonor"
]
},
"rdfs:label": "Strain background",
"rdfs:comment": "The specific parent strain designation of a non-human donor."
},
"strain_name": {
"@id": "/policy/strain_name",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/FlyDonor",
"/policy/MouseDonor",
"/policy/WormDonor"
]
},
"rdfs:label": "Strain name",
"rdfs:comment": "The specific strain designation of a non-human donor."
},
"genotype": {
"@id": "/policy/genotype",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/FlyDonor",
"/policy/MouseDonor",
"/policy/WormDonor"
]
},
"rdfs:label": "Strain genotype",
"rdfs:comment": [
"The genotype of the strain according to accepted nomenclature conventions.",
"The genotype of the strain according to accepted nomenclature conventions: http://flybase.org/wiki/FlyBase:Nomenclature",
"The genotype of the strain according to accepted nomenclature conventions: http://www.wormbase.org/about/userguide/nomenclature#k89607hgcf24ea13jbid5--10."
]
},
"parent_strains": {
"@id": "/policy/parent_strains",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/FlyDonor",
"/policy/MouseDonor",
"/policy/WormDonor"
]
},
"rdfs:label": "Parent strain",
"rdfs:comment": "A donor ID of a parent strain, if known.",
"rdfs:range": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/FlyDonor",
"/policy/MouseDonor",
"/policy/WormDonor"
]
}
},
"HumanDonor": {
"@id": "/policy/HumanDonor",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Donor",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/human_donor.json"
},
"HumanDonorCollection": {
"@id": "/policy/HumanDonorCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"ethnicity": {
"@id": "/policy/ethnicity",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HumanDonor",
"rdfs:label": "Ethnicity"
},
"parents": {
"@id": "/policy/parents",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStep",
"/policy/HumanDonor"
]
},
"rdfs:label": "Parent",
"rdfs:comment": [
"A precusor step.",
"Biological parent of this donor."
],
"rdfs:range": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStep",
"/policy/HumanDonor"
]
}
},
"siblings": {
"@id": "/policy/siblings",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HumanDonor",
"rdfs:label": "Sibling",
"rdfs:comment": "A donor that has at least one parent in common.",
"rdfs:range": "/policy/HumanDonor"
},
"twin": {
"@id": "/policy/twin",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HumanDonor",
"rdfs:label": "Twin",
"rdfs:comment": "A human donor that is a twin sibling of this human donor.",
"rdfs:range": "/policy/HumanDonor"
},
"twin_type": {
"@id": "/policy/twin_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HumanDonor",
"rdfs:label": "Twin type"
},
"children": {
"@id": "/policy/children",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HumanDonor",
"rdfs:range": "/policy/HumanDonor"
},
"MouseDonor": {
"@id": "/policy/MouseDonor",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Donor",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/mouse_donor.json"
},
"MouseDonorCollection": {
"@id": "/policy/MouseDonorCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"WormDonor": {
"@id": "/policy/WormDonor",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Donor",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/worm_donor.json"
},
"WormDonorCollection": {
"@id": "/policy/WormDonorCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"num_times_outcrossed": {
"@id": "/policy/num_times_outcrossed",
"@type": "rdf:Property",
"rdfs:domain": "/policy/WormDonor",
"rdfs:label": "Number of times outcrossed",
"rdfs:comment": "The number of out/backcrossed when constructing the strain"
},
"outcrossed_strain": {
"@id": "/policy/outcrossed_strain",
"@type": "rdf:Property",
"rdfs:domain": "/policy/WormDonor",
"rdfs:label": "Outcrossed strain background",
"rdfs:comment": "The strain used for backcrossing.",
"rdfs:range": "/policy/WormDonor"
},
"Experiment": {
"@id": "/policy/Experiment",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Dataset",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/experiment.json"
},
"ExperimentCollection": {
"@id": "/policy/ExperimentCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"date_submitted": {
"@id": "/policy/date_submitted",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment",
"rdfs:label": "Date submitted",
"rdfs:comment": "The date that the experiment received all required replicates and files"
},
"assay_pipeline": {
"@id": "/policy/assay_pipeline",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment",
"rdfs:label": "Pipeline",
"rdfs:comment": "Pipeline referred to by the assay.",
"rdfs:range": "/policy/Pipeline"
},
"possible_controls": {
"@id": "/policy/possible_controls",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment",
"rdfs:label": "Control",
"rdfs:comment": "An experiment that contains files that can serve as a scientific control for this experiment.",
"rdfs:range": "/policy/Experiment"
},
"internal_status": {
"@id": "/policy/internal_status",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment",
"rdfs:label": "Internal status",
"rdfs:comment": "The status of an experiment in the DCC process."
},
"pipeline_error_detail": {
"@id": "/policy/pipeline_error_detail",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment",
"rdfs:label": "Pipeline error message",
"rdfs:comment": "Explanation of why the experiment failed pipeline analysis."
},
"replicates": {
"@id": "/policy/replicates",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment",
"rdfs:range": "/policy/Replicate"
},
"biosample_summary": {
"@id": "/policy/biosample_summary",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment",
"rdfs:label": "Biosample summary"
},
"assay_slims": {
"@id": "/policy/assay_slims",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment"
},
"assay_title": {
"@id": "/policy/assay_title",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment",
"rdfs:label": "Assay title"
},
"category_slims": {
"@id": "/policy/category_slims",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment"
},
"type_slims": {
"@id": "/policy/type_slims",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment"
},
"objective_slims": {
"@id": "/policy/objective_slims",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment"
},
"related_series": {
"@id": "/policy/related_series",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment",
"rdfs:range": "/policy/Series"
},
"replication_type": {
"@id": "/policy/replication_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Experiment",
"rdfs:label": "Replication type",
"rdfs:comment": "Calculated field that indicates the replication model"
},
"Replicate": {
"@id": "/policy/Replicate",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/replicate.json"
},
"ReplicateCollection": {
"@id": "/policy/ReplicateCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"antibody": {
"@id": "/policy/antibody",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Replicate",
"rdfs:label": "Antibody",
"rdfs:comment": "For Immunoprecipitation assays, the antibody used.",
"rdfs:range": "/policy/AntibodyLot"
},
"biological_replicate_number": {
"@id": "/policy/biological_replicate_number",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Replicate",
"rdfs:label": "Biological replicate",
"rdfs:comment": "Data collection under the same methods using a different biological source, measuring the variability in the biological source."
},
"technical_replicate_number": {
"@id": "/policy/technical_replicate_number",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Replicate",
"rdfs:label": "Technical replicate",
"rdfs:comment": "Data collection under the same methods using the same biological source, measuring the variability in the method."
},
"experiment": {
"@id": "/policy/experiment",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Replicate",
"rdfs:label": "Experiment",
"rdfs:comment": "The experiment the replicate belongs to.",
"rdfs:range": "/policy/Experiment"
},
"rbns_protein_concentration": {
"@id": "/policy/rbns_protein_concentration",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Replicate",
"rdfs:label": "RBNS protein concentration",
"rdfs:comment": "For use only with RNA Bind-n-Seq replicates to indicate the protein concentration."
