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elixir
metadata-tools
Commits
c93d0261
Commit
c93d0261
authored
Nov 13, 2019
by
Pinar Alper
Browse files
some fields moved from dataset/project to core
parent
23c487ac
Changes
3
Hide whitespace changes
Inline
Side-by-side
metadata_tools/resources/elu-core.json
View file @
c93d0261
...
...
@@ -24,6 +24,54 @@
},
"elu_accession"
:
{
"type"
:
"string"
},
"elu_uuid"
:
{
"type"
:
"string"
},
"other_external_id"
:
{
"type"
:
"string"
},
"contacts"
:
{
"type"
:
"array"
,
"items"
:
{
"type"
:
"object"
,
"properties"
:
{
"first_name"
:
{
"type"
:
"string"
},
"last_name"
:
{
"type"
:
"string"
},
"role"
:
{
"type"
:
"string"
,
"enum"
:
[
"Principal_Investigator"
,
"Researcher"
,
"Data_Manager"
,
"Data_Protection_Officer"
,
"Legal_Representative"
,
"Other"
]
},
"email"
:
{
"type"
:
"string"
,
"format"
:
"email"
},
"affiliations"
:
{
"type"
:
"array"
,
"items"
:
{
"type"
:
"string"
}
}
},
"required"
:
[
"first_name"
,
"last_name"
,
"role"
,
"email"
,
"institution"
]
}
}
}
}
...
...
metadata_tools/resources/elu-dataset.json
View file @
c93d0261
{
"description"
:
"
Dataset
Schema"
,
"description"
:
"
ELIXIR Luxembourg Projects
Schema"
,
"schema"
:
{
"title"
:
"A JSON Schema for describing
Datasets within the ELIXIR Data Submission System
."
,
"title"
:
"A JSON Schema for describing
biomedical research Projects
."
,
"$schema"
:
"http://json-schema.org/draft-04/schema#"
,
"type"
:
"object"
,
"
required
"
:
[
"title"
,
"source_type"
,
"data_types"
"
allOf
"
:
[
{
"$ref"
:
"https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/elu-core.json"
}
],
"properties"
:
{
"title"
:
{
"type"
:
"string"
},
"submission_id"
:
{
"project"
:
{
"type"
:
"string"
},
"source_type"
:
{
"type"
:
"string"
,
"enum"
:
[
"From_Collaborator"
,
"From_Repository"
,
"Own_Cohort"
,
"From_Elixir_Data_Submitter"
]
},
"local_custodian"
:
{
"data_declarations"
:
{
"type"
:
"array"
,
"minItems"
:
1
,
"items"
:
[
{
"type"
:
"string"
}
]
"items"
:
{
"$ref"
:
"#/definitions/elu:data"
}
},
"
use_restriction
s"
:
{
"
storage
s"
:
{
"type"
:
"array"
,
"items"
:
{
"type"
:
"object"
,
"properties"
:
{
"ga4gh_code"
:
{
"type"
:
"string"
,
"enum"
:
[
"NRES"
,
"GRU(CC)"
,
"HMB(CC)"
,
"DS-[XX](CC)"
,
"POA"
,
"RS-[XX]"
,
"RUO"
,
"NMDS"
,
"GSO"
,
"NPU"
,
"PUB"
,
"COL-[XX]"
,
"RTN"
,
"IRB"
,
"GS-[XX]"
,
"MOR-[XX]"
,
"TS-[XX]"
,
"US"
,
"PS"
,
"IS"
]
},
"note"
:
{
"type"
:
"string"
}
},
"required"
:
[
"ga4gh_code"
,
"note"
]
"$ref"
:
"#/definitions/elu:storage"
}
},
"
data_type
s"
:
{
"
transfer
s"
:
{
"type"
:
"array"
,
"items"
:
{
"type"
:
"string"
,
"enum"
:
[
"Omics_data"
,
"Genotype_data"
,
"Whole_genome_sequencing"
,
"Exome_sequencing"
,
"Genomics_variant_array"
,
"RNASeq"
,
"Genetic_and_derived_genetic_data"
,
"Transcriptome_array"
,
"Methylation_array"
,
"MicroRNA_array"
,
"Metabolomics"
,
"Metagenomics"
,
"Proteomics"
,
"Other_omics_data"
,
"Clinical_Imaging"
,
"Cell_Imaging"
,
"Human_subject_data"
,
"Clinical_data"
,
"Lifestyle_data"
,
"Socio_Economic_Data"
,
"Environmental_Data"
,
"Other_Phenotype_data"
,
"Other"
]
},
"data_type_notes"
:
{
"type"
:
"string"
},
"other_external_id"
:
{
"type"
:
"string"
},
"access_category"
:
{
"type"
:
"string"
},
"subject_categories"
:
{
"type"
:
"array"
,
"items"
:
{
"type"
:
"string"
,
"enum"
:
[
"cases"
,
"controls"
,
"cases_and_controls"
]
"$ref"
:
"#/definitions/elu:transfer"
}
}
},
"definitions"
:
{
"elu:storage"
:
{
"type"
:
"object"
,
"properties"
:
{
"platform"
:
"string"
,
"location"
:
"string"
,
"accesses"
:
{
"type"
:
"array"
,
"items"
:
{
"type"
:
"string"
}
}
},
"source_project"
:
{
"type"
