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Class: Experiment

Represents a sequencing experiment that has been carried out within a study, based on biological samples, and providing data files as output. Subsequent analysis of output data is described by the Analysis entity.

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

 classDiagram
    class Experiment
    click Experiment href "../Experiment/"
      Experiment : antibody_target





        Experiment --> "0..1" Term : antibody_target
        click Term href "../Term/"



      Experiment : assay_type





        Experiment --> "1" Term : assay_type
        click Term href "../Term/"



      Experiment : biological_processes





        Experiment --> "*" Term : biological_processes
        click Term href "../Term/"



      Experiment : design_description

      Experiment : experiment_external_id

      Experiment : experiment_id

      Experiment : experiment_label

      Experiment : experiment_samples





        Experiment --> "1..*" InputSource : experiment_samples
        click InputSource href "../InputSource/"



      Experiment : experiment_study_ref

      Experiment : instrument





        Experiment --> "0..1" Term : instrument
        click Term href "../Term/"



      Experiment : library_layout





        Experiment --> "0..1" Term : library_layout
        click Term href "../Term/"



      Experiment : molecule_type





        Experiment --> "1" Term : molecule_type
        click Term href "../Term/"



      Experiment : sequencing_protocol

Example

Example JSON 
{
  "antibody_target": {
    "id": "SO:0001707",
    "label": "H3K9Me3"
  },
  "assay_type": {
    "id": "obi:OBI_0000716",
    "label": "ChIP-seq assay"
  },
  "biological_processes": [
    {
      "id": "GO:0140999",
      "label": "histone H3K4 trimethyltransferase activity"
    }
  ],
  "design_description": "https://www.encodeproject.org/documents/92cd1386-ccad-450a-b5a6-ad49983e7e3f/@@download/attachment/wgEncodeUwHistone.release5.html.pdf",
  "experiment_external_id": "encode:ENCSR000DPJ",
  "experiment_id": "experiment:ENCSR000DPJ",
  "experiment_label": "H3K9me3 ChIP-seq on human AG04450",
  "experiment_samples": [
    {
      "biological_replicate_labels": [
        "1",
        "2"
      ],
      "inputsource_ref": "sample:ENCBS004ENC",
      "qualified_relation": "prov:used",
      "technical_replicate_labels": [
        "1_1",
        "2_1"
      ]
    }
  ],
  "experiment_study_ref": "study:E-GEOD-35583",
  "instrument": {
    "id": "obi:OBI_0002128",
    "label": "Illumina Genome Analyzer"
  },
  "library_layout": {
    "id": "obi:OBI_0000736",
    "label": "single fragment library"
  },
  "molecule_type": {
    "id": "SO:0000991",
    "label": "genomic_DNA"
  }
}

Slots

Name Cardinality and Range Description Inheritance
experiment_external_id 0..1
Curie		 External, globally unique identifier for the experiment. direct
experiment_id 1
Curie		 Internal identifier for the experiment (unique within the metadata deposit). direct
experiment_label 1
String		 A human-readable description of the experiment, short enough to be used for listings within software user interfaces, tables, illustration legends, etc. direct
experiment_study_ref 1
Curie		 Internal reference to the study within which the experiment has been carried out. direct
experiment_samples 1..*
InputSource		 External or internal references to samples used in the experiment. Internal references should refer to Sample objects. direct
molecule_type 1
Term		 Specifies the type of source material that is being sequenced. direct
assay_type 1
Term		 Sequencing technique intended for this library. direct
design_description 0..1
String		 The high-level experiment design including layout, protocol. direct
library_layout 0..1
Term		 Whether the library was built as paired-end, or single-end. direct
instrument 0..1
Term		 Technology platform used to perform nucleic acid sequencing, including name and/or number associated with a specific sequencing instrument model. It is recommended to be as specific as possible for this property (e.g. if the model/revision are available, providing that instead of just the instrument maker). direct
sequencing_protocol 0..1
Uriorcurie		 Set of rules which guides how the sequencing protocol was followed. Change-tracking services such as Protocol.io or GitHub are encouraged instead of dumping free text in this field. direct
antibody_target 0..1
Term		 The target of the antibody used in the experiment. direct
biological_processes *
Term		 Biological processes illuminated by the experiment. direct