},
"rbns_protein_concentration_units": {
"@id": "/policy/rbns_protein_concentration_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Replicate",
"rdfs:label": "RBNS protein concentration units"
},
"File": {
"@id": "/policy/File",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/file.json"
},
"FileCollection": {
"@id": "/policy/FileCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"external_accession": {
"@id": "/policy/external_accession",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "External accession",
"rdfs:comment": "For files that were not accessioned at our site but have an accession elsewhere."
},
"read_count": {
"@id": "/policy/read_count",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Read count",
"rdfs:comment": "Number of reads in fastq file."
},
"file_format": {
"@id": "/policy/file_format",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "File format"
},
"file_format_type": {
"@id": "/policy/file_format_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Specific file format type",
"rdfs:comment": "Files of type bed and gff require further specification"
},
"file_format_specifications": {
"@id": "/policy/file_format_specifications",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:range": "/policy/Document"
},
"restricted": {
"@id": "/policy/restricted",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Restricted file",
"rdfs:comment": "A flag to indicate whether this file is subject to restricted access"
},
"no_file_available": {
"@id": "/policy/no_file_available",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "No file available",
"rdfs:comment": "A flag to indicate whether this file is available to download. It may also not exist if it is the result of an unproductive analysis."
},
"submitted_file_name": {
"@id": "/policy/submitted_file_name",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Original file name",
"rdfs:comment": "The local file name used at time of submission."
},
"md5sum": {
"@id": "/policy/md5sum",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "MD5sum",
"rdfs:comment": "The md5sum of the file being transferred."
},
"content_md5sum": {
"@id": "/policy/content_md5sum",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Content MD5sum",
"rdfs:comment": "The MD5sum of the uncompressed file."
},
"fastq_signature": {
"@id": "/policy/fastq_signature",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Flowcell based fastq signature part",
"rdfs:comment": "Fastq file flowcell based unique signature to reference a file."
},
"file_size": {
"@id": "/policy/file_size",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "File size",
"rdfs:comment": "File size specified in bytes."
},
"platform": {
"@id": "/policy/platform",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Platform",
"rdfs:comment": "The measurement device used to collect data.",
"rdfs:range": "/policy/Platform"
},
"platforms_multiple_files": {
"@id": "/policy/platforms_multiple_files",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Platform multiple files",
"rdfs:comment": "The measurement device used to collect data"
},
"read_length": {
"@id": "/policy/read_length",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Read length",
"rdfs:comment": "For high-throughput sequencing, the number of contiguous nucleotides determined by sequencing."
},
"read_length_zip_files": {
"@id": "/policy/read_length_zip_files",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Read length for zipped files",
"rdfs:comment": "For high-throughput sequencing, the number of contiguous nucleotides determined by sequencing"
},
"run_type": {
"@id": "/policy/run_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Run type for sequencing files",
"rdfs:comment": "Indicates if file is part of a single or paired end sequencing run"
},
"bed_file_state": {
"@id": "/policy/bed_file_state",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "State",
"rdfs:comment": "Options peak number, cell type, gene name of linked promoter, variant name, chromatin state, gene name of linked binding sites, no assigned name"
},
"bed_file_value": {
"@id": "/policy/bed_file_value",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Value",
"rdfs:comment": "number of samples, peak darkness, co-accesibility score, deltaSVM score, no assigned value"
},
"paired_end": {
"@id": "/policy/paired_end",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Paired End Identifier",
"rdfs:comment": "Which read of the pair the file represents (in case of paired end sequencing run)"
},
"paired_with": {
"@id": "/policy/paired_with",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "File pairing",
"rdfs:comment": "The paired end fastq that corresponds with this file.",
"rdfs:range": "/policy/File"
},
"mapped_read_length": {
"@id": "/policy/mapped_read_length",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Mapped read length",
"rdfs:comment": "The length of the reads actually mapped, if the original read length was clipped."
},
"mapped_run_type": {
"@id": "/policy/mapped_run_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Mapped run type for bam files",
"rdfs:comment": "The mapped run type of the alignment file which may differ from the fastqs it is derived from."
},
"flowcell_details": {
"@id": "/policy/flowcell_details",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Flowcell details"
},
"output_type": {
"@id": "/policy/output_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Output type",
"rdfs:comment": "A description of the file's purpose or contents."
},
"derived_from": {
"@id": "/policy/derived_from",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:range": "/policy/File"
},
"controlled_by": {
"@id": "/policy/controlled_by",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:range": "/policy/File"
},
"dataset": {
"@id": "/policy/dataset",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Dataset",
"rdfs:comment": "The experiment or dataset the file belongs to.",
"rdfs:range": "/policy/Dataset"
},
"replicate": {
"@id": "/policy/replicate",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Replicate",
"rdfs:comment": "The experimental replicate designation for the file.",
"rdfs:range": "/policy/Replicate"
},
"genome_annotation": {
"@id": "/policy/genome_annotation",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Genome annotation",
"rdfs:comment": "Genome annotation that file was generated with."
},
"step_run": {
"@id": "/policy/step_run",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/BismarkQualityMetric",
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric",
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/DuplicatesQualityMetric",
"/policy/EdwbamstatsQualityMetric",
"/policy/File",
"/policy/FilteringQualityMetric",
"/policy/GenericQualityMetric",
"/policy/HistoneChipSeqQualityMetric",
"/policy/HotspotQualityMetric",
"/policy/IDRQualityMetric",
"/policy/IdrSummaryQualityMetric",
"/policy/MadQualityMetric",
"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/StarQualityMetric",
"/policy/TrimmingQualityMetric"
]
},
"rdfs:label": [
"Analysis Step",
"Analysis step run"
],
"rdfs:comment": [
"Reference to analysis step run in pipeline",
"The run instance of the step used to generate the file."
],
"rdfs:range": "/policy/AnalysisStepRun"
},
"content_error_detail": {
"@id": "/policy/content_error_detail",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Content error detail",
"rdfs:comment": "Explanation of why the file failed the automated content checks."
},
"revoke_detail": {
"@id": "/policy/revoke_detail",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Revoke error detail",
"rdfs:comment": "Explanation of why the file was revoked."
},
"href": {
"@id": "/policy/href",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Download URL",
"rdfs:comment": "The download path for S3 to obtain the actual file."
},
"upload_credentials": {
"@id": "/policy/upload_credentials",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Upload Credentials",
"rdfs:comment": "The upload credentials for S3 to submit the file content."
},
"read_length_units": {
"@id": "/policy/read_length_units",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Read length units",
"rdfs:comment": "The units for read length."
},
"biological_replicates": {
"@id": "/policy/biological_replicates",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Biological replicate number",
"rdfs:comment": "The identifying number of each relevant biological replicate"
},
"technical_replicates": {
"@id": "/policy/technical_replicates",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Technical replicate number",
"rdfs:comment": "The identifying number of each relevant technical replicate"
},
"analysis_step_version": {
"@id": "/policy/analysis_step_version",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/AnalysisStepRun",
"/policy/File"
]
},
"rdfs:label": "Analysis Step Version",
"rdfs:comment": [
"Reference to template step in pipeline",
"The step version of the pipeline from which this file is an output."
],
"rdfs:range": "/policy/AnalysisStepVersion"
},
"output_category": {
"@id": "/policy/output_category",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "Output category",
"rdfs:comment": "The overall catagory of the file content."