:
"string"
},
"source_repository"
:
{
"type"
:
"string"
},
"de_identification"
:
{
"type"
:
"string"
,
"enum"
:
[
"anonymized"
,
"pseudonymized"
]
},
"consent_status"
:
{
"type"
:
"string"
,
"enum"
:
[
"heterogeneous"
,
"homogeneous"
]
},
"involves_samples"
:
{
"type"
:
"boolean"
},
"has_special_subjects"
:
{
"type"
:
"boolean"
},
"special_subject_notes"
:
{
"type"
:
"string"
"elu:transfer"
:
{
"type"
:
"object"
,
"properties"
:
{
"partner"
:
"string"
,
"transfer_details"
:
"string"
,
"transfer_date"
:
{
"type"
:
"string"
,
"pattern"
:
"^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
}
}
},
"samples_location"
:
{
"type"
:
"string"
},
"data_notes"
:
{
"type"
:
"string"
"elu:data"
:
{
"type"
:
"object"
,
"properties"
:
{
"title"
:
{
"type"
:
"string"
},
"use_restrictions"
:
{
"type"
:
"array"
,
"items"
:
{
"type"
:
"object"
,
"properties"
:
{
"ga4gh_code"
:
{
"type"
:
"string"
,
"enum"
:
[
"NRES"
,
"GRU(CC)"
,
"HMB(CC)"
,
"DS-[XX](CC)"
,
"POA"
,
"RS-[XX]"
,
"RUO"
,
"NMDS"
,
"GSO"
,
"NPU"
,
"PUB"
,
"COL-[XX]"
,
"RTN"
,
"IRB"
,
"GS-[XX]"
,
"MOR-[XX]"
,
"TS-[XX]"
,
"US"
,
"PS"
,
"IS"
]
},
"note"
:
{
"type"
:
"string"
}
},
"required"
:
[
"ga4gh_code"
,
"note"
]
}
},
"data_types"
:
{
"type"
:
"array"
,
"items"
:
{
"type"
:
"string"
,
"enum"
:
[
"Omics_data"
,
"Genotype_data"
,
"Whole_genome_sequencing"
,
"Exome_sequencing"
,
"Genomics_variant_array"
,
"RNASeq"
,
"Genetic_and_derived_genetic_data"
,
"Transcriptome_array"
,
"Methylation_array"
,
"MicroRNA_array"
,
"Metabolomics"
,
"Metagenomics"
,
"Proteomics"
,
"Other_omics_data"
,
"Clinical_Imaging"
,
"Cell_Imaging"
,
"Human_subject_data"
,
"Clinical_data"
,
"Lifestyle_data"
,
"Socio_Economic_Data"
,
"Environmental_Data"
,
"Other_Phenotype_data"
,
"Other"
]
},
"data_type_notes"
:
{
"type"
:
"string"
},
"access_category"
:
{
"type"
:
"string"
,
"enum"
:
[
"open-access"
,
"controlled-access"
]
},
"subjects_category"
:
{
"type"
:
"array"
,
"items"
:
{
"type"
:
"string"
,
"enum"
:
[
"cases"
,
"controls"
,
"cases_and_controls"
]
}
},
"de_identification"
:
{
"type"
:
"string"
,
"enum"
:
[
"anonymized"
,
"pseudonymized"
]
},
"consent_status"
:
{
"type"
:
"string"
,
"enum"
:
[
"heterogeneous"
,
"homogeneous"
]
},
"has_special_subjects"
:
{
"type"
:
"boolean"
},
"special_subjects_description"
:
{
"type"
:
"string"
},
"embargo_date"
:
{
"type"
:
"string"
,
"pattern"
:
"^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
},
"storage_end_date"
:
{
"type"
:
"string"
,
"pattern"
:
"^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
},
"storage_duration_criteria"
:
{
"type"
:
"string"
,
"pattern"
:
"^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
}
}
}
}
}
}
}
}
...
...
metadata_tools/resources/elu-project.json
View file @
c93d0261
...
...
@@ -29,50 +29,12 @@
"type"
:
"string"
},
"start_date"
:
{
"type"
:
"string"
"type"
:
"string"
,
"pattern"
:
"^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
},
"contacts"
:
{
"type"
:
"array"
,
"minItems"
:
1
,
"items"
:
{
"type"
:
"object"
,
"properties"
:
{
"first_name"
:
{
"type"
:
"string"
},
"last_name"
:
{
"type"
:
"string"
},
"role"
:
{
"type"
:
"string"
,
"enum"
:
[
"Principal_Investigator"
,
"Researcher"
,
"Data_Manager"
,
"Data_Protection_Officer"
,
"Legal_Representative"
,
"Other"
]
},
"email"
:
{
"type"
:
"string"
,
"format"
:
"email"
},
"affiliations"
:
{
"type"
:
"array"
,
"items"
:
{
"type"
:
"string"
}
}
},
"required"
:
[
"first_name"
,
"last_name"
,
"role"
,
"email"
,
"institution"
]
}
"end_date"
:
{
"type"
:
"string"
,
"pattern"
:
"^[0-9]{4}-[0-9]{2}-[0-9]{2}$"
}
}
}
...
...
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