Class: File Meta Data (FileMetaData)

Representation of file metadata for NCPI

classDiagram class FileMetaData click FileMetaData href "../FileMetaData/" FileMetaData : adaptor_trimmed FileMetaData : assay_strategy FileMetaData : file_meta_data_id FileMetaData : is_paired_end FileMetaData : library_prep FileMetaData : library_selection FileMetaData : meta_data_type FileMetaData --> "1" EnumFileMetaDataType : meta_data_type click EnumFileMetaDataType href "../EnumFileMetaDataType/" FileMetaData : platform_instrument FileMetaData : reference_genome FileMetaData : samples FileMetaData --> "*" Sample : samples click Sample href "../Sample/" FileMetaData : strandedness FileMetaData : target_region FileMetaData : workflow_tool FileMetaData : workflow_type

Slots

Name	Cardinality and Range	Description	Inheritance
file_meta_data_id	1 String	Representation of file metadata for NCPI	direct
meta_data_type	1 EnumFileMetaDataType	Clarify which type of meta data this file has recorded	direct
assay_strategy	1 Uriorcurie	e	direct
platform_instrument	1 Uriorcurie	e	direct
library_prep	0..1 Uriorcurie	e	direct
library_selection	0..1 Uriorcurie		direct
strandedness	0..1 Uriorcurie	stranded, unstranded	direct
target_region	0..1 Uriorcurie	Target region	direct
is_paired_end	0..1 Uriorcurie	True, False	direct
adaptor_trimmed	0..1 Uriorcurie	True, False	direct
reference_genome	0..1 Uriorcurie	GRCh37, GRCh38	direct
workflow_type	0..1 Uriorcurie	e	direct
workflow_tool	0..1 Uriorcurie	e	direct
samples	* Sample	e	direct

Usages

used by	used in	type	used
NCPIFile	file_meta_data_id	range	FileMetaData

Identifier and Mapping Information

Annotations

property	value
fhir_resource	Observation
fhir_profile	https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file-metadata

Schema Source

from schema: https://carrollaboratory.github.io/kfi-fhir-input

Mappings

Mapping Type	Mapped Value
self	kfi_fhir_sparks:FileMetaData
native	kfi_fhir_sparks:FileMetaData

LinkML Source

Direct

name: FileMetaData
annotations:
  fhir_resource:
    tag: fhir_resource
    value: Observation
  fhir_profile:
    tag: fhir_profile
    value: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file-metadata
description: Representation of file metadata for NCPI
title: File Meta Data
from_schema: https://carrollaboratory.github.io/kfi-fhir-input
slots:
- file_meta_data_id
- meta_data_type
- assay_strategy
- platform_instrument
- library_prep
- library_selection
- strandedness
- target_region
- is_paired_end
- adaptor_trimmed
- reference_genome
- workflow_type
- workflow_tool
- samples
slot_usage:
  file_meta_data_id:
    name: file_meta_data_id
    annotations:
      db_column:
        tag: db_column
        value: file_meta_data_id
      target_slot:
        tag: target_slot
        value: file_meta_data_id
    identifier: true
    range: string
    required: true
    multivalued: false

Induced

name: FileMetaData
annotations:
  fhir_resource:
    tag: fhir_resource
    value: Observation
  fhir_profile:
    tag: fhir_profile
    value: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-file-metadata
description: Representation of file metadata for NCPI
title: File Meta Data
from_schema: https://carrollaboratory.github.io/kfi-fhir-input
slot_usage:
  file_meta_data_id:
    name: file_meta_data_id
    annotations:
      db_column:
        tag: db_column
        value: file_meta_data_id
      target_slot:
        tag: target_slot
        value: file_meta_data_id
    identifier: true
    range: string
    required: true
    multivalued: false
attributes:
  file_meta_data_id:
    name: file_meta_data_id
    annotations:
      db_column:
        tag: db_column
        value: file_meta_data_id
      target_slot:
        tag: target_slot
        value: file_meta_data_id
    description: Representation of file metadata for NCPI
    title: File Meta Data
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    identifier: true
    alias: file_meta_data_id
    owner: FileMetaData
    domain_of:
    - NCPIFile
    - FileMetaData
    range: string
    required: true
    multivalued: false
  meta_data_type:
    name: meta_data_type
    description: Clarify which type of meta data this file has recorded
    title: Meta Data Type
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: meta_data_type
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: EnumFileMetaDataType
    required: true
    multivalued: false
  assay_strategy:
    name: assay_strategy
    description: e.g., Whole Genome Sequencing
    title: Assay Strategy
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: assay_strategy
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: true
    multivalued: false
  platform_instrument:
    name: platform_instrument
    description: e.g., Illumina HiSeq2000
    title: Platform Instrument
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: platform_instrument
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: true
    multivalued: false
  library_prep:
    name: library_prep
    description: e.g., polyA
    title: Library Prep
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: library_prep
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: false
    multivalued: false
  library_selection:
    name: library_selection
    description: '...'
    title: Library Selection
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: library_selection
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: false
    multivalued: false
  strandedness:
    name: strandedness
    description: stranded, unstranded
    title: Strandedness
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: strandedness
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: false
    multivalued: false
  target_region:
    name: target_region
    description: Target region
    title: Target Region
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: target_region
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: false
    multivalued: false
  is_paired_end:
    name: is_paired_end
    description: True, False
    title: Is Paired End
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: is_paired_end
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: false
    multivalued: false
  adaptor_trimmed:
    name: adaptor_trimmed
    description: True, False
    title: Adaptor Trimmed
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: adaptor_trimmed
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: false
    multivalued: false
  reference_genome:
    name: reference_genome
    description: GRCh37, GRCh38
    title: Reference Genome
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: reference_genome
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: false
    multivalued: false
  workflow_type:
    name: workflow_type
    description: e.g., alignment, somatic
    title: Workflow Type
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: workflow_type
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: false
    multivalued: false
  workflow_tool:
    name: workflow_tool
    description: e.g., BAM-MEM, GATK-Haplotype Caller
    title: Workflow Tool
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: workflow_tool
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: uriorcurie
    required: false
    multivalued: false
  samples:
    name: samples
    description: e.g., Reference(sample)
    title: Samples associated with the file's content
    from_schema: https://carrollaboratory.github.io/kfi-fhir-input
    rank: 1000
    alias: samples
    owner: FileMetaData
    domain_of:
    - FileMetaData
    range: Sample
    required: false
    multivalued: true