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Class: Analysis

Represents the computational processing applied to data from a sequencing experiment, or from another analysis. This can be described at the level of individual analysis steps in a workflow/pipeline, or more generally for the workflow/pipeline as a whole.

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

 classDiagram
    class Analysis
    click Analysis href "../Analysis/"
      Analysis : analysis_description

      Analysis : analysis_external_id

      Analysis : analysis_id

      Analysis : analysis_input_sources





        Analysis --> "1..*" InputSource : analysis_input_sources
        click InputSource href "../InputSource/"



      Analysis : analysis_label

      Analysis : analysis_main_tool





        Analysis --> "0..1" Any : analysis_main_tool
        click Any href "../Any/"



      Analysis : analysis_main_tool_version

      Analysis : analysis_protocol

      Analysis : analysis_study_ref

      Analysis : analysis_type





        Analysis --> "1" Term : analysis_type
        click Term href "../Term/"



      Analysis : analysis_workflow

Example

Example JSON 
{
  "analysis_description": "ENCODE3 ChIP-seq pipeline on GRCH38 with replicated peak calling using MACS.",
  "analysis_external_id": "encode:ENCAN718KHT",
  "analysis_id": "analysis:ENCAN718KHT",
  "analysis_input_sources": [
    {
      "biological_replicate_labels": [
        "1",
        "2"
      ],
      "inputsource_ref": "experiment:ENCSR000DPJ",
      "qualified_relation": "prov:wasInformedBy",
      "technical_replicate_labels": [
        "1_1",
        "2_1"
      ]
    },
    {
      "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": "https://bioschemas.org/FormalParameter",
      "technical_replicate_labels": [
        "1_1",
        "2_1"
      ]
    }
  ],
  "analysis_label": "ENCODE3 ChIP-seq pipeline, GRCH38, replicated peak calling",
  "analysis_main_tool": "biotools:macs",
  "analysis_main_tool_version": "2.10",
  "analysis_protocol": "https://www.encodeproject.org/documents/7009beb8-340b-4e71-b9db-53bb020c7fe2/@@download/attachment/ChIP-seq_pipeline_overview.pdf",
  "analysis_study_ref": "study:S-EPMC7391744",
  "analysis_type": {
    "id": "edam:operation_3222",
    "label": "Peak calling"
  },
  "analysis_workflow": "encode:ENCPL272XAE"
}

Slots

Name Cardinality and Range Description Inheritance
analysis_external_id 0..1
Curie		 External, globally unique identifier for the experiment. direct
analysis_id 1
Curie		 Internal identifier for the experiment (unique within the metadata deposit). direct
analysis_label 1
String		 A human-readable description of the analysis, short enough to be used for listings within software user interfaces, tables, illustration legends, etc. direct
analysis_description 0..1
String		 Human-readable description of the analysis. direct
analysis_study_ref 0..1
Curie		 Internal reference to the study within which the analysis has been carried out. direct
analysis_input_sources 1..*
InputSource		 External or internal references to sources for the input data analyzed. Internal references should lead to FileCollection, File, Experiment, or Analysis objects. direct
analysis_type 1
Term		 The type of analysis carried out. direct
analysis_main_tool 0..1
Any or 
String or 
Curie		 Main software tool used for the analysis. direct
analysis_main_tool_version 0..1
String		 Version of the main software tool used for the analysis. direct
analysis_protocol 0..1
Uriorcurie		 Document describing the analysis protocol that was followed. direct
analysis_workflow 0..1
Uriorcurie		 External reference to the analysis workflow, with availability in at least one machine-operable form (e.g. CWL, Nextflow, ...). direct

Usages

used by used in type used
Bundle analyses range Analysis

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

LinkML Source

Direct

name: Analysis
description: Represents the computational processing applied to data from a sequencing
  experiment, or from another analysis. This can be described at the level of individual
  analysis steps in a workflow/pipeline, or more generally for the workflow/pipeline
  as a whole.
from_schema: https://w3id.org/fga-wg/schema/bundle
slots:
- analysis_external_id
- analysis_id
- analysis_label
- analysis_description
- analysis_study_ref
- analysis_input_sources
- analysis_type
- analysis_main_tool
- analysis_main_tool_version
- analysis_protocol
- analysis_workflow

