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submission.yaml
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submission.yaml
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id: https://w3id.org/GHGA-Submission-Metadata-Schema
name: GHGA-Submission-Metadata-Schema
description: >-
The submission centric metadata schema for the German Human Genome-Phenome Archive (GHGA).
version: 2.0.0
imports:
- linkml:types
prefixes:
COB: https://purl.obolibrary.org/obo/COB_
EFO: https://www.ebi.ac.uk/efo/EFO_
GHGA: https://w3id.org/GHGA/
HANCESTRO: https://purl.obolibrary.org/obo/HANCESTRO_
SIO: https://semanticscience.org/resource/SIO_
biolink: https://w3id.org/biolink/vocab/
linkml: https://w3id.org/linkml/
GSSO: https://purl.obolibrary.org/obo/gsso/releases/2.0.5/gsso.owl
DUO: https://purl.obolibrary.org/obo/duo/releases/2021-02-23/duo.owl
NCIT: https://purl.obolibrary.org/obo/ncit/releases/2022-08-19/ncit.owl
topic: https://raw.githubusercontent.com/edamontology/edamontology/main/EDAM_dev.owl
format: https://raw.githubusercontent.com/edamontology/edamontology/main/EDAM_dev.owl
GENEPIO: https://purl.obolibrary.org/obo/genepio/releases/2023-08-19/genepio.owl
default_prefix: GHGA
default_range: string
default_curi_maps:
- obo_context
- idot_context
- semweb_context
classes:
Attribute:
description: >-
A key/value pair that further characterizes an entity.
slots:
- key
- key_type
- value
- value_type
exact_mappings:
- SIO:000614
slot_usage:
key:
required: true
key_type:
required: false
value:
required: true
value_type:
required: false
AttributeMixin:
mixin: true
description: Mixin for entities that can have one or more attributes.
slots:
- attributes
slot_usage:
attributes:
required: false
inlined: true
inlined_as_list: true
AliasMixin:
mixin: true
description: Mixin for entities that can be assigned an alias at the time of metadata submission.
slots:
- alias
slot_usage:
alias:
required: true
IdentifiedByAliasMixin:
mixin: true
abstract: true
is_a: AliasMixin
slot_usage:
alias:
identifier: true
Study:
mixins:
- IdentifiedByAliasMixin
- AttributeMixin
description: >-
A Study is an experimental investigation of a particular phenomenon. It involves a detailed examination and analysis of a subject to learn more about the phenomenon being studied.
slots:
- title
- description
- types
- ega_accession
- affiliations
slot_usage:
title:
description: >-
A comprehensive title for this Study.
required: true
description:
description: >-
A detailed description (abstract) that describes the goals of this Study.
required: true
types:
description: >-
One or more types of this Study (e.g., Cancer Genomics, Epigenetics, Exome Sequencing).
range: StudyTypeEnum
required: true
ega_accession:
required: false
affiliations:
description: >-
The affiliations associated with this Study.
required: true
attributes:
description: >-
One or more attributes that further characterize this Study.
Experiment:
mixins:
- IdentifiedByAliasMixin
- AttributeMixin
description: >-
An Experiment is an investigation that consists of a coordinated set of actions and observations designed to generate data with the goal of verifying, falsifying, or establishing the validity of a hypothesis.
exact_mappings:
- SIO:000994
slots:
- experiment_method
- title
- description
- type
- ega_accession
- sample
slot_usage:
experiment_method:
description: >-
The alias of one or more Experiment Methods that are associated with this Experiment.
required: true
inlined: false
title:
description: >-
The title for this Experiment (e.g., GHGAE_PBMC_RNAseq).
required: true
description:
description: >-
A detailed description of this Experiment.
required: true
type:
description: >-
The type of this Experiment.
required: false
ega_accession:
description: >-
The EGA accession of the 'Run' entity (EGAR).
required: false
sample:
description: The alias of one or more Samples that are associated with this Experiment.
required: true
inlined: false
ExperimentMethod:
mixins:
- IdentifiedByAliasMixin
- AttributeMixin
description: >-
The Experiment Method captures technical metadata describing the parameters used to generate output from the Sample.
