| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| alignment_details • Phased • Sorted | array of enum • min items: 1 • unique | Additional details about sequencing alignment. |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Sequencing Reads | array of enum • min items: 1 • unique • default: ['Sequencing Reads'] | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_type • Aligned Reads • In Silico Generated | array of enum • min items: 1 • unique • default: ['Aligned Reads'] | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| extra_files_creds | object • calculated | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| flow_cell_barcode | string | Flow cell barcode for sequencing that generated this file. |
| flow_cell_lane | integer • min value: 1 | Flow cell lane for sequencing that generated this file. |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| n50 | number • min value: 0 | The sequence length of the shortest read at 50% of the total sequencing dataset sorted by read length (bp). |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| reference_genome | ReferenceGenome • string | Reference genome used for alignment. See values here |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_ALIGNED-READS_[A-Z0-9-_.]{4,}$ |
| submitted_md5sum | string • format: hex | Submitted MD5 checksum of the file. |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| alignment_details • Phased • Sorted | array of enum • min items: 1 • unique | Additional details about sequencing alignment. |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Sequencing Reads | array of enum • min items: 1 • unique • default: ['Sequencing Reads'] | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_generation_summary . target_read_count | array of string | - |
| data_type • Aligned Reads • In Silico Generated | array of enum • min items: 1 • unique • default: ['Aligned Reads'] | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| extra_files_creds | object • calculated | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| flow_cell_barcode | string | Flow cell barcode for sequencing that generated this file. |
| flow_cell_lane | integer • min value: 1 | Flow cell lane for sequencing that generated this file. |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| n50 | number • min value: 0 | The sequence length of the shortest read at 50% of the total sequencing dataset sorted by read length (bp). |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| reference_genome | ReferenceGenome • string | Reference genome used for alignment. See values here |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_ALIGNED-READS_[A-Z0-9-_.]{4,}$ |
| submitted_md5sum | string • format: hex | Submitted MD5 checksum of the file. |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| aliases | array of string • unique • restricted | Institution-specific ID (e.g. bgm:cohort-1234-a). Must adhere to (regex) pattern: ^[^\s\\\/]+:[^\s\\\/]+$ |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Genome Annotation • Genome Region • Germline Variant Calls • Quality Control • RNA Quantification • Reference Conversion • Reference Genome • Reference Transcriptome • Sequencing Reads • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_type • Aligned Reads • CNV • Chain File • Gene Expression • Gene Model • Image • In Silico Generated • Indel • Index • MEI • Reference Sequence • SNV • SV • Sequence Interval • Statistics • Transcript Expression • Unaligned Reads | array of enum • min items: 1 • unique | - |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | Version for the item. Must adhere to (regex) pattern: ^([0-9]+.)*[0-9]+$ |
| Property | Type | Description |
|---|---|---|
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| aliases | array of string • unique • restricted | Institution-specific ID (e.g. bgm:cohort-1234-a). Must adhere to (regex) pattern: ^[^\s\\\/]+:[^\s\\\/]+$ |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Genome Annotation • Genome Region • Germline Variant Calls • Quality Control • RNA Quantification • Reference Conversion • Reference Genome • Reference Transcriptome • Sequencing Reads • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_generation_summary . target_read_count | array of string | - |
| data_type • Aligned Reads • CNV • Chain File • Gene Expression • Gene Model • Image • In Silico Generated • Indel • Index • MEI • Reference Sequence • SNV • SV • Sequence Interval • Statistics • Transcript Expression • Unaligned Reads | array of enum • min items: 1 • unique | - |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | Version for the item. Must adhere to (regex) pattern: ^([0-9]+.)*[0-9]+$ |
| Property | Type | Description |
|---|---|---|
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| adapter_inclusion_method • Ligation • Not Applicable • Tagmentation | array of enum • min items: 1 • unique | Method of library preparation from an analyte. |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| amplification_method • MALBAC • MDA • Not Applicable • PCR • PTA | array of enum • min items: 1 • unique | Amplification method used to increase library products. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| description | string | Plain text description of the item. |
| display_title | string • calculated | - |
| enzymes | array of string • min items: 1 • unique | Enzymes used in fragmentation. Required if fragmentation_method contains Restriction Enzyme or Transposase. |
| fragmentation_method • Not Applicable • Restriction Enzyme • Sonication • Transposase | array of enum • min items: 1 • unique | Method used for nucleotide fragmentation. |