},
"quality_metrics": {
"@id": "/policy/quality_metrics",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:range": "/policy/QualityMetric"
},
"file_type": {
"@id": "/policy/file_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/File",
"rdfs:label": "File type",
"rdfs:comment": "The concatenation of file_format and file_format_type"
},
"GeneticModification": {
"@id": "/policy/GeneticModification",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/genetic_modification.json"
},
"GeneticModificationCollection": {
"@id": "/policy/GeneticModificationCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"category": {
"@id": "/policy/category",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "Category",
"rdfs:comment": "The category/type of the genetic modification performed."
},
"zygosity": {
"@id": "/policy/zygosity",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "Modification zygosity",
"rdfs:comment": "The zygosity of the genetic modification."
},
"modified_site_by_target_id": {
"@id": "/policy/modified_site_by_target_id",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "Modification site",
"rdfs:comment": "The name (ENCODE target ID) of the gene whose expression or product is modified by the genetic modification.",
"rdfs:range": "/policy/Target"
},
"modified_site_by_coordinates": {
"@id": "/policy/modified_site_by_coordinates",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "Modification site",
"rdfs:comment": "Genomic coordinates specifying the location of the modification."
},
"modified_site_by_sequence": {
"@id": "/policy/modified_site_by_sequence",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "Modification site",
"rdfs:comment": "Genomic sequence specifying location of the modification."
},
"modified_site_nonspecific": {
"@id": "/policy/modified_site_nonspecific",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "Modification site",
"rdfs:comment": "Site of modification that is not known (i.e. is random, not targeted)."
},
"introduced_tags": {
"@id": "/policy/introduced_tags",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "Introduced tag",
"rdfs:comment": "Protein tag introduced in the modification."
},
"introduced_sequence": {
"@id": "/policy/introduced_sequence",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "Introduced sequence",
"rdfs:comment": "If modification_type = insertion or replacement, the newly introduced sequence via the modification."
},
"method": {
"@id": "/policy/method",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "Method",
"rdfs:comment": "The method used to produce the described genetic modification."
},
"rnai_sequences": {
"@id": "/policy/rnai_sequences",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "RNAi sequence",
"rdfs:comment": "Sequences of the inhibitory RNA."
},
"guide_rna_sequences": {
"@id": "/policy/guide_rna_sequences",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "guide RNA sequence",
"rdfs:comment": "guide RNA sequence used in the experiment."
},
"RVD_sequence_pairs": {
"@id": "/policy/RVD_sequence_pairs",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "RVD sequence pair",
"rdfs:comment": "The pair of repeat variable diresidue sequences of the TAL effectors that recognize the left and right half sites at a particular location. e.g. NI,NG,NI,HD,NG,NN,NG,NG,NN,HD,NI,NI,NI,NI,NM,HD,HD,NG"
},
"reagents": {
"@id": "/policy/reagents",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:label": "Reagent",
"rdfs:comment": "Details for where a reagent used to produce the described genetic modification can be obtained, if applicable."
},
"biosamples_modified": {
"@id": "/policy/biosamples_modified",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:range": "/policy/Biosample"
},
"donors_modified": {
"@id": "/policy/donors_modified",
"@type": "rdf:Property",
"rdfs:domain": "/policy/GeneticModification",
"rdfs:range": "/policy/Donor"
},
"Image": {
"@id": "/policy/Image",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/image.json"
},
"ImageCollection": {
"@id": "/policy/ImageCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"Page": {
"@id": "/policy/Page",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/page.json"
},
"PageCollection": {
"@id": "/policy/PageCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"parent": {
"@id": "/policy/parent",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Page",
"rdfs:label": "Parent Page",
"rdfs:range": "/policy/Page"
},
"news": {
"@id": "/policy/news",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Page",
"rdfs:label": "News post",
"rdfs:comment": "Page is a news post"
},
"news_excerpt": {
"@id": "/policy/news_excerpt",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Page",
"rdfs:label": "Excerpt of news post to display on lists of news posts",
"rdfs:comment": "News post excerpt"
},
"news_keywords": {
"@id": "/policy/news_keywords",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Page",
"rdfs:label": "News keyword",
"rdfs:comment": "A keyword for news post filtering."
},
"layout": {
"@id": "/policy/layout",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Page",
"rdfs:label": "Page Layout",
"rdfs:comment": "Hierarchical description of the page layout."
},
"canonical_uri": {
"@id": "/policy/canonical_uri",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Page",
"rdfs:label": "Canonical URI"
},
"year_released": {
"@id": "/policy/year_released",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Page",
"rdfs:label": "Year"
},
"AnalysisStep": {
"@id": "/policy/AnalysisStep",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/analysis_step.json"
},
"AnalysisStepCollection": {
"@id": "/policy/AnalysisStepCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"step_label": {
"@id": "/policy/step_label",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStep",
"rdfs:label": "Step label",
"rdfs:comment": "Unique label of the analysis step using a naming system where the pipeline, software used, the purpose is described, e.g. rampage-grit-peak-calling-step"
},
"major_version": {
"@id": "/policy/major_version",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStep",
"rdfs:label": "Major version",
"rdfs:comment": "The major version of the analysis step."
},
"analysis_step_types": {
"@id": "/policy/analysis_step_types",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStep",
"rdfs:label": "Type"
},
"input_file_types": {
"@id": "/policy/input_file_types",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStep",
"rdfs:label": "Input file type",
"rdfs:comment": "A file type used as input for the analysis."
},
"output_file_types": {
"@id": "/policy/output_file_types",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStep",
"rdfs:label": "Output file type",
"rdfs:comment": "A file type generated as output for the analysis."
},
"qa_stats_generated": {
"@id": "/policy/qa_stats_generated",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStep",
"rdfs:label": "QA statistic",
"rdfs:comment": "A QA statistic generated by the analysis."
},
"pipelines": {
"@id": "/policy/pipelines",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStep",
"rdfs:range": "/policy/Pipeline"
},
"current_version": {
"@id": "/policy/current_version",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStep",
"rdfs:label": "Current version",
"rdfs:range": "/policy/AnalysisStepVersion"
},
"AnalysisStepRun": {
"@id": "/policy/AnalysisStepRun",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/analysis_step_run.json"
},
"AnalysisStepRunCollection": {
"@id": "/policy/AnalysisStepRunCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"dx_applet_details": {
"@id": "/policy/dx_applet_details",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStepRun",
"rdfs:label": "DNA Nexus applet detail"
},
"AnalysisStepVersion": {
"@id": "/policy/AnalysisStepVersion",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/analysis_step_version.json"
},
"AnalysisStepVersionCollection": {
"@id": "/policy/AnalysisStepVersionCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"minor_version": {
"@id": "/policy/minor_version",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStepVersion",
"rdfs:label": "Minor version",
"rdfs:comment": "The minor version of the analysis step"
},
"analysis_step": {
"@id": "/policy/analysis_step",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStepVersion",
"rdfs:label": "Analysis Step",
"rdfs:comment": "Reference to template step in pipeline",
"rdfs:range": "/policy/AnalysisStep"
},
"software_versions": {
"@id": "/policy/software_versions",
"@type": "rdf:Property",
"rdfs:domain": "/policy/AnalysisStepVersion",
"rdfs:range": "/policy/SoftwareVersion"
},
"Pipeline": {
"@id": "/policy/Pipeline",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/pipeline.json"
},
"PipelineCollection": {
"@id": "/policy/PipelineCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"assay_term_names": {
"@id": "/policy/assay_term_names",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Pipeline",
"rdfs:label": "Assay name",
"rdfs:comment": "OBI (Ontology for Biomedical Investigations) ontology term for the assay."
