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Class: FileCollection

A collection of files, according to some selection criteria. In the context of the "FAIRification of Genomic Annotations" data model, we are mainly interested in "GenomicAnnotationFile" entities, but other types of files can also be contained in a collection, e.g. raw data files such as FASTQ files.

URI: https://w3id.org/fga-wg/schema/bundle/FileCollection

 classDiagram
    class FileCollection
    click FileCollection href "../FileCollection/"
      FileCollection : deposit_versioned_ref

      FileCollection : filecollection_contact





        FileCollection --> "0..1" Contact : filecollection_contact
        click Contact href "../Contact/"



      FileCollection : filecollection_description





        FileCollection --> "0..1" Any : filecollection_description
        click Any href "../Any/"



      FileCollection : filecollection_external_id

      FileCollection : filecollection_id

      FileCollection : filecollection_input_sources





        FileCollection --> "*" InputSource : filecollection_input_sources
        click InputSource href "../InputSource/"



      FileCollection : filecollection_label

Example

Example JSON 
{
  "deposit_versioned_ref": "doi:10.1234/zenodo.12345679",
  "filecollection_contact": {
    "contact_id": "bioproject:PRJNA234466",
    "email": "info@ihec-epigenomes.org",
    "name": "International Human Epigenome Consortium"
  },
  "filecollection_description": "ENCODE dataset in the International Human Epigenome Consortium (IHEC) data portal, enhanced with metadata from the ENCODE data portal.",
  "filecollection_id": "filecollection:ihec_encode",
  "filecollection_input_sources": [
    {
      "inputsource_external_ref": "https://epigenomesportal.ca/ihec/grid.html?build=2020-10&assembly=4&institutions=4",
      "qualified_relation": "prov:wasDerivedFrom",
      "version": "2020-10"
    },
    {
      "inputsource_external_ref": "https://www.encodeproject.org",
      "qualified_relation": "prov:hadPrimarySource"
    }
  ],
  "filecollection_label": "IHEC data portal: ENCODE dataset"
}

Slots

Name Cardinality and Range Description Inheritance
filecollection_external_id 0..1
Curie		 External, globally unique identifier for the file collection (in most cases, this will not exist). direct
filecollection_id 1
Curie		 Internal identifier for the file collection (unique within the metadata deposit). direct
filecollection_label 1
String		 A human-readable description of the file collection, short enough to be used for listings within software user interfaces, tables, illustration legends, etc. direct
filecollection_description 0..1
Any or 
String or 
Uri		 Human-readable description of the file collection. direct
filecollection_input_sources *
InputSource		 References to other input sources from which this file collection was derived. direct
deposit_versioned_ref 1
Curie		 Reference to versioned id of deposit containing this file collection. direct
filecollection_contact 0..1
Contact		 Contact point to the creator and/or maintainer of the file collection. direct

Usages

used by used in type used
Bundle file_collections range FileCollection

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/fga-wg/schema/bundle

Mappings

Mapping Type Mapped Value
self https://w3id.org/fga-wg/schema/bundle/FileCollection
native https://w3id.org/fga-wg/schema/bundle/FileCollection

LinkML Source

Direct

name: FileCollection
description: A collection of files, according to some selection criteria. In the context
  of the "FAIRification of Genomic Annotations" data model, we are mainly interested
  in "GenomicAnnotationFile" entities, but other types of files can also be contained
  in a collection, e.g. raw data files such as FASTQ files.
from_schema: https://w3id.org/fga-wg/schema/bundle
slots:
- filecollection_external_id
- filecollection_id
- filecollection_label
- filecollection_description
- filecollection_input_sources
- deposit_versioned_ref
- filecollection_contact

Induced

name: FileCollection
description: A collection of files, according to some selection criteria. In the context
  of the "FAIRification of Genomic Annotations" data model, we are mainly interested
  in "GenomicAnnotationFile" entities, but other types of files can also be contained
  in a collection, e.g. raw data files such as FASTQ files.
from_schema: https://w3id.org/fga-wg/schema/bundle
attributes:
  filecollection_external_id:
    name: filecollection_external_id
    description: External, globally unique identifier for the file collection (in
      most cases, this will not exist).
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: FileCollection
    domain_of:
    - FileCollection
    range: curie
    required: false
  filecollection_id:
    name: filecollection_id
    description: 'Internal identifier for the file collection (unique within the metadata
      deposit). '
    examples:
    - value: filecollection:ihec_encode
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    identifier: true
    owner: FileCollection
    domain_of:
    - FileCollection
    range: curie
    required: true
  filecollection_label:
    name: filecollection_label
    description: A human-readable description of the file collection, short enough
      to be used for listings within software user interfaces, tables, illustration
      legends, etc.
    examples:
    - value: 'IHEC data portal: ENCODE dataset'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: FileCollection
    domain_of:
    - FileCollection
    range: string
    required: true
    pattern: ^.{1,60}$
  filecollection_description:
    name: filecollection_description
    description: Human-readable description of the file collection.
    examples:
    - value: ENCODE dataset in the International Human Epigenome Consortium (IHEC)
        data portal, enhanced with metadata from the ENCODE data portal.
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: FileCollection
    domain_of:
    - FileCollection
    range: Any
    any_of:
    - range: string
    - range: uri
  filecollection_input_sources:
    name: filecollection_input_sources
    description: References to other input sources from which this file collection
      was derived.
    examples:
    - object:
        inputsource_external_ref: https://epigenomesportal.ca/ihec/grid.html?build=2020-10&assembly=4&institutions=4
        qualified_relation: prov:wasDerivedFrom
        version: 2020-10
    - object:
        inputsource_external_ref: https://www.encodeproject.org
        qualified_relation: prov:hadPrimarySource
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: FileCollection
    domain_of:
    - FileCollection
    range: InputSource
    multivalued: true
  deposit_versioned_ref:
    name: deposit_versioned_ref
    description: Reference to versioned id of deposit containing this file collection.
    examples:
    - value: doi:10.1234/zenodo.12345679
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: FileCollection
    domain_of:
    - FileCollection
    range: curie
    required: true
  filecollection_contact:
    name: filecollection_contact
    description: Contact point to the creator and/or maintainer of the file collection.
    examples:
    - object:
        name: International Human Epigenome Consortium
        contact_id: bioproject:PRJNA234466
        email: info@ihec-epigenomes.org
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: FileCollection
    domain_of:
    - FileCollection
    range: Contact