slots:
- name
- description
- type
- library_type
- library_selection_methods
- library_preparation
- library_preparation_kit_retail_name
- library_preparation_kit_manufacturer
- primer
- end_bias
- target_regions
- rnaseq_strandedness
- instrument_model
- sequencing_center
- sequencing_read_length
- sequencing_layout
- target_coverage
- flow_cell_id
- flow_cell_type
- sample_barcode_read
- ega_accession
slot_usage:
name:
description: >-
A short name identifying this Experiment Method.
required: true
description:
description: >-
A short description of this Experiment Method.
required: true
type:
description: >-
The type associated with this Experiment Method.
required: true
library_type:
required: true
library_selection_methods:
required: true
library_preparation:
required: true
library_preparation_kit_retail_name:
required: false
recommended: true
library_preparation_kit_manufacturer:
required: false
recommended: true
primer:
required: false
recommended: true
end_bias:
required: false
recommended: true
target_regions:
required: false
rnaseq_strandedness:
required: false
recommended: true
instrument_model:
required: true
sequencing_center:
required: false
recommended: true
sequencing_read_length:
required: false
sequencing_layout:
required: true
target_coverage:
required: false
flow_cell_id:
required: false
recommended: true
flow_cell_type:
required: false
recommended: true
sample_barcode_read:
required: false
recommended: true
ega_accession:
description: >-
The EGA accession of the 'Experiment' entity (EGAX).
required: false
attributes:
description: >-
One or more attributes that further characterize this Experiment Method.
Sample:
mixins:
- IdentifiedByAliasMixin
- AttributeMixin
description: >-
A Sample is a limited quantity of something to be used for testing, analysis, inspection, investigation, demonstration, or trial use.
It is prepared from a Biospecimen.
exact_mappings:
- SIO:001050
- biolink:MaterialSample
slots:
- individual
- name
- type
- biological_replicate
- description
- storage
- disease_or_healthy
- case_control_status
- ega_accession
- xref
- biospecimen_name
- biospecimen_type
- biospecimen_description
- biospecimen_age_at_sampling
- biospecimen_vital_status_at_sampling
- biospecimen_tissue_term
- biospecimen_tissue_id
- biospecimen_isolation
- biospecimen_storage
slot_usage:
individual:
description: >-
The alias of the Individual entity from which this Biospecimen or Sample was derived.
inlined: false
required: true
name:
description: >-
A descriptive name of this Sample (e.g., GHGAS_Blood_Sample1 or GHGAS_PBMC_RNAseq_S1).
This property must not include any personally identifiable data.
required: true
type:
description: >-
The type of the Sample.
range: SampleTypeEnum
required: false
biological_replicate:
recommended: true
description:
description: >-
A concise description about the Sample source, the collection method, and the protocol which was followed to process this Sample.
required: true
storage:
required: false
recommended: true
disease_or_healthy:
required: false
recommended: true
case_control_status:
required: true
ega_accession:
required: false
xref:
description: >-
One or more cross-references for this Sample (e.g., this Sample may have an EBI BioSamples accession ID).
required: false
biospecimen_name:
description: >-
A descriptive name of this Biospecimen (e.g., GHGAB_caudate_nucleus_biospecimen).
This property must not include any personally identifiable data.
required: false
recommended: true
biospecimen_type:
description: >-
The type of Biospecimen.
required: false
recommended: true
biospecimen_description:
description: >-
A concise description about the Biospecimen source, the collection method, and the protocol which was followed to process this Biospecimen.
required: false
biospecimen_age_at_sampling:
required: true
biospecimen_vital_status_at_sampling:
required: false
recommended: true
biospecimen_tissue_term:
required: false
recommended: true
biospecimen_tissue_id:
required: false
recommended: true
biospecimen_isolation:
description: >-
Method or device employed for collecting/isolating this Biospecimen.
required: false
recommended: true
biospecimen_storage:
description: >-
Methods by which this Biospecimen is stored.
required: false
recommended: true
Individual:
mixins:
- IdentifiedByAliasMixin
aliases: ["subject", "patient"]
description: >-
An Individual is a Person who is participating in a Study.
slots:
- phenotypic_features_terms
- phenotypic_features_ids
- diagnosis_ids
- diagnosis_terms
- sex
- geographical_region_term
- geographical_region_id
- ancestry_terms
- ancestry_ids
slot_usage:
phenotypic_features_terms:
required: false
recommended: true
phenotypic_features_ids:
required: false
recommended: true
diagnosis_ids:
required: false
recommended: true
diagnosis_terms:
required: false
recommended: true
sex:
required: true
geographical_region_term:
required: false
geographical_region_id:
required: false
ancestry_terms:
required: false
ancestry_ids:
required: false
Analysis:
mixins:
- IdentifiedByAliasMixin
aliases: ["data analysis"]
description: >-
An Analysis is a data transformation that transforms input data to output data.