},
"data_type": {
"@id": "/policy/data_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Pipeline",
"rdfs:label": "Data Type"
},
"analysis_steps": {
"@id": "/policy/analysis_steps",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Pipeline",
"rdfs:label": "Analysis step",
"rdfs:comment": "A particular computational analysis step used by the pipeline.",
"rdfs:range": "/policy/AnalysisStep"
},
"standards_page": {
"@id": "/policy/standards_page",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Pipeline",
"rdfs:label": "Standards page for this pipeline",
"rdfs:comment": "An link to a page describing the standards for this pipeline.",
"rdfs:range": "/policy/Page"
},
"pipeline_type": {
"@id": "/policy/pipeline_type",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Pipeline",
"rdfs:label": "Pipeline Type",
"rdfs:comment": "Type of pipeline: wdl, snakemake, ruffus, cwl, github_readme, text_file, notebook"
},
"workflow_language": {
"@id": "/policy/workflow_language",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Pipeline",
"rdfs:label": "Workflow Language",
"rdfs:comment": "Language used if workflow script"
},
"pipeline_output": {
"@id": "/policy/pipeline_output",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Pipeline",
"rdfs:label": "Pipeline Output",
"rdfs:comment": "Outputs produced by the pipeline"
},
"pipeline_chain": {
"@id": "/policy/pipeline_chain",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Pipeline",
"rdfs:label": "Pipeline chain",
"rdfs:comment": "An link to pipelines in same chain",
"rdfs:range": "/policy/Pipeline"
},
"pipeline_version": {
"@id": "/policy/pipeline_version",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Pipeline",
"rdfs:label": "Pipeline version",
"rdfs:comment": "The pipeline version."
},
"pipeline_newer_version": {
"@id": "/policy/pipeline_newer_version",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Pipeline",
"rdfs:label": "Pipeline Latest version",
"rdfs:comment": "The pipeline latest version."
},
"BismarkQualityMetric": {
"@id": "/policy/BismarkQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/bismark_quality_metric.json"
},
"QualityMetric": {
"@id": "/policy/QualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": "/policy/Item"
},
"BismarkQualityMetricCollection": {
"@id": "/policy/BismarkQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"quality_metric_of": {
"@id": "/policy/quality_metric_of",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/BismarkQualityMetric",
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric",
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/DuplicatesQualityMetric",
"/policy/EdwbamstatsQualityMetric",
"/policy/FilteringQualityMetric",
"/policy/GenericQualityMetric",
"/policy/HistoneChipSeqQualityMetric",
"/policy/HotspotQualityMetric",
"/policy/IDRQualityMetric",
"/policy/IdrSummaryQualityMetric",
"/policy/MadQualityMetric",
"/policy/SamtoolsFlagstatsQualityMetric",
"/policy/SamtoolsStatsQualityMetric",
"/policy/StarQualityMetric",
"/policy/TrimmingQualityMetric"
]
},
"rdfs:label": "File",
"rdfs:comment": "A particular file associated with this quality metric.",
"rdfs:range": "/policy/File"
},
"Sequences%20analysed%20in%20total": {
"@id": "/policy/Sequences%20analysed%20in%20total",
"@type": "rdf:Property",
"rdfs:domain": "/policy/BismarkQualityMetric",
"rdfs:label": "Sequences analysed in total",
"rdfs:comment": "Total number of reads analysed by Bismark for WGBS"
},
"lambda%20Sequences%20analysed%20in%20total": {
"@id": "/policy/lambda%20Sequences%20analysed%20in%20total",
"@type": "rdf:Property",
"rdfs:domain": "/policy/BismarkQualityMetric",
"rdfs:label": "lambda Sequences analysed in total",
"rdfs:comment": "Total number of reads analysed by Bismark for WGBS vs. lambda phage genome"
},
"Mapping%20efficiency": {
"@id": "/policy/Mapping%20efficiency",
"@type": "rdf:Property",
"rdfs:domain": "/policy/BismarkQualityMetric",
"rdfs:label": "Mapping efficiency",
"rdfs:comment": "Bismark mapping efficiency for WGBS vs. reference genome"
},
"lambda%20Mapping%20efficiency": {
"@id": "/policy/lambda%20Mapping%20efficiency",
"@type": "rdf:Property",
"rdfs:domain": "/policy/BismarkQualityMetric",
"rdfs:label": "lambda Mapping efficiency",
"rdfs:comment": "Bismark mapping efficiency for WGBS vs. lambda phage genome"
},
"lambda%20C%20methylated%20in%20CpG%20context": {
"@id": "/policy/lambda%20C%20methylated%20in%20CpG%20context",
"@type": "rdf:Property",
"rdfs:domain": "/policy/BismarkQualityMetric",
"rdfs:label": "lambda C methylated in CpG context",
"rdfs:comment": "Bismark mapping efficiency for WGBS vs. lambda phage genome"
},
"lambda%20C%20methylated%20in%20CHG%20context": {
"@id": "/policy/lambda%20C%20methylated%20in%20CHG%20context",
"@type": "rdf:Property",
"rdfs:domain": "/policy/BismarkQualityMetric",
"rdfs:label": "lambda C methylated in CHG context",
"rdfs:comment": "Bismark mapping efficiency for WGBS vs. lambda phage genome"
},
"lambda%20C%20methylated%20in%20CHH%20context": {
"@id": "/policy/lambda%20C%20methylated%20in%20CHH%20context",
"@type": "rdf:Property",
"rdfs:domain": "/policy/BismarkQualityMetric",
"rdfs:label": "lambda C methylated in CHH context",
"rdfs:comment": "Bismark mapping efficiency for WGBS vs. lambda phage genome"
},
"C%20methylated%20in%20CHH%20context": {
"@id": "/policy/C%20methylated%20in%20CHH%20context",
"@type": "rdf:Property",
"rdfs:domain": "/policy/BismarkQualityMetric",
"rdfs:label": "C methylated in CHH context",
"rdfs:comment": "Bismark mapping efficiency for WGBS vs. reference genome"
},
"C%20methylated%20in%20CHG%20context": {
"@id": "/policy/C%20methylated%20in%20CHG%20context",
"@type": "rdf:Property",
"rdfs:domain": "/policy/BismarkQualityMetric",
"rdfs:label": "C methylated in CHG context",
"rdfs:comment": "Bismark mapping efficiency for WGBS vs. reference genome"
},
"C%20methylated%20in%20CpG%20context": {
"@id": "/policy/C%20methylated%20in%20CpG%20context",
"@type": "rdf:Property",
"rdfs:domain": "/policy/BismarkQualityMetric",
"rdfs:label": "C methylated in CpG context",
"rdfs:comment": "Bismark mapping efficiency for WGBS vs. reference genome"
},
"ChipSeqFilterQualityMetric": {
"@id": "/policy/ChipSeqFilterQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/chipseq_filter_quality_metric.json"
},
"ChipSeqFilterQualityMetricCollection": {
"@id": "/policy/ChipSeqFilterQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"NSC": {
"@id": "/policy/NSC",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric"
]
},
"rdfs:label": "Normalized strand cross-correlation",
"rdfs:comment": "Normalized strand cross-correlation = FRAGLEN_CC / MIN_CC. Ratio of strand cross-correlation at estimated fragment length to the minimum cross-correlation over all shifts."