| insert_selection_method • Affinity Enrichment • Hybrid Selection • Not applicable • PCR • PolyA Enrichment • PolyT Enrichment • rRNA Depletion | array of enum • min items: 1 • unique | Method for selecting inserts included in library. |
| preparation_kits | PreparationKit • array of string • min items: 1 • unique | Links to associated preparation kits. |
| rna_seq_protocol • TruSeq • Watchmaker | enum of string | Protocol used for RNA-seq assays. |
| size_selection_method • Gel Electrophoresis • Magnetic Beads • Not Applicable | array of enum • min items: 1 • unique | Method for selecting fragment sizes. |
| status • deleted • draft • in review ← default • obsolete • public • released • restricted | enum of string • default: in review | - |
| strand • First Stranded • Not Applicable • Second Stranded • Unstranded | enum of string | Library stranded-ness. |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_LIBRARY-PREPARATION_[A-Z0-9-_.]{4,}$ |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| treatments | Treatment • array of string • min items: 1 • unique | Link to associated treatments performed during library preparation. |
| trim_adapter_sequence | boolean | Whether trimming adapter sequence is recommended. |
| uuid | string | Unique ID by which this object is identified. |
| Property | Type | Description |
|---|---|---|
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| adapter_inclusion_method • Ligation • Not Applicable • Tagmentation | array of enum • min items: 1 • unique | Method of library preparation from an analyte. |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| amplification_method • MALBAC • MDA • Not Applicable • PCR • PTA | array of enum • min items: 1 • unique | Amplification method used to increase library products. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| description | string | Plain text description of the item. |
| display_title | string • calculated | - |
| enzymes | array of string • min items: 1 • unique | Enzymes used in fragmentation. Required if fragmentation_method contains Restriction Enzyme or Transposase. |
| fragmentation_method • Mechanical • Not Applicable • Restriction Enzyme • Sonication • Transposase | array of enum • min items: 1 • unique | Method used for nucleotide fragmentation. |
| insert_selection_method • Affinity Enrichment • Hybrid Selection • Not applicable • PCR • PolyA Enrichment • PolyT Enrichment • rRNA Depletion | array of enum • min items: 1 • unique | Method for selecting inserts included in library. |
| preparation_kits | PreparationKit • array of string • min items: 1 • unique | Links to associated preparation kits. |
| rna_seq_protocol • TruSeq • Watchmaker | enum of string | Protocol used for RNA-seq assays. |
| size_selection_method • Gel Electrophoresis • Magnetic Beads • Not Applicable | array of enum • min items: 1 • unique | Method for selecting fragment sizes. |
| status • deleted • draft • in review ← default • obsolete • public • released • restricted | enum of string • default: in review | - |
| strand • First Stranded • Not Applicable • Second Stranded • Unstranded | enum of string | Library stranded-ness. |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_LIBRARY-PREPARATION_[A-Z0-9-_.]{4,}$ |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| treatments | Treatment • array of string • min items: 1 • unique | Link to associated treatments performed during library preparation. |
| trim_adapter_sequence | boolean | Whether trimming adapter sequence is recommended. |
| uuid | string | Unique ID by which this object is identified. |
| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| aliases | array of string • unique • restricted | Institution-specific ID (e.g. bgm:cohort-1234-a). Must adhere to (regex) pattern: ^[^\s\\\/]+:[^\s\\\/]+$ |
| alignment_details • Phased • Sorted | array of enum • min items: 1 • unique | Additional details about sequencing alignment. |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Genome Annotation • Genome Region • Germline Variant Calls • Quality Control • RNA Quantification • Reference Conversion • Reference Genome • Reference Transcriptome • Sequencing Reads • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_type • Aligned Reads • CNV • Chain File • Gene Expression • Gene Model • Image • In Silico Generated • Indel • Index • MEI • Reference Sequence • SNV • SV • Sequence Interval • Statistics • Transcript Expression • Unaligned Reads | array of enum • min items: 1 • unique | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| output_status • Final Output | enum of string | Output status of this file within the MetaWorkflowRun. |
| paired_with | OutputFile • string | Link to associated paired-end file, if applicable. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| read_pair_number • Not Applicable • R1 • R2 | enum of string | Read pair number, if paired-end. |
| reference_genome | ReferenceGenome • string | Reference genome used for alignment. See values here |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| aliases | array of string • unique • restricted | Institution-specific ID (e.g. bgm:cohort-1234-a). Must adhere to (regex) pattern: ^[^\s\\\/]+:[^\s\\\/]+$ |
| alignment_details • Phased • Sorted | array of enum • min items: 1 • unique | Additional details about sequencing alignment. |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Genome Annotation • Genome Region • Germline Variant Calls • Quality Control • RNA Quantification • Reference Conversion • Reference Genome • Reference Transcriptome • Sequencing Reads • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_generation_summary . target_read_count | array of string | - |