slots:
- analysis_method
- title
- description
- type
- ega_accession
- research_data_files
slot_usage:
analysis_method:
description: >-
The alias of the Analysis Method that is associated with this Analysis.
required: true
inlined: false
title:
required: true
description:
description: >-
A description summarizing how this Analysis was carried out (e.g., description of computational tools, pipelines, workflows).
required: false
type:
description: >-
The type of this Analysis.
required: false
ega_accession:
description: >-
The EGA accession of the 'Analysis' entity (EGAZ).
required: false
research_data_files:
description: >-
One or more aliases of the Research Data Files that this Analysis used as input to create Process Data Files.
required: true
inlined: false
AnalysisMethod:
mixins:
- IdentifiedByAliasMixin
description: >-
An Analysis Method captures the workflow steps that were performed to analyze data obtained from an Experiment.
slots:
- name
- description
- type
- workflow_name
- workflow_version
- workflow_repository
- workflow_doi
- workflow_tasks
- parameters
- software_versions
slot_usage:
name:
description: >-
A name identifying this Analysis Method.
required: true
description:
required: true
type:
required: true
workflow_name:
required: true
workflow_version:
required: false
recommended: true
workflow_repository:
required: true
workflow_doi:
required: true
workflow_tasks:
required: false
recommended: true
parameters:
recommended: true
required: false
inlined: true
inlined_as_list: true
software_versions:
recommended: true
required: false
inlined: true
inlined_as_list: true
Dataset:
mixins:
- IdentifiedByAliasMixin
description: >-
A Dataset is a collection of Files that is prepared for distribution and is tied to a Data Access Policy.
exact_mappings:
- SIO:000089
slots:
- title
- description
- types
- ega_accession
- data_access_policy
- study
slot_usage:
title:
description: >-
A title for this Dataset.
required: true
description:
description: >-
A description summarizing this Dataset.
required: true
types:
description: >-
The type of this Dataset.
required: true
ega_accession:
required: false
data_access_policy:
description: >-
The Data Access Policy that applies to this Dataset.
required: true
inlined: false
study:
description: >-
The Study associated with this Dataset.
required: true
inlined: false
DataAccessPolicy:
mixins:
- IdentifiedByAliasMixin
description: >-
A Data Access Policy specifies under which circumstances, legal or otherwise, a user can have access to one or more Datasets belonging to one or more Studies.
slots:
- name
- description
- policy_text
- policy_url
- data_use_permission_term
- data_use_permission_id
- data_use_modifier_terms
- data_use_modifier_ids
- ega_accession
- data_access_committee
slot_usage:
name:
description: >-
A name for this Data Access Policy.
required: true
description:
description: >-
A short description for this Data Access Policy.
required: true
policy_text:
required: true
policy_url:
required: false
recommended: true
data_use_permission_term:
description: >-
The Data Use Permission associated with this Data Use Policy. The used term should be a descendant of 'DUO:0000001: data use permission' (e.g., no restriction).
required: true
data_use_permission_id:
description: >-
The DUO ID corresponding to the Data Use Permission term (e.g., DUO:0000004).
required: true
data_use_modifier_terms:
description: >-
One or more Data Use Modifiers for the Data Use Permission associated with this Data Use Policy. The used terms should be descendants of 'DUO:0000017: data use modifier' (e.g., clinical care use).
Please use 'USER_SPECIFIC_RESTRICTION' if no other modifier applies.
required: false
recommended: true
data_use_modifier_ids:
description: >-
The DUO IDs corresponding to the Data Use Modifier terms (e.g., DUO:0000043).
required: false
recommended: true
ega_accession:
required: false
data_access_committee:
description: >-
The Data Access Committee linked to this Data Use Policy.
required: true
inlined: false
DataAccessCommittee:
mixins:
- IdentifiedByAliasMixin
description: >-
A group of members that are delegated to grant access to one or more datasets after ensuring the criteria for data sharing has been met,
and request for data use does not raise ethical and/or legal concerns.
slots:
- email
- institute
- ega_accession
slot_usage:
email:
description: >-
The email of the Data Access Committee (e.g., DAC[at]email.com).