},
"RSC": {
"@id": "/policy/RSC",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric"
]
},
"rdfs:label": [
"Relative cross correlation coefficient",
"Relative cross-correlation coefficient"
],
"rdfs:comment": [
"Relative cross correlation coefficient. Ratio of strand cross-correlation at fragment length and at read length",
"Relative cross correlation coefficient. Ratio of strand cross-correlation at fragment length and at read length"
]
},
"PBC1": {
"@id": "/policy/PBC1",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric"
]
},
"rdfs:label": "PCR bottlenecking coefficient 1",
"rdfs:comment": [
"PCR Bottlenecking coefficient 1 = M1/M_DISTINCT where M1: number of genomic locations where exactly one read maps uniquely, M_DISTINCT: number of distinct genomic locations to which some read maps uniquely",
"PCR Bottlenecking coefficient 1 = Single-read Locations / Distinct Locations"
]
},
"PBC2": {
"@id": "/policy/PBC2",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric"
]
},
"rdfs:label": "PCR bottlenecking coefficient 2",
"rdfs:comment": [
"PCR Bottlenecking coefficient 2 (indicates library complexity) = M1/M2 where M1: number of genomic locations where only one read maps uniquely and M2: number of genomic locations where 2 reads map uniquely",
"PCR Bottlenecking coefficient 2 (indicates library complexity) = Single-read Locations / Multi-read Locations"
]
},
"fragment%20length": {
"@id": "/policy/fragment%20length",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric"
]
},
"rdfs:label": [
"Fragment length",
"fragment length"
],
"rdfs:comment": "Fragment length/strandshift. This is the estimated fragment length/strand shift for each dataset as estimated by strand cross-correlation analysis"
},
"NRF": {
"@id": "/policy/NRF",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric"
]
},
"rdfs:label": "Non-redundant fraction",
"rdfs:comment": [
"Non redundant fraction (indicates library complexity). Distinct Locations Mapped / Sampled Reads",
"Non redundant fraction (indicates library complexity). Number of distinct unique mapping reads (i.e. after removing duplicates) / Total number of reads"
]
},
"cross_correlation_plot": {
"@id": "/policy/cross_correlation_plot",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/ChipSeqFilterQualityMetric",
"/policy/ComplexityXcorrQualityMetric"
]
},
"rdfs:label": "QC metric document metadata",
"rdfs:comment": "Cross-correlation plot"
},
"ComplexityXcorrQualityMetric": {
"@id": "/policy/ComplexityXcorrQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/complexity_xcorr_quality_metric.json"
},
"ComplexityXcorrQualityMetricCollection": {
"@id": "/policy/ComplexityXcorrQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"sample%20size": {
"@id": "/policy/sample%20size",
"@type": "rdf:Property",
"rdfs:domain": "/policy/ComplexityXcorrQualityMetric",
"rdfs:label": "Sample size",
"rdfs:comment": "Total reads sampled (pairs if applicable)"
},
"paired-end": {
"@id": "/policy/paired-end",
"@type": "rdf:Property",
"rdfs:domain": "/policy/ComplexityXcorrQualityMetric",
"rdfs:label": "Paired-end",
"rdfs:comment": "Reads are paired-ended"
},
"read%20length": {
"@id": "/policy/read%20length",
"@type": "rdf:Property",
"rdfs:domain": "/policy/ComplexityXcorrQualityMetric",
"rdfs:label": "Read length",
"rdfs:comment": "Read length"
},
"CorrelationQualityMetric": {
"@id": "/policy/CorrelationQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/correlation_quality_metric.json"
},
"CorrelationQualityMetricCollection": {
"@id": "/policy/CorrelationQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"Pearson%20correlation": {
"@id": "/policy/Pearson%20correlation",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/CorrelationQualityMetric",
"/policy/CpgCorrelationQualityMetric",
"/policy/MadQualityMetric"
]
},
"rdfs:label": "Pearson correlation",
"rdfs:comment": [
"Pearson correlation coefficient of replicates from quantification",
"Pearson's R correlation",
"Pearson's correlation of CpG pairs with at least 10 reads each"
]
},
"Spearman%20correlation": {
"@id": "/policy/Spearman%20correlation",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/CorrelationQualityMetric",
"/policy/MadQualityMetric"
]
},
"rdfs:label": "Spearman correlation",
"rdfs:comment": [
"Spearman correlation coefficient of replicates from quantification",
"Spearman's rank correlation"
]
},
"Items": {
"@id": "/policy/Items",
"@type": "rdf:Property",
"rdfs:domain": "/policy/CorrelationQualityMetric",
"rdfs:label": "Items",
"rdfs:comment": "Count of items from two different datasets that are being correlated"
},
"Standard%20deviation": {
"@id": "/policy/Standard%20deviation",
"@type": "rdf:Property",
"rdfs:domain": "/policy/CorrelationQualityMetric",
"rdfs:label": "Standard deviation",
"rdfs:comment": "Standard deviation of difference"
},
"MAD%20of%20log%20ratios": {
"@id": "/policy/MAD%20of%20log%20ratios",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/CorrelationQualityMetric",
"/policy/MadQualityMetric"
]
},
"rdfs:label": "MAD of log ratios",
"rdfs:comment": "Mean-Average-Deviation (MAD) of replicate log ratios from quantification"
},
"Details": {
"@id": "/policy/Details",
"@type": "rdf:Property",
"rdfs:domain": "/policy/CorrelationQualityMetric",
"rdfs:label": "Details",
"rdfs:comment": "Description of methods"
},
"CpgCorrelationQualityMetric": {
"@id": "/policy/CpgCorrelationQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/cpg_correlation_quality_metric.json"
},
"CpgCorrelationQualityMetricCollection": {
"@id": "/policy/CpgCorrelationQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"CpG%20pairs": {
"@id": "/policy/CpG%20pairs",
"@type": "rdf:Property",
"rdfs:domain": "/policy/CpgCorrelationQualityMetric",
"rdfs:label": "CpG pairs",
"rdfs:comment": "CpG pairs"
},
"CpG%20pairs%20with%20atleast%2010%20reads%20each": {
"@id": "/policy/CpG%20pairs%20with%20atleast%2010%20reads%20each",
"@type": "rdf:Property",
"rdfs:domain": "/policy/CpgCorrelationQualityMetric",
"rdfs:label": "CpG pairs with at least 10 reads each",
"rdfs:comment": "CpG pairs with atleast 10 reads each"
},
"DuplicatesQualityMetric": {
"@id": "/policy/DuplicatesQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/duplicates_quality_metric.json"
},
"DuplicatesQualityMetricCollection": {
"@id": "/policy/DuplicatesQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"Reads%20Examined": {
"@id": "/policy/Reads%20Examined",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "Reads Examined",
"rdfs:comment": "Total number of paired and unpaired reads examined"
},
"Read%20Duplicates": {
"@id": "/policy/Read%20Duplicates",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "Read Duplicates",
"rdfs:comment": "Total number of paired and unpaired read duplicates"
},
"UMI%20Read%20Duplicates": {
"@id": "/policy/UMI%20Read%20Duplicates",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "UMI Read Duplicates",
"rdfs:comment": "Number of UMI flagged read duplicates"
},
"Percent%20Duplication": {
"@id": "/policy/Percent%20Duplication",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "Percent Duplication",
"rdfs:comment": "Percent of reads that are duplicates"
},
"Read%20Pairs%20Examined": {
