AnalysisMethod¶
Description¶
An Analysis Method captures the workflow steps that were performed to analyze data obtained from an Experiment.
Fields¶
name¶
description : A name identifying this Analysis Method.
required : True
data type : string
description¶
description : Description of an entity.
required : True
data type : string
type¶
description : The type of an entity. Note: Not to be confused with rdf:type.
required : True
data type : string
workflow_name¶
description : The workflow name.
required : True
data type : string
workflow_version¶
description : The workflow version.
required : False
data type : string
workflow_repository¶
description : The workflow repository (e.g., the URL).
required : True
data type : string
workflow_doi¶
description : A digital object identifier for the workflow. Can be a publication or the workflow commit that was used for the Analysis.
required : True
data type : string
workflow_tasks¶
description : Tasks performed by the workflow
required : False
data type : string
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).
required : False
data type : Attribute
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').
required : False
data type : Attribute
reference_name¶
description : Name or identifier of the reference, e.g., "hg38", "dbSNP"
required : False
data type : string
reference_type¶
description : Type of reference data used
required : False
data type : Controlled Vocabulary
Permissible Values
| Permissible Values | Description |
|---|---|
GENOME |
Reference genome sequence |
SNP |
SNP reference database |
INDEL |
Indel reference set |
TRANSCRIPTOME |
Transcript sequences |
HAPLOTYPE |
Haplotype panels |
VCF |
Variant call format reference |
BED |
BED-formatted genomic regions |
REPEATMASKER |
RepeatMasker annotations |
OTHER |
Other types of references |
reference_source¶
description : Source or provider of the reference, e.g., "UCSC", "Ensembl"
required : False
data type : string
reference_link¶
description : URL to the reference
required : False
data type : string
reference_version¶
description : Version or release identifier of the reference data
required : False
data type : string
attributes¶
description : Key/value pairs corresponding to an entity.
required : False
data type : Attribute
alias¶
description : The alias for an entity at the time of submission.
required : True
data type : string