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152 changes: 152 additions & 0 deletions
152
site-config/anvil-cmg/dev/dataDictionary/data-dictionary.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,152 @@ | ||
| { | ||
| "classes": [ | ||
| { | ||
| "name": "Activity", | ||
| "description": "A table describing the activities performed on biosamples or files that resulted in the generation of additional files. The anvil_activity table is used to capture activity provenance that does not fit into the other activity tables described in the schema (such as file indexing, file checksums, etc.).", | ||
| "key": "activities", | ||
| "label": "Activity", | ||
| "attributes": [ | ||
| { | ||
| "key": "activities.activity_type", | ||
| "label": "Activity Type", | ||
| "description": "A reference to the type of activity, preferably using an identifier in a recommended standard ontology." | ||
| }, | ||
| { | ||
| "key": "activities.data_modality", | ||
| "label": "Data Modality", | ||
| "description": "A table describing the activities performed on biosamples or files that resulted in the generation of additional files. The anvil_activity table is used to capture activity provenance that does not fit into the other activity tables described in the schema (such as file indexing, file checksums, etc.)." | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "name": "BioSample", | ||
| "description": "Contains information about the sample(s) included in the dataset.", | ||
| "key": "biosamples", | ||
| "label": "BioSample", | ||
| "attributes": [ | ||
| { | ||
| "key": "biosamples.anatomical_site", | ||
| "label": "Anatomical Site", | ||
| "description": "A human-readable reference to the site within the organism from which the biosample was taken." | ||
| }, | ||
| { | ||
| "key": "biosamples.biosample_id", | ||
| "label": "BioSample Id", | ||
| "description": "A unique identifier for the biosample." | ||
| }, | ||
| { | ||
| "key": "biosamples.biosample_type", | ||
| "label": "BioSample Type", | ||
| "description": "A human-readable reference to the type of biosample represented by the record." | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "name": "Dataset", | ||
| "description": "A dataset is a collection of related files and associated metadata that share the same consent and access permissions.", | ||
| "key": "datasets", | ||
| "label": "Dataset", | ||
| "attributes": [ | ||
| { | ||
| "key": "accessible", | ||
| "label": "Access", | ||
| "description": "Indicates whether the user has permission to access the given dataset. For open-access datasets, this value will always be \"Granted\". For controlled-access datasets, it will be \"Required\" if the user is not logged in. If the user is logged in, the value will reflect their specific access permissions for the dataset." | ||
| }, | ||
| { | ||
| "key": "datasets.accessible", | ||
| "label": "Access", | ||
| "description": "Indicates whether the user has permission to access the given dataset. For open-access datasets, this value will always be \"Granted\". For controlled-access datasets, it will be \"Required\" if the user is not logged in. If the user is logged in, the value will reflect their specific access permissions for the dataset." | ||
| }, | ||
| { | ||
| "key": "datasets.consent_group", | ||
| "label": "Consent Group", | ||
| "description": "Consent group or consent groups related to a dataset." | ||
| }, | ||
| { | ||
| "key": "datasets.registered_identifier", | ||
| "label": "Registered Identifier", | ||
| "description": "Unique ID used to identify this dataset in an external database. For example, the DUOS identifier for datasets registered in DUOS." | ||
| }, | ||
| { | ||
| "key": "datasets.title", | ||
| "label": "Title", | ||
| "description": "A human-readable property that identifies the dataset which the dataset belongs to." | ||
| }, | ||
| { | ||
| "key": "diagnoses.disease", | ||
| "label": "Diagnosis", | ||
| "description": "A human-readable property that identifies a disease or condition has been reported in this entity." | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "name": "Diagnosis", | ||
| "description": "Contains information about conditions or diagnoses related to the donor of a biosample.", | ||
| "key": "diagnoses", | ||
| "label": "Diagnosis", | ||
| "attributes": [ | ||
| { | ||
| "key": "diagnoses.disease", | ||
| "label": "Diagnosis", | ||
| "description": "A human-readable property that identifies a disease or condition has been reported in this entity." | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "name": "Donor", | ||
| "description": "Demographic and phenotypic information about the donor.", | ||
| "key": "donors", | ||
| "label": "Donor", | ||
| "attributes": [ | ||
| { | ||
| "key": "donors.donor_id", | ||
| "label": "Donor Id", | ||
| "description": "A unique identifier for the donor." | ||
| }, | ||
| { | ||
| "key": "donors.organism_type", | ||
| "label": "Organism Type", | ||
| "description": "A human-readable reference to the organism type." | ||
| }, | ||
| { | ||
| "key": "donors.phenotypic_sex", | ||
| "label": "Phenotypic Sex", | ||
| "description": "A reference to the BiologicalSex of the Donor organism. \"An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. [PATO_0001894]" | ||
| }, | ||
| { | ||
| "key": "donors.reported_ethnicity", | ||
| "label": "Reported Ethnicity", | ||
| "description": "A property that relects a Human Donor's reported ethnic origins. Note this may contain both Race and Ethnicity information as define by the US Department of Interior (DOI) https://www.doi.gov/pmb/eeo/directives/race-data" | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "name": "File", | ||
| "description": "Information for files associated with the dataset.", | ||
| "key": "files", | ||
| "label": "File", | ||
| "attributes": [ | ||
| { | ||
| "key": "drs_uri", | ||
| "label": "DRS URI", | ||
| "description": "A Uniform Resource Identifier (URI) that follows the GA4GH Data Repository Service (DRS) specification. It provides a standardized way to reference and access digital objects, such as files, within compliant data repositories. The DRS URI enables interoperability across systems by allowing authorized users and tools to retrieve dataset contents through a consistent interface." | ||
| }, | ||
| { | ||
| "key": "files.file_format", | ||
| "label": "File Format", | ||
| "description": "An indication of the format of an electronic file; include the full file extension including compression extensions. Usually aligns with file extension (e.g. bam, sam, text, csv, etc.)" | ||
| }, | ||
| { | ||
| "key": "files.file_name", | ||
| "label": "File Name", | ||
| "description": "The name of the file." | ||
| }, | ||
| { | ||
| "key": "files.file_size", | ||
| "label": "File Size", | ||
| "description": "Size of file in megabytes." | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } |
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