"@id": "/policy/Read%20Pairs%20Examined",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "Read Pairs Examined",
"rdfs:comment": "Number of read pairs examined by picard"
},
"Read%20Pair%20Duplicates": {
"@id": "/policy/Read%20Pair%20Duplicates",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "Read Pair Duplicates",
"rdfs:comment": "Number of read pairs detected as duplicates by picard"
},
"Read%20Pair%20Optical%20Duplicates": {
"@id": "/policy/Read%20Pair%20Optical%20Duplicates",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "Read Pair Optical Duplicates",
"rdfs:comment": "Number of read pairs detected as optical duplicates by picard"
},
"Unmapped%20Reads": {
"@id": "/policy/Unmapped%20Reads",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "Unmapped Reads",
"rdfs:comment": "Number of unmapped detected by picard"
},
"Unpaired%20Reads%20Examined": {
"@id": "/policy/Unpaired%20Reads%20Examined",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "Unpaired Reads Examined",
"rdfs:comment": "Number of unpaired reads examined by picard"
},
"Unpaired%20Read%20Duplicates": {
"@id": "/policy/Unpaired%20Read%20Duplicates",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "Unpaired Read Duplicates",
"rdfs:comment": "Number of unpaired reads detected as duplicates by picard"
},
"Estimated%20Library%20Size": {
"@id": "/policy/Estimated%20Library%20Size",
"@type": "rdf:Property",
"rdfs:domain": "/policy/DuplicatesQualityMetric",
"rdfs:label": "Estimated Library Size",
"rdfs:comment": "Library size in reads as estimated by picard"
},
"EdwbamstatsQualityMetric": {
"@id": "/policy/EdwbamstatsQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/edwbamstats_quality_metric.json"
},
"EdwbamstatsQualityMetricCollection": {
"@id": "/policy/EdwbamstatsQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"alignedBy": {
"@id": "/policy/alignedBy",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "Aligner used",
"rdfs:comment": "The aligner used"
},
"isPaired": {
"@id": "/policy/isPaired",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "Is paired end flag",
"rdfs:comment": "If alignment is from paired-end reads this will be set to 1"
},
"isSortedByTarget": {
"@id": "/policy/isSortedByTarget",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "Is sorted by target flag",
"rdfs:comment": "If the bam is sorted by target location, this is set to 1; if sorted by name, this is set to 0"
},
"mappedCount": {
"@id": "/policy/mappedCount",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "# of mapped reads",
"rdfs:comment": "Count of mapped reads"
},
"readBaseCount": {
"@id": "/policy/readBaseCount",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "# of bases in reads",
"rdfs:comment": "Count of total bases in reads"
},
"readCount": {
"@id": "/policy/readCount",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "# of reads",
"rdfs:comment": "Count of all reads"
},
"readSizeMax": {
"@id": "/policy/readSizeMax",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "Longest read length",
"rdfs:comment": "Longest read"
},
"readSizeMean": {
"@id": "/policy/readSizeMean",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "Mean read length",
"rdfs:comment": "Mean size of all reads"
},
"readSizeMin": {
"@id": "/policy/readSizeMin",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "Shortest read length",
"rdfs:comment": "Shortest read"
},
"readSizeStd": {
"@id": "/policy/readSizeStd",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "SD of read length",
"rdfs:comment": "Standard deviation of read size"
},
"targetBaseCount": {
"@id": "/policy/targetBaseCount",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "# of covered bases in target",
"rdfs:comment": "Number of bases covered in target (e.g. on chromosomes)"
},
"targetSeqCount": {
"@id": "/policy/targetSeqCount",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "# of target sequences",
"rdfs:comment": "Count of target sequences (e.g. chromosomes)"
},
"u4mReadCount": {
"@id": "/policy/u4mReadCount",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "# of random sampled unique reads",
"rdfs:comment": "Number of randomly sampled uniquely mapped items used in complexity calculation"
},
"u4mUniquePos": {
"@id": "/policy/u4mUniquePos",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "# of positions sampled unique reads map to",
"rdfs:comment": "Number of unique positions that sampled uniquely mapped reads were mapped to"
},
"u4mUniqueRatio": {
"@id": "/policy/u4mUniqueRatio",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "Ratio of unique positions to uniquely mapped reads",
"rdfs:comment": "Ratio of unique positions to uniquely mapped reads"
},
"uniqueMappedCount": {
"@id": "/policy/uniqueMappedCount",
"@type": "rdf:Property",
"rdfs:domain": "/policy/EdwbamstatsQualityMetric",
"rdfs:label": "# of uniquely mapped reads",
"rdfs:comment": "Count of reads uniquely mapped"
},
"FilteringQualityMetric": {
"@id": "/policy/FilteringQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/filtering_quality_metric.json"
},
"FilteringQualityMetricCollection": {
"@id": "/policy/FilteringQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"pre-filter%20all%20reads": {
"@id": "/policy/pre-filter%20all%20reads",
"@type": "rdf:Property",
"rdfs:domain": "/policy/FilteringQualityMetric",
"rdfs:label": "Total reads after filtering",
"rdfs:comment": "Count of all reads prior to filtering"
},
"pre-filter%20mapped%20reads": {
"@id": "/policy/pre-filter%20mapped%20reads",
"@type": "rdf:Property",
"rdfs:domain": "/policy/FilteringQualityMetric",
"rdfs:label": "Mapped reads before filtering",
"rdfs:comment": "Count of mapped reads prior to filtering"
},
"post-filter%20all%20reads": {
"@id": "/policy/post-filter%20all%20reads",
"@type": "rdf:Property",
"rdfs:domain": "/policy/FilteringQualityMetric",
"rdfs:label": "Mapped reads after filtering",
"rdfs:comment": "Count of all reads after filtering"
},
"post-filter%20mapped%20reads": {
"@id": "/policy/post-filter%20mapped%20reads",
"@type": "rdf:Property",
"rdfs:domain": "/policy/FilteringQualityMetric",
"rdfs:label": "Total reads after filtering",
"rdfs:comment": "Count of mapped reads after filtering"
},
"GenericQualityMetric": {
"@id": "/policy/GenericQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/generic_quality_metric.json"
},
"GenericQualityMetricCollection": {
"@id": "/policy/GenericQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"HistoneChipSeqQualityMetric": {
"@id": "/policy/HistoneChipSeqQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/histone_chipseq_quality_metric.json"
},
"HistoneChipSeqQualityMetricCollection": {
"@id": "/policy/HistoneChipSeqQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"nreads": {
"@id": "/policy/nreads",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HistoneChipSeqQualityMetric",
"rdfs:label": "# of reads",
"rdfs:comment": "# of starting reads in the pool (if replicated) or experiment (if unreplicated)"
},
"nreads_in_peaks": {
"@id": "/policy/nreads_in_peaks",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HistoneChipSeqQualityMetric",
"rdfs:label": "# of reads in peaks",
"rdfs:comment": "# of reads that fall within peaks."