Induced

name: Analysis
description: Represents the computational processing applied to data from a sequencing
  experiment, or from another analysis. This can be described at the level of individual
  analysis steps in a workflow/pipeline, or more generally for the workflow/pipeline
  as a whole.
from_schema: https://w3id.org/fga-wg/schema/bundle
attributes:
  analysis_external_id:
    name: analysis_external_id
    description: External, globally unique identifier for the experiment.
    examples:
    - value: encode:ENCAN718KHT
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Analysis
    domain_of:
    - Analysis
    range: curie
  analysis_id:
    name: analysis_id
    description: 'Internal identifier for the experiment (unique within the metadata
      deposit). '
    examples:
    - value: analysis:ENCAN718KHT
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    identifier: true
    owner: Analysis
    domain_of:
    - Analysis
    range: curie
    required: true
  analysis_label:
    name: analysis_label
    description: A human-readable description of the analysis, short enough to be
      used for listings within software user interfaces, tables, illustration legends,
      etc.
    examples:
    - value: ENCODE3 ChIP-seq pipeline, GRCH38, replicated peak calling
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Analysis
    domain_of:
    - Analysis
    range: string
    required: true
    pattern: ^.{1,60}$
  analysis_description:
    name: analysis_description
    description: Human-readable description of the analysis.
    examples:
    - value: ENCODE3 ChIP-seq pipeline on GRCH38 with replicated peak calling using
        MACS.
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Analysis
    domain_of:
    - Analysis
    range: string
  analysis_study_ref:
    name: analysis_study_ref
    description: Internal reference to the study within which the analysis has been
      carried out.
    examples:
    - value: study:S-EPMC7391744
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Analysis
    domain_of:
    - Analysis
    range: curie
  analysis_input_sources:
    name: analysis_input_sources
    description: External or internal references to sources for the input data analyzed.
      Internal references should lead to FileCollection, File, Experiment, or Analysis
      objects.
    examples:
    - object:
        inputsource_ref: experiment:ENCSR000DPJ
        qualified_relation: prov:wasInformedBy
        biological_replicate_labels:
        - '1'
        - '2'
        technical_replicate_labels:
        - '1_1'
        - '2_1'
    - object:
        inputsource_external_ref: https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15
        qualified_relation: https://bioschemas.org/FormalParameter
        biological_replicate_labels:
        - '1'
        - '2'
        technical_replicate_labels:
        - '1_1'
        - '2_1'
        date_of_retrieval: '2016-04-19'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Analysis
    domain_of:
    - Analysis
    range: InputSource
    required: true
    multivalued: true
  analysis_type:
    name: analysis_type
    description: The type of analysis carried out.
    examples:
    - object:
        id: edam:operation_3222
        label: Peak calling
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Analysis
    domain_of:
    - Analysis
    range: Term
    required: true
  analysis_main_tool:
    name: analysis_main_tool
    description: Main software tool used for the analysis.
    examples:
    - value: biotools:macs
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Analysis
    domain_of:
    - Analysis
    range: Any
    any_of:
    - range: string
    - range: curie
  analysis_main_tool_version:
    name: analysis_main_tool_version
    description: Version of the main software tool used for the analysis.
    examples:
    - value: '2.10'
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Analysis
    domain_of:
    - Analysis
    range: string
  analysis_protocol:
    name: analysis_protocol
    description: Document describing the analysis protocol that was followed.
    examples:
    - value: https://www.encodeproject.org/documents/7009beb8-340b-4e71-b9db-53bb020c7fe2/@@download/attachment/ChIP-seq_pipeline_overview.pdf
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Analysis
    domain_of:
    - Analysis
    range: uriorcurie
  analysis_workflow:
    name: analysis_workflow
    description: External reference to the analysis workflow, with availability in
      at least one machine-operable form (e.g. CWL, Nextflow, ...).
    examples:
    - value: encode:ENCPL272XAE
    from_schema: https://w3id.org/fga-wg/schema/bundle
    rank: 1000
    owner: Analysis
    domain_of:
    - Analysis
    range: uriorcurie