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Class: WorkflowRun

A computational processing workflow execution

URI: lambdaber:WorkflowRun

classDiagram class WorkflowRun click WorkflowRun href "../WorkflowRun/" NamedThing <|-- WorkflowRun click NamedThing href "../NamedThing/" WorkflowRun : additional_software WorkflowRun : completed_at WorkflowRun : compute_resources WorkflowRun --> "0..1" ComputeResources : compute_resources click ComputeResources href "../ComputeResources/" WorkflowRun : deposited_to_pdb WorkflowRun : description WorkflowRun : experiment_id WorkflowRun : id WorkflowRun : indexer_module WorkflowRun : integrator_module WorkflowRun : ligands_cofactors WorkflowRun : ncs_used WorkflowRun : number_of_waters WorkflowRun : outlier_rejection_method WorkflowRun : output_files WorkflowRun --> "*" DataFile : output_files click DataFile href "../DataFile/" WorkflowRun : parameters_file_path WorkflowRun : pdb_id WorkflowRun : phasing_method WorkflowRun --> "0..1" PhasingMethodEnum : phasing_method click PhasingMethodEnum href "../PhasingMethodEnum/" WorkflowRun : processing_level WorkflowRun : processing_notes WorkflowRun : processing_parameters WorkflowRun : refinement_resolution_a WorkflowRun : restraints_other WorkflowRun : scaler_module WorkflowRun : search_model_pdb_id WorkflowRun : software_name WorkflowRun : software_version WorkflowRun : started_at WorkflowRun : title WorkflowRun : tls_used WorkflowRun : validation_report_path WorkflowRun : workflow_code WorkflowRun : workflow_type WorkflowRun --> "1" WorkflowTypeEnum : workflow_type click WorkflowTypeEnum href "../WorkflowTypeEnum/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
workflow_code 1
String		 Human-friendly identifier for the computational workflow run (e direct
workflow_type 1
WorkflowTypeEnum		 Type of processing workflow direct
experiment_id 1
String		 Reference to the source experiment direct
processing_level 0..1
Integer		 Processing level (0=raw, 1=corrected, 2=derived, 3=model) direct
software_name 1
String		 Software used for processing direct
software_version 0..1
String		 Software version direct
additional_software 0..1
String		 Additional software used in pipeline direct
processing_parameters 0..1
String		 Parameters used in processing direct
parameters_file_path 0..1
String		 Path to parameters file or text of key parameters direct
indexer_module 0..1
String		 Indexing module used (e direct
integrator_module 0..1
String		 Integration module used direct
scaler_module 0..1
String		 Scaling module used (e direct
outlier_rejection_method 0..1
String		 Method for rejecting outlier reflections direct
phasing_method 0..1
PhasingMethodEnum		 Phasing method used for X-ray crystallography structure determination direct
search_model_pdb_id 0..1
String		 PDB ID of search model for molecular replacement direct
tls_used 0..1
Boolean		 Whether TLS (Translation/Libration/Screw) refinement was used direct
ncs_used 0..1
Boolean		 Whether Non-Crystallographic Symmetry restraints were used direct
restraints_other 0..1
String		 Other restraints applied during refinement direct
ligands_cofactors 0..1
String		 Ligands or cofactors modeled in the structure direct
number_of_waters 0..1
Integer		 Number of water molecules modeled direct
refinement_resolution_a 0..1
Float		 Resolution cutoff used for refinement in Angstroms direct
deposited_to_pdb 0..1
Boolean		 Whether structure was deposited to PDB direct
pdb_id 0..1
String		 PDB accession code if deposited direct
validation_report_path 0..1
String		 Path to validation report direct
processing_notes 0..1
String		 Additional notes about processing direct
compute_resources 0..1
ComputeResources		 Computational resources used direct
started_at 0..1
String		 Workflow start time direct
completed_at 0..1
String		 Workflow completion time direct
output_files *
DataFile		 Output files generated direct
id 1
Uriorcurie		 Globally unique identifier as an IRI or CURIE for machine processing and exte... NamedThing
title 0..1
String		 NamedThing
description 0..1
String		 NamedThing

Usages

used by used in type used
Study workflow_runs range WorkflowRun

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/lambda-ber-schema/

Mappings

Mapping Type Mapped Value
self lambdaber:WorkflowRun
native lambdaber:WorkflowRun

LinkML Source

Direct

name: WorkflowRun
description: A computational processing workflow execution
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  workflow_code:
    name: workflow_code
    description: Human-friendly identifier for the computational workflow run (e.g.,
      'MOTION-CORR-RUN-001', 'RELION-REFINE-240815'). Used for tracking processing
      pipelines and computational provenance.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    required: true
  workflow_type:
    name: workflow_type
    description: Type of processing workflow
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: WorkflowTypeEnum
    required: true
  experiment_id:
    name: experiment_id
    description: Reference to the source experiment
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: string
    required: true
  processing_level:
    name: processing_level
    description: Processing level (0=raw, 1=corrected, 2=derived, 3=model)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: integer
    minimum_value: 0
    maximum_value: 4
  software_name:
    name: software_name
    description: Software used for processing
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    required: true
  software_version:
    name: software_version
    description: Software version
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  additional_software:
    name: additional_software
    description: Additional software used in pipeline
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  processing_parameters:
    name: processing_parameters
    description: Parameters used in processing
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  parameters_file_path:
    name: parameters_file_path
    description: Path to parameters file or text of key parameters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  indexer_module:
    name: indexer_module
    description: Indexing module used (e.g., MOSFLM, XDS)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  integrator_module:
    name: integrator_module
    description: Integration module used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  scaler_module:
    name: scaler_module
    description: Scaling module used (e.g., AIMLESS, SCALA)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  outlier_rejection_method:
    name: outlier_rejection_method
    description: Method for rejecting outlier reflections