},
"npeak_overlap": {
"@id": "/policy/npeak_overlap",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HistoneChipSeqQualityMetric",
"rdfs:label": "# of overlapping peaks",
"rdfs:comment": "# peaks overlapping with true replicate or pooled pseudoreplicate peaks"
},
"Fp": {
"@id": "/policy/Fp",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/HistoneChipSeqQualityMetric",
"/policy/IDRQualityMetric"
]
},
"rdfs:label": "FRiP score from pooled pseudoreplicate peaks",
"rdfs:comment": [
"Fraction reads in IDR peaks (FRiP) from pooled pseudoreplicates",
"Fraction reads in replicated/stable narrowPeaks (FRiP) from pooled pseudoreplicates"
]
},
"Ft": {
"@id": "/policy/Ft",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/HistoneChipSeqQualityMetric",
"/policy/IDRQualityMetric"
]
},
"rdfs:label": "FRiP score from true replicate peaks",
"rdfs:comment": [
"Fraction reads in IDR peaks (FRiP) from true replicates",
"Fraction reads in replicated/stable narrowPeaks (FRiP) from true replicates"
]
},
"F1": {
"@id": "/policy/F1",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/HistoneChipSeqQualityMetric",
"/policy/IDRQualityMetric"
]
},
"rdfs:label": "FRiP score from rep1 self-pseudoreplicate peaks",
"rdfs:comment": [
"Fraction reads in peaks (FRiP) from replicate 1 self-pseudoreplicates or the number of stable peaks that pass the internal pseudoreplication IDR threshold, when self-pseudoreplication is done on unreplicated experiments.",
"Fraction reads in replicated/stable narrowPeaks (FRiP) from replicate 1 self-pseudoreplicates or the number of stable peaks that pass internal pseudoreplication, when self-pseudoreplication is done on unreplicated experiments."
]
},
"F2": {
"@id": "/policy/F2",
"@type": "rdf:Property",
"rdfs:domain": {
"@type": "owl:Class",
"owl:unionOf": [
"/policy/HistoneChipSeqQualityMetric",
"/policy/IDRQualityMetric"
]
},
"rdfs:label": "FRiP score from rep2 self-pseudoreplicate peaks",
"rdfs:comment": [
"Fraction reads in peaks (FRiP) from replicate 2 self-pseudoreplicates",
"Fraction reads in replicated/stable narrowPeaks (FRiP) from replicate 2 self-pseudoreplicates"
]
},
"HotspotQualityMetric": {
"@id": "/policy/HotspotQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/hotspot_quality_metric.json"
},
"HotspotQualityMetricCollection": {
"@id": "/policy/HotspotQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"SPOT1%20score": {
"@id": "/policy/SPOT1%20score",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HotspotQualityMetric",
"rdfs:label": "SPOT1 score",
"rdfs:comment": "SPOT score as calculated by Hotspot1"
},
"SPOT2%20score": {
"@id": "/policy/SPOT2%20score",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HotspotQualityMetric",
"rdfs:label": "SPOT2 score",
"rdfs:comment": "SPOT score as calculated by Hotspot2"
},
"hotspot%20count": {
"@id": "/policy/hotspot%20count",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HotspotQualityMetric",
"rdfs:label": "# of hotspots",
"rdfs:comment": "Count of hotspots discovered by Hotspot2"
},
"peaks%20count": {
"@id": "/policy/peaks%20count",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HotspotQualityMetric",
"rdfs:label": "# of peaks",
"rdfs:comment": "Count of peaks discovered by Hotspot2"
},
"total%20tags": {
"@id": "/policy/total%20tags",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HotspotQualityMetric",
"rdfs:label": "# of read tags provided",
"rdfs:comment": "Count of read tags provided to Hotspot"
},
"hotspot%20tags": {
"@id": "/policy/hotspot%20tags",
"@type": "rdf:Property",
"rdfs:domain": "/policy/HotspotQualityMetric",
"rdfs:label": "# of read tags that were in hotspots",
"rdfs:comment": "Count of read tags discovered to be in hotspots"
},
"IDRQualityMetric": {
"@id": "/policy/IDRQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/idr_quality_metric.json"
},
"IDRQualityMetricCollection": {
"@id": "/policy/IDRQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"Np": {
"@id": "/policy/Np",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "# pooled pseudoreplicate peaks",
"rdfs:comment": "Number of peaks from pooled pseudoreplicates"
},
"Nt": {
"@id": "/policy/Nt",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "# true replicate peaks",
"rdfs:comment": "Number of peaks from true replicates"
},
"N1": {
"@id": "/policy/N1",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "# rep1 self-pseudoreplicate peaks",
"rdfs:comment": "Number of peaks from replicate 1 self-pseudoreplicates or the number of stable peaks that pass the internal pseudoreplication IDR threshold, when self-pseudoreplication is done on unreplicated experiments."
},
"N2": {
"@id": "/policy/N2",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "# rep2 self-pseudoreplicate peaks",
"rdfs:comment": "Number of peaks from replicate 2 self-pseudoreplicates"
},
"IDR_cutoff": {
"@id": "/policy/IDR_cutoff",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "IDR cutoff",
"rdfs:comment": "IDR cutoff threshold for this experiment"
},
"self_consistency_ratio": {
"@id": "/policy/self_consistency_ratio",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "Self-consistency ratio",
"rdfs:comment": "IDR self-consistency ratio for this experiment"
},
"rescue_ratio": {
"@id": "/policy/rescue_ratio",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "Rescue ratio",
"rdfs:comment": "IDR rescue ratio for this experiment"
},
"reproducibility_test": {
"@id": "/policy/reproducibility_test",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "IDR reproducibility",
"rdfs:comment": "IDR reproducibility test result for this experiment"
},
"N_optimal": {
"@id": "/policy/N_optimal",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "# optimal IDR peaks",
"rdfs:comment": "Number of peaks in the IDR optimal set"
},
"N_conservative": {
"@id": "/policy/N_conservative",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "# conservative IDR peaks",
"rdfs:comment": "Number of peaks in the IDR conservative set"
},
"IDR_plot_true": {
"@id": "/policy/IDR_plot_true",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "True replicate IDR plot",
"rdfs:comment": "IDR dispersion plot for true replicates"
},
"IDR_plot_rep1_pr": {
"@id": "/policy/IDR_plot_rep1_pr",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "Rep 1 pseudoreplicate IDR plot",
"rdfs:comment": "IDR dispersion plot for replicate 1 pseudo-replicates"
},
"IDR_plot_rep2_pr": {
"@id": "/policy/IDR_plot_rep2_pr",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "Rep2 pseudoreplicate IDR plot",
"rdfs:comment": "IDR dispersion plot for replicate 2 pseudo-replicates"
},
"IDR_plot_pool_pr": {
"@id": "/policy/IDR_plot_pool_pr",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "Pooled pseudoreplicate IDR plot",
"rdfs:comment": "IDR dispersion plot for pool pseudo-replicates"
},
"IDR_parameters_true": {
"@id": "/policy/IDR_parameters_true",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "True replicate IDR run parameters",
"rdfs:comment": "IDR run parameters for true replicates"
},