Usages

used by used in type used
Bundle experiments range Experiment

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

LinkML Source

Direct

name: Experiment
description: Represents a sequencing experiment that has been carried out within a
  study, based on biological samples, and providing data files as output. Subsequent
  analysis of output data is described by the Analysis entity.
from_schema: https://w3id.org/fga-wg/schema/bundle
slots:
- experiment_external_id
- experiment_id
- experiment_label
- experiment_study_ref
- experiment_samples
- molecule_type
- assay_type
- design_description
- library_layout
- instrument
- sequencing_protocol
- antibody_target
- biological_processes

Induced

name: Experiment
description: Represents a sequencing experiment that has been carried out within a
  study, based on biological samples, and providing data files as output. Subsequent
  analysis of output data is described by the Analysis entity.
from_schema: https://w3id.org/fga-wg/schema/bundle
attributes:
  experiment_external_id:
    name: experiment_external_id
    description: External, globally unique identifier for the experiment.
    examples:
    - value: encode:ENCSR000DPJ
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: curie
  experiment_id:
    name: experiment_id
    description: Internal identifier for the experiment (unique within the metadata
      deposit).
    examples:
    - value: experiment:ENCSR000DPJ
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    identifier: true
    owner: Experiment
    domain_of:
    - Experiment
    range: curie
    required: true
  experiment_label:
    name: experiment_label
    description: A human-readable description of the experiment, short enough to be
      used for listings within software user interfaces, tables, illustration legends,
      etc.
    examples:
    - value: H3K9me3 ChIP-seq on human AG04450
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: string
    required: true
    pattern: ^.{1,60}$
  experiment_study_ref:
    name: experiment_study_ref
    description: Internal reference to the study within which the experiment has been
      carried out.
    examples:
    - value: study:E-GEOD-35583
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: curie
    required: true
  experiment_samples:
    name: experiment_samples
    description: External or internal references to samples used in the experiment.
      Internal references should refer to Sample objects.
    examples:
    - object:
        inputsource_ref: sample:ENCBS004ENC
        qualified_relation: prov:used
        biological_replicate_labels:
        - '1'
        - '2'
        technical_replicate_labels:
        - '1_1'
        - '2_1'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: InputSource
    required: true
    multivalued: true
  molecule_type:
    name: molecule_type
    description: Specifies the type of source material that is being sequenced.
    examples:
    - object:
        id: SO:0000991
        label: genomic_DNA
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: Term
    required: true
  assay_type:
    name: assay_type
    description: Sequencing technique intended for this library.
    examples:
    - object:
        id: obi:OBI_0000716
        label: ChIP-seq assay
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: Term
    required: true
  design_description:
    name: design_description
    description: The high-level experiment design including layout, protocol.
    examples:
    - value: https://www.encodeproject.org/documents/92cd1386-ccad-450a-b5a6-ad49983e7e3f/@@download/attachment/wgEncodeUwHistone.release5.html.pdf
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: string
  library_layout:
    name: library_layout
    description: Whether the library was built as paired-end, or single-end.
    examples:
    - object:
        id: obi:OBI_0000736
        label: single fragment library
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: Term
  instrument:
    name: instrument
    description: Technology platform used to perform nucleic acid sequencing, including
      name and/or number associated with a specific sequencing instrument model. It
      is recommended to be as specific as possible for this property (e.g. if the
      model/revision are available, providing that instead of just the instrument
      maker).
    examples:
    - object:
        id: obi:OBI_0002128
        label: Illumina Genome Analyzer
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: Term
  sequencing_protocol:
    name: sequencing_protocol
    description: Set of rules which guides how the sequencing protocol was followed.
      Change-tracking services such as Protocol.io or GitHub are encouraged instead
      of dumping free text in this field.
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: uriorcurie
  antibody_target:
    name: antibody_target
    description: The target of the antibody used in the experiment.
    examples:
    - object:
        id: SO:0001707
        label: H3K9Me3
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: Term
  biological_processes:
    name: biological_processes
    description: Biological processes illuminated by the experiment.
    examples:
    - object:
        id: GO:0140999
        label: histone H3K4 trimethyltransferase activity
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Experiment
    domain_of:
    - Experiment
    range: Term
    multivalued: true