This property must not include any personally identifiable data.
required: true
institute:
required: true
ega_accession:
required: false
Publication:
mixins:
- IdentifiedByAliasMixin
description: >-
A Publication represents an article that is published. The minimum expectation is that the publication has a valid DOI.
slots:
- study
- title
- abstract
- author
- year
- journal
- doi
- xref
slot_usage:
study:
description: >-
The Study entity associated with this Publication.
required: true
inlined: false
title:
description: >-
The title for this Publication.
required: false
abstract:
required: false
author:
description: >-
Author(s) of this Publication.
required: false
year:
required: false
journal:
required: false
doi:
required: true
xref:
description: >-
One or more cross-references for this Publication.
required: false
File:
mixins:
- IdentifiedByAliasMixin
description: >-
A file is an object that contains information generated from a process, either an Experiment or an Analysis.
slots:
- name
- dataset
- ega_accession
- included_in_submission
slot_usage:
name:
description: >-
The given filename.
required: true
dataset:
description: >-
The Dataset alias associated with this File.
inlined: false
required: true
ega_accession:
required: false
included_in_submission:
required: true
ResearchDataFile:
is_a: File
description: >-
A Research Data File is a File that contains raw data originating from an Experiment.
slots:
- format
- technical_replicate
- sequencing_lane_id
- experiments
slot_usage:
format:
description: The file format of the Research Data File (e.g., FASTQ, uBAM, FASTA).
required: true
range: ResearchDataFileFormatEnum
technical_replicate:
required: true
sequencing_lane_id:
required: false
recommended: true
experiments:
description: >-
The aliases of the Experiments that produced this Research Data File.
required: true
inlined: false
ProcessDataFile:
is_a: File
description: >-
A Process Data File is a File that contains data produced by an Analysis or workflow.
slots:
- format
- analysis
slot_usage:
format:
description: The file format of the Process Data File (e.g., CRAM, BAM).
required: true
range: ProcessDataFileFormatEnum
analysis:
description: >-
The alias of the Analysis that produced this Process Data File.
required: true
inlined: false
ExperimentMethodSupportingFile:
is_a: File
description: >-
An Experiment Method Supporting File is a File that contains additional information relevant for the Experiment Method, such as (unstructured) protocols.
slots:
- format
- experiment_method
slot_usage:
format:
description: The file format of the Supporting File (e.g., TXT, JSON).
required: true
range: SupportingFileFormatEnum
experiment_method:
required: true
inlined: false
AnalysisMethodSupportingFile:
is_a: File
description: >-
An Analysis Method Supporting File is a File that contains additional information relevant for the Analysis Method, such as (unstructured) protocols or task descriptions.
slots:
- format
- analysis_method
slot_usage:
format:
description: The file format of the Supporting File (e.g., TXT, JSON).
required: true
range: SupportingFileFormatEnum
analysis_method:
required: true
inlined: false
IndividualSupportingFile:
is_a: File
description: >-
An Individual Supporting File is a File that contains additional information relevant for the Individual, such as ped-files, phenopackets or imaging data.
slots:
- format
- individual
slot_usage:
format:
description: The file format of the Supporting File (e.g., TXT, JSON).
required: true
range: SupportingFileFormatEnum
individual:
required: true
inlined: false
Submission:
tree_root: true
description: >-
A grouping entity that represents information about one or more entities.
A submission can be considered as a set of inter-related (and inter-connected)
entities that represent a data submission to GHGA.
slots:
- analyses
- analysis_methods
- data_access_committees
- data_access_policies
- datasets
- individuals
- publications
- samples
- experiments
- experiment_methods
- studies
- research_data_files
- process_data_files
- experiment_method_supporting_files
- analysis_method_supporting_files
- individual_supporting_files
slot_usage:
studies:
description: >-
Study entities associated with this Submission.
required: true
inlined: true
inlined_as_list: true
samples:
description: >-
One or more Sample entities associated with this Submission.
required: true
inlined: true
inlined_as_list: true
individuals:
description: >-
One or more Individual entities associated with this Submission.
required: true
inlined: true
inlined_as_list: true
experiments:
description: >-
One or more Experiment entities associated with this Submission.