"IDR_parameters_rep1_pr": {
"@id": "/policy/IDR_parameters_rep1_pr",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "Rep1 pseudoreplicate IDR run parameters",
"rdfs:comment": "IDR run parameters for replicate 1 pseudo-replicates"
},
"IDR_parameters_rep2_pr": {
"@id": "/policy/IDR_parameters_rep2_pr",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "Rep2 pseudoreplicate IDR run parameters",
"rdfs:comment": "IDR run parameters for replicate 2 pseudo-replicates"
},
"IDR_parameters_pool_pr": {
"@id": "/policy/IDR_parameters_pool_pr",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IDRQualityMetric",
"rdfs:label": "Pooled pseudoreplicate IDR run parameters",
"rdfs:comment": "IDR run parameters for pool pseudo-replicates"
},
"IdrSummaryQualityMetric": {
"@id": "/policy/IdrSummaryQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/idr_summary_quality_metric.json"
},
"IdrSummaryQualityMetricCollection": {
"@id": "/policy/IdrSummaryQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"Final%20parameter%20values%20%28mu%2C%20sigma%2C%20rho%2C%20and%20mix%29": {
"@id": "/policy/Final%20parameter%20values%20%28mu%2C%20sigma%2C%20rho%2C%20and%20mix%29",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IdrSummaryQualityMetric",
"rdfs:comment": ""
},
"IDR%20cutoff": {
"@id": "/policy/IDR%20cutoff",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IdrSummaryQualityMetric",
"rdfs:label": "IDR cutoff",
"rdfs:comment": "IDR: IDR cutoff"
},
"Initial%20parameter%20values%20%28mu%2C%20sigma%2C%20rho%2C%20and%20mix%29": {
"@id": "/policy/Initial%20parameter%20values%20%28mu%2C%20sigma%2C%20rho%2C%20and%20mix%29",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IdrSummaryQualityMetric",
"rdfs:comment": ""
},
"Number%20of%20peaks%20passing%20IDR%20cutoff": {
"@id": "/policy/Number%20of%20peaks%20passing%20IDR%20cutoff",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IdrSummaryQualityMetric",
"rdfs:label": "# of IDR passing peaks",
"rdfs:comment": "IDR: Number of peaks passing IDR cutoff"
},
"Number%20of%20reported%20peaks": {
"@id": "/policy/Number%20of%20reported%20peaks",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IdrSummaryQualityMetric",
"rdfs:label": "# of reported peaks",
"rdfs:comment": "IDR: Number of reported peaks"
},
"Percent%20peaks%20passing%20IDR%20cutoff": {
"@id": "/policy/Percent%20peaks%20passing%20IDR%20cutoff",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IdrSummaryQualityMetric",
"rdfs:label": "% IDR passing peaks",
"rdfs:comment": "IDR: Percent peaks passing IDR cutoff"
},
"Percent%20reported%20peaks": {
"@id": "/policy/Percent%20reported%20peaks",
"@type": "rdf:Property",
"rdfs:domain": "/policy/IdrSummaryQualityMetric",
"rdfs:label": "% reported peaks",
"rdfs:comment": "IDR: Percent reported peaks"
},
"MadQualityMetric": {
"@id": "/policy/MadQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/mad_quality_metric.json"
},
"MadQualityMetricCollection": {
"@id": "/policy/MadQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"SD%20of%20log%20ratios": {
"@id": "/policy/SD%20of%20log%20ratios",
"@type": "rdf:Property",
"rdfs:domain": "/policy/MadQualityMetric",
"rdfs:label": "SD of log ratios",
"rdfs:comment": "Standard Deviation of replicate log ratios from quantification"
},
"SamtoolsFlagstatsQualityMetric": {
"@id": "/policy/SamtoolsFlagstatsQualityMetric",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/QualityMetric",
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/samtools_flagstats_quality_metric.json"
},
"SamtoolsFlagstatsQualityMetricCollection": {
"@id": "/policy/SamtoolsFlagstatsQualityMetricCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"processing_stage": {
"@id": "/policy/processing_stage",
"@type": "rdf:Property",
"rdfs:domain": "/policy/SamtoolsFlagstatsQualityMetric",
"rdfs:label": "Processing stage",
"rdfs:comment": "The degree of post-mapping processing to which the statistics apply"
},
"diff_chroms": {
"@id": "/policy/diff_chroms",
"@type": "rdf:Property",
"rdfs:domain": "/policy/SamtoolsFlagstatsQualityMetric",
"rdfs:label": "# reads with mate mapped to diff chr passing QC",
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"rdfs:domain": "/policy/TrimmingQualityMetric",
"rdfs:label": "PE read-pairs trimmed",
"rdfs:comment": "Total number read-pairs trimmed"
},
"SE%20reads%20processed": {
"@id": "/policy/SE%20reads%20processed",
"@type": "rdf:Property",
"rdfs:domain": "/policy/TrimmingQualityMetric",
"rdfs:label": "SE reads processed",
"rdfs:comment": "Total number (single-end) reads processed"
},
"SE%20reads%20trimmed": {
"@id": "/policy/SE%20reads%20trimmed",
"@type": "rdf:Property",
"rdfs:domain": "/policy/TrimmingQualityMetric",
"rdfs:label": "SE reads trimmed",
"rdfs:comment": "Total number (single-end) reads trimmed"
},
"Target": {
"@id": "/policy/Target",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/target.json"
},
"TargetCollection": {
"@id": "/policy/TargetCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"dbxref": {
"@id": "/policy/dbxref",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Target",
"rdfs:label": "External identifier",
"rdfs:comment": "A unique identifier from external resource (e.g. HGNC, GeneID, UniProtKB or ENSEMBL)."
},
"gene_name": {
"@id": "/policy/gene_name",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Target",
"rdfs:label": "Gene name",
"rdfs:comment": "HGNC or MGI identifier for the target."
},
"label": {
"@id": "/policy/label",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Target",
"rdfs:label": "Common name with modification",
"rdfs:comment": "Common name for the target including post-translational modifications, if any."
},
"investigated_as": {
"@id": "/policy/investigated_as",
"@type": "rdf:Property",
"rdfs:domain": "/policy/Target"
},
"User": {
"@id": "/policy/User",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Item"
],
"rdfs:seeAlso": "/profiles/user.json"
},
"UserCollection": {
"@id": "/policy/UserCollection",
"@type": "rdfs:Class",
"rdfs:subClassOf": [
"/policy/Collection"
]
},
"email": {
"@id": "/policy/email",
"@type": "rdf:Property",
"rdfs:domain": "/policy/User",
"rdfs:label": "Email"
},
"first_name": {
"@id": "/policy/first_name",
"@type": "rdf:Property",
"rdfs:domain": "/policy/User",
"rdfs:label": "First name",
"rdfs:comment": "The user's first (given) name."
},
"last_name": {
"@id": "/policy/last_name",
"@type": "rdf:Property",
"rdfs:domain": "/policy/User",
"rdfs:label": "Last name",
"rdfs:comment": "The user's last (family) name."
},
"submits_for": {
"@id": "/policy/submits_for",
"@type": "rdf:Property",
"rdfs:domain": "/policy/User",
"rdfs:comment": "A lab user is authorized to submit for.",
"rdfs:range": "/policy/Lab"
},
"groups": {
"@id": "/policy/groups",
"@type": "rdf:Property",
"rdfs:domain": "/policy/User"
},
"viewing_groups": {
"@id": "/policy/viewing_groups",
"@type": "rdf:Property",
"rdfs:domain": "/policy/User"
},
"job_title": {
"@id": "/policy/job_title",
"@type": "rdf:Property",
"rdfs:domain": "/policy/User",
"rdfs:label": "Job title"
}
}
}