| data_type • Aligned Reads • CNV • Chain File • Gene Expression • Gene Model • Image • In Silico Generated • Indel • Index • MEI • Reference Sequence • SNV • SV • Sequence Interval • Statistics • Transcript Expression • Unaligned Reads | array of enum • min items: 1 • unique | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| output_status • Final Output | enum of string | Output status of this file within the MetaWorkflowRun. |
| paired_with | OutputFile • string | Link to associated paired-end file, if applicable. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| read_pair_number • Not Applicable • R1 • R2 | enum of string | Read pair number, if paired-end. |
| reference_genome | ReferenceGenome • string | Reference genome used for alignment. See values here |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| aliases | array of string • unique • restricted | Institution-specific ID (e.g. bgm:cohort-1234-a). Must adhere to (regex) pattern: ^[^\s\\\/]+:[^\s\\\/]+$ |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Genome Annotation • Genome Region • Germline Variant Calls • Quality Control • RNA Quantification • Reference Conversion • Reference Genome • Reference Transcriptome • Sequencing Reads • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_type • Aligned Reads • CNV • Chain File • Gene Expression • Gene Model • Image • In Silico Generated • Indel • Index • MEI • Reference Sequence • SNV • SV • Sequence Interval • Statistics • Transcript Expression • Unaligned Reads | array of enum • min items: 1 • unique | - |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| url | string • format: uri | An external resource with additional information about the item. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| aliases | array of string • unique • restricted | Institution-specific ID (e.g. bgm:cohort-1234-a). Must adhere to (regex) pattern: ^[^\s\\\/]+:[^\s\\\/]+$ |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Genome Annotation • Genome Region • Germline Variant Calls • Quality Control • RNA Quantification • Reference Conversion • Reference Genome • Reference Transcriptome • Sequencing Reads • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_generation_summary . target_read_count | array of string | - |
| data_type • Aligned Reads • CNV • Chain File • Gene Expression • Gene Model • Image • In Silico Generated • Indel • Index • MEI • Reference Sequence • SNV • SV • Sequence Interval • Statistics • Transcript Expression • Unaligned Reads | array of enum • min items: 1 • unique | - |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| url | string • format: uri | An external resource with additional information about the item. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Genome Annotation • Genome Region • Germline Variant Calls • Quality Control • RNA Quantification • Reference Conversion • Reference Genome • Reference Transcriptome • Sequencing Reads • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_type • Aligned Reads • CNV • Chain File • Gene Expression • Gene Model • Image • In Silico Generated • Indel • Index • MEI • Reference Sequence • SNV • SV • Sequence Interval • Statistics • Transcript Expression • Unaligned Reads | array of enum • min items: 1 • unique | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| extra_files_creds | object • calculated | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_SUBMITTED-FILE_[A-Z0-9-_.]{4,}$ |
| submitted_md5sum | string • format: hex | Submitted MD5 checksum of the file. |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Genome Annotation • Genome Region • Germline Variant Calls • Quality Control • RNA Quantification • Reference Conversion • Reference Genome • Reference Transcriptome • Sequencing Reads • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_generation_summary . target_read_count | array of string | - |
| data_type • Aligned Reads • CNV • Chain File • Gene Expression • Gene Model • Image • In Silico Generated • Indel • Index • MEI • Reference Sequence • SNV • SV • Sequence Interval • Statistics • Transcript Expression • Unaligned Reads | array of enum • min items: 1 • unique | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| extra_files_creds | object • calculated | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_SUBMITTED-FILE_[A-Z0-9-_.]{4,}$ |
| submitted_md5sum | string • format: hex | Submitted MD5 checksum of the file. |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Sequencing Reads | array of enum • min items: 1 • unique • default: ['Sequencing Reads'] | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_type • Unaligned Reads | array of enum • min items: 1 • unique • default: ['Unaligned Reads'] | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| extra_files_creds | object • calculated | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| flow_cell_barcode | string | Flow cell barcode for sequencing that generated this file. |
| flow_cell_lane | integer • min value: 1 | Flow cell lane for sequencing that generated this file. |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| n50 | number • min value: 0 | The sequence length of the shortest read at 50% of the total sequencing dataset sorted by read length (bp). |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| paired_with | UnalignedReads • string | Link to associated R1 paired-end file, if applicable (For R2 files only). |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| read_pair_number • Not Applicable • R1 • R2 | enum of string | Read pair number, if paired-end. |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_UNALIGNED-READS_[A-Z0-9-_.]{4,}$ |
