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Class: InputSource

General object representing the source of data files, samples, or other entities used as input to a process or a result. An input source refering to a single file or sample object will represent that item only, while an input source referring to a container or process may represent a number of disctinct input items. InputSource also contains information about the type of relationship, replication labelling, versioning and retrieval date.

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

 classDiagram
    class InputSource
    click InputSource href "../InputSource/"
      InputSource : biological_replicate_labels

      InputSource : database_accessions





        InputSource --> "*" Any : database_accessions
        click Any href "../Any/"



      InputSource : date_of_retrieval

      InputSource : inputsource_external_ref

      InputSource : inputsource_ref

      InputSource : qualified_relation

      InputSource : technical_replicate_labels

      InputSource : version

Example

Example JSON 
{
  "biological_replicate_labels": [
    "1",
    "2"
  ],
  "date_of_retrieval": "2016-04-19",
  "inputsource_external_ref": "https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15",
  "qualified_relation": "bioschemas:FormalParameter",
  "technical_replicate_labels": [
    "1_1",
    "1_2"
  ]
}

Slots

Name Cardinality and Range Description Inheritance
inputsource_external_ref 0..1
Uriorcurie		 Reference to an external entity as the input source, using a globally unique identifier or an URL. External references will in most cases refer to a database, data record, data file, website or other data source. One of "inputsource_external_ref" or "inputsource_ref" must be specified. direct
inputsource_ref 0..1
Curie		 Reference to an internal object as the input source using a local identifier. Entities to be used as an internal input source includes FileCollection, Sample, Experiment, Analysis or File as restricted by the description of the field where the input source is used. One of "inputsource_external_ref" or "inputsource_ref" must be specified. direct
database_accessions *
Any or 
String or 
Curie		 Accession numbers for database records used as input source. Used in connection with "inputsource_external_ref". direct
qualified_relation 1
Uriorcurie		 A description of the relationship with the input source. direct
biological_replicate_labels *
String		 Labels denoting the biological replicates within which the relation is defined, if any. direct
technical_replicate_labels *
String		 Labels denoting the technical replicates within which the relation is defined, if any. direct
version 0..1
String		 Version information for the retrieval from the input source. direct
date_of_retrieval 0..1
Date		 Date of retrieval from the input source, typically used to timestamp downloading data from a database or URL. direct

Usages

used by used in type used
BundleMetadata bundle_input_sources range InputSource
Analysis analysis_input_sources range InputSource
Experiment experiment_samples range InputSource
File file_input_sources range InputSource
FileCollection filecollection_input_sources range InputSource
GenomicAnnotationFile file_input_sources range InputSource

Rules

Rule Applied Preconditions Postconditions Elseconditions
slot_conditions {'qualified_relation': {'value_presence': 'PRESENT'}}

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/InputSource
native https://w3id.org/fga-wg/schema/bundle/InputSource

LinkML Source

Direct

name: InputSource
description: General object representing the source of data files, samples, or other
  entities used as input to a process or a result. An input source refering to a single
  file or sample object will represent that item only, while an input source referring
  to a container or process may represent a number of disctinct input items. InputSource
  also contains information about the type of relationship, replication labelling,
  versioning and retrieval date.
from_schema: https://w3id.org/fga-wg/schema/bundle
slots:
- inputsource_external_ref
- inputsource_ref
- database_accessions
- qualified_relation
- biological_replicate_labels
- technical_replicate_labels
- version
- date_of_retrieval
rules:
- preconditions:
    slot_conditions:
      qualified_relation:
        name: qualified_relation
        value_presence: PRESENT
  postconditions:
    exactly_one_of:
    - slot_conditions:
        inputsource_external_ref:
          name: inputsource_external_ref
          required: true
    - slot_conditions:
        inputsource_ref:
          name: inputsource_ref
          required: true

Induced

name: InputSource
description: General object representing the source of data files, samples, or other
  entities used as input to a process or a result. An input source refering to a single
  file or sample object will represent that item only, while an input source referring
  to a container or process may represent a number of disctinct input items. InputSource
  also contains information about the type of relationship, replication labelling,
  versioning and retrieval date.
from_schema: https://w3id.org/fga-wg/schema/bundle
attributes:
  inputsource_external_ref:
    name: inputsource_external_ref
    description: Reference to an external entity as the input source, using a globally
      unique identifier or an URL. External references will in most cases refer to
      a database, data record, data file, website or other data source. One of "inputsource_external_ref"
      or "inputsource_ref" must be specified.
    examples:
    - value: https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: InputSource
    domain_of:
    - InputSource
    range: uriorcurie
  inputsource_ref:
    name: inputsource_ref
    description: Reference to an internal object as the input source using a local
      identifier. Entities to be used as an internal input source includes FileCollection,
      Sample, Experiment, Analysis or File as restricted by the description of the
      field where the input source is used. One of "inputsource_external_ref" or "inputsource_ref"
      must be specified.
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: InputSource
    domain_of:
    - InputSource
    range: curie
  database_accessions:
    name: database_accessions
    description: Accession numbers for database records used as input source. Used
      in connection with "inputsource_external_ref".
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: InputSource
    domain_of:
    - InputSource
    range: Any
    multivalued: true
    any_of:
    - range: string
    - range: curie
  qualified_relation:
    name: qualified_relation
    description: A description of the relationship with the input source.
    examples:
    - value: bioschemas:FormalParameter
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: InputSource
    domain_of:
    - InputSource
    range: uriorcurie
    required: true
  biological_replicate_labels:
    name: biological_replicate_labels
    description: Labels denoting the biological replicates within which the relation
      is defined, if any.
    examples:
    - value: '1'
    - value: '2'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: InputSource
    domain_of:
    - InputSource
    range: string
    multivalued: true
  technical_replicate_labels:
    name: technical_replicate_labels
    description: Labels denoting the technical replicates within which the relation
      is defined, if any.
    examples:
    - value: '1_1'
    - value: '1_2'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: InputSource
    domain_of:
    - InputSource
    range: string
    multivalued: true
  version:
    name: version
    description: Version information for the retrieval from the input source.
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: InputSource
    domain_of:
    - InputSource
    range: string
  date_of_retrieval:
    name: date_of_retrieval
    description: Date of retrieval from the input source, typically used to timestamp
      downloading data from a database or URL.
    examples:
    - value: '2016-04-19'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: InputSource
    domain_of:
    - InputSource
    range: date
rules:
- preconditions:
    slot_conditions:
      qualified_relation:
        name: qualified_relation
        value_presence: PRESENT
  postconditions:
    exactly_one_of:
    - slot_conditions:
        inputsource_external_ref:
          name: inputsource_external_ref
          required: true
    - slot_conditions:
        inputsource_ref:
          name: inputsource_ref
          required: true