required: true
inlined: true
inlined_as_list: true
analyses:
description: >-
One or more Analysis entities associated with this Submission.
required: true
inlined: true
inlined_as_list: true
experiment_methods:
description: >-
The Experiment Methods that are part of this Submission.
required: true
inlined: true
inlined_as_list: true
analysis_methods:
description: >-
The Analysis Methods that are part of this Submission.
required: true
inlined: true
inlined_as_list: true
datasets:
description: >-
One or more Dataset entities that are part of this Submission.
required: true
inlined: true
inlined_as_list: true
data_access_policies:
description: >-
The Data Access Policies that apply to the Datasets in this Submission.
required: true
inlined: true
inlined_as_list: true
data_access_committees:
description: >-
The Data Access Committees that apply to the Data Access Policies in this Submission.
required: true
inlined: true
inlined_as_list: true
publications:
description: >-
One or more Publication entities associated with this Submission.
required: true
inlined: true
inlined_as_list: true
research_data_files:
description: >-
One or more Research Data Files associated with this Submission.
required: true
inlined: true
inlined_as_list: true
process_data_files:
description: >-
One or more Process Data Files associated with this Submission.
required: true
inlined: true
inlined_as_list: true
experiment_method_supporting_files:
description: >-
One or more Experiment Method Supporting Files associated with this Submission.
required: true
inlined: true
inlined_as_list: true
analysis_method_supporting_files:
description: >-
One or more Analysis Method Supporting Files associated with this Submission.
required: true
inlined: true
inlined_as_list: true
individual_supporting_files:
description: >-
One or more Individual Supporting Files associated with this Submission.
required: true
inlined: true
inlined_as_list: true
slots:
alias:
description: The alias for an entity at the time of submission.
description:
description: Description of an entity.
exact_mappings:
- SIO:000185
key:
description: The key of an attribute.
key_type:
description: A semantic type that characterizes the attribute key (e.g., oxygen saturation measurement (MAXO:0000616)).
value:
description: The value for an attribute (e.g., a numerical value without the units).
value_type:
description: The value_type that characterizes the attribute value (e.g., percentage (SIO:001413)).
attributes:
description: Key/value pairs corresponding to an entity.
range: Attribute
multivalued: true
parameters:
description: Key/value pairs where key corresponds to a parameter name and value corresponds to a parameter value (e.g., 'aligner' = 'star_salmon', 'hisat2_build_memory' = '200.GB', 'split_fastq' = 50000000).
range: Attribute
multivalued: true
software_versions:
description: key/value pairs where key corresponds to a software name and value corresponds to a version descriptor (e.g., `salmon` = '1.3.0', `trim-galore` = '0.6.6', `bedtools` = '2.29.2').
range: Attribute
multivalued: true
type:
description: >-
The type of an entity.
Note: Not to be confused with rdf:type.
types:
description: >-
The types of an entity.
Note: Not to be confused with rdf:type.
multivalued: True
name:
description: The name for an entity.
title:
description: The title that describes an entity.
xref:
description: Database cross references for an entity.
multivalued: true
study:
description: The Study associated with an entity.
range: Study
studies:
description: The Study associated with an entity.
range: Study
multivalued: True
publications:
description: The Publication associated with an entity.
range: Publication
multivalued: True
sample:
description: The Sample associated with an entity.
range: Sample
samples:
description: The Samples associated with an entity.
range: Sample
multivalued: true
experiments:
description: The Experiments associated with an entity.
range: Experiment
multivalued: true
experiment_method:
description: The Experiment Method associated with an entity.
range: ExperimentMethod
experiment_methods:
description: The Experiment Methods associated with an entity.
range: ExperimentMethod
multivalued: true
analyses:
description: The Analyses associated with an entity.
range: Analysis
multivalued: true
analysis:
description: The Analysis associated with an entity.
range: Analysis
analysis_method:
description: The Analysis Process associated with an entity.
range: AnalysisMethod
analysis_methods:
description: The Analysis Processes associated with an entity.
range: AnalysisMethod
multivalued: true
workflow_name:
description: The workflow name.
workflow_version:
description: The workflow version.
workflow_repository:
description: The workflow repository (e.g., the URL).
workflow_doi:
description: A digital object identifier for the workflow. Can be a publication or the workflow commit that was used for the Analysis.