| submitted_md5sum | string • format: hex | Submitted MD5 checksum of the file. |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Sequencing Reads | array of enum • min items: 1 • unique • default: ['Sequencing Reads'] | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_generation_summary . target_read_count | array of string | - |
| data_type • Unaligned Reads | array of enum • min items: 1 • unique • default: ['Unaligned Reads'] | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| extra_files_creds | object • calculated | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| flow_cell_barcode | string | Flow cell barcode for sequencing that generated this file. |
| flow_cell_lane | integer • min value: 1 | Flow cell lane for sequencing that generated this file. |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| n50 | number • min value: 0 | The sequence length of the shortest read at 50% of the total sequencing dataset sorted by read length (bp). |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| paired_with | UnalignedReads • string | Link to associated R1 paired-end file, if applicable (For R2 files only). |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| read_pair_number • Not Applicable • R1 • R2 | enum of string | Read pair number, if paired-end. |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_UNALIGNED-READS_[A-Z0-9-_.]{4,}$ |
| submitted_md5sum | string • format: hex | Submitted MD5 checksum of the file. |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| comparators | array of string | Link to comparator sample files used for normal matching. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Germline Variant Calls • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_type • CNV • Indel • MEI • SNV • SV | array of enum • min items: 1 • unique | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_databases | array of string | External databases used for filtering variant calls. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| extra_files_creds | object • calculated | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| filtering_methods | array of string | Filtering methods used in variant calling. |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| mode • Paired • Single Sample | enum of string | Mode used for variant calling. |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| reference_genome | ReferenceGenome • string | Reference genome used for alignment. See values here |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_VARIANT-CALLS_[A-Z0-9-_.]{4,}$ |
| submitted_md5sum | string • format: hex | Submitted MD5 checksum of the file. |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |
| Property | Type | Description |
|---|---|---|
| access_status • Open • Protected | enum of string | Access status for the file contents. |
| accession | string | A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.] |
| alternate_accessions | array of string • restricted | Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.] |
| analysis_summary | object • calculated | - |
| analysis_summary . reference_genome | string | - |
| analysis_summary . software | array of string | - |
| analytes | Analyte • array of string • unique • calculated | Analytes associated with the file. |
| annotated_filename | string • unique | Filename containing controlled metadata. |
| assays | Assay • array of string • unique • calculated | Assays associated with the file. |
| comparators | array of string | Link to comparator sample files used for normal matching. |
| consortia | Consortium • array of string • unique • restricted | Consortia associated with this item. See values here |
| content_md5sum | string • format: hex | The MD5 checksum of the uncompressed file. |
| data_category • Germline Variant Calls • Somatic Variant Calls | array of enum • min items: 1 • unique | Category for information in the file. |
| data_generation_summary | object • calculated | Summary of data generation. |
| data_generation_summary . assays | array of string | - |
| data_generation_summary . data_category | array of string | - |
| data_generation_summary . data_type | array of string | - |
| data_generation_summary . sequencing_center | string | - |
| data_generation_summary . sequencing_platforms | array of string | - |
| data_generation_summary . submission_centers | array of string | - |
| data_generation_summary . target_group_coverage | array of string | - |
| data_generation_summary . target_read_count | array of string | - |
| data_type • CNV • Indel • MEI • SNV • SV | array of enum • min items: 1 • unique | - |
| dataset • colo829_snv_indel_challenge_data • colo829bl • colo829blt_50to1 • colo829blt_in_silico • colo829t • hapmap • hg002 • hg00438 • hg005 • hg02257 • hg02486 • hg02622 • lb_fibroblast • lb_ipsc_1 • lb_ipsc_2 • lb_ipsc_4 • lb_ipsc_52 • lb_ipsc_60 • mei_detection_challenge_data • tissue | enum of string | Dataset associated with the file. |
| derived_from | File • array of string • min items: 1 • unique | Link to files used as input to create this file. |
| description | string | Plain text description of the item. |
| display_title | string • calculated | A calculated title for every object. |
| donors | Donor • array of string • unique • calculated | Donors associated with the file. |
| external_databases | array of string | External databases used for filtering variant calls. |
| external_quality_metrics | ExternalQualityMetric • array of string • min items: 1 • unique | Link to externally-generated QC metrics associated with file. |
| extra_files | array of object • min items: 1 • restricted | Links to extra files on s3 that don't have associated metadata. |
| extra_files . file_format | FileFormat • string | See values here |
| extra_files . file_size | integer | - |
| extra_files . filename | string | - |
| extra_files . href | string | - |
| extra_files . md5sum | string • format: hex | - |
| extra_files . status • archived • current • deleted • in review • inactive • obsolete • replaced • shared • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| extra_files_creds | object • calculated | - |
| file_access_status • Open • Protected | enum of string • calculated | Access status for the file contents. |
| file_format | FileFormat • string | Format for the file. See values here |
| file_sets | FileSet • array of string • min items: 1 • unique | Link to file sets associated with this file. |
| file_size | integer | Size of file on disk. |
| file_status_tracking | object • calculated | - |
| file_status_tracking . in review | string • format: date-time | - |
| file_status_tracking . public | string • format: date-time | - |
| file_status_tracking . released | string • format: date-time | - |
| file_status_tracking . released_date | string • format: date | - |
| file_status_tracking . restricted | string • format: date-time | - |
| file_status_tracking . uploaded | string • format: date-time | - |
| file_status_tracking . uploading | string • format: date-time | - |
| file_summary | object • calculated | - |
| file_summary . access_status | string | - |
| file_summary . annotated_name | string | - |
| file_summary . consortia | array of string | - |
| file_summary . file_format | string | - |
| file_summary . file_size | string | - |
| file_summary . md5sum | string | - |
| file_summary . uuid | string | Unique ID by which this object is identified. |
| filename | string | The local file name used at time of submission. Must be alphanumeric, with the exception of the following special characters: '+=,.@-_'. Must adhere to (regex) pattern: ^[\w+=,.@-]*$ |
| filtering_methods | array of string | Filtering methods used in variant calling. |
| href | string • calculated | Use this link to download this file. |
| libraries | Library • array of string • unique • calculated | Libraries associated with the file. |
| md5sum | string • format: hex | The MD5 checksum of the file being transferred. |
| meta_workflow_run_inputs | MetaWorkflowRun • array of string • calculated | - |
| meta_workflow_run_outputs | MetaWorkflowRun • array of string • calculated | - |
| mode • Paired • Single Sample | enum of string | Mode used for variant calling. |
| notes_to_tsv | array of string • restricted | - |
| o2_path | string | Path to file on O2. |
| quality_metrics | QualityMetric • array of string • min items: 1 • unique • restricted | Associated QC reports. |
| reference_genome | ReferenceGenome • string | Reference genome used for alignment. See values here |
| s3_lifecycle_category • ignore • long_term_access • long_term_access_long_term_archive • long_term_archive • no_storage • short_term_access • short_term_access_long_term_archive • short_term_archive | enum of string | The lifecycle category determines how long a file remains in a certain storage class. If set to ignore, lifecycle management will have no effect on this file. |
| s3_lifecycle_last_checked | string • format: date | date-time | Date when the lifecycle status of the file was last checked. |
| s3_lifecycle_status • deep archive • deleted • glacier • infrequent access • standard ← default | enum of string • default: standard | Current S3 storage class of this object. [Files in Standard and Infrequent Access are accessible without restriction. Files in Glacier and Deep Archive need to be requested and cannot be downloaded] |
| sample_sources | Tissue • array of string • unique • calculated | Sample sources (e.g. cell lines or tissues) associated with the file. |
| sample_summary | object • calculated | - |
| sample_summary . analytes | array of string | - |
| sample_summary . donor_ids | array of string | - |
| sample_summary . sample_descriptions | array of string | - |
| sample_summary . sample_names | array of string | - |
| sample_summary . studies | array of string | - |
| sample_summary . tissues | array of string | - |
| samples | Sample • array of string • unique • calculated | Samples associated with the file. |
| sequencing | Sequencing • array of string • unique • calculated | Sequencing associated with the file. |
| sequencing_center | SubmissionCenter • string | Sequencing Center. See values here |
| software | Software • array of string • min items: 1 • unique | Link to software used to create this file. |
| status • archived • deleted • in review • obsolete • public • released • restricted • retracted • to be uploaded by workflow • upload failed • uploaded • uploading ← default | enum of string • default: uploading | - |
| submission_centers | SubmissionCenter • array of string • unique | Submission Centers that created this item. See values here |
| submitted_id | string | Unique identifier for the item assigned by the submitter. Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_VARIANT-CALLS_[A-Z0-9-_.]{4,}$ |
| submitted_md5sum | string • format: hex | Submitted MD5 checksum of the file. |
| tags | array of string • min string length: 1 • max string length: 50 • unique • restricted | Key words that can tag an item - useful for filtering. Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$ |
| tsv_notes | string • calculated | Notes that go into the metadata.tsv file. |
| upload_credentials | object • calculated | - |
| upload_key | string • calculated | File object name in S3. |
| uuid | string | Unique ID by which this object is identified. |
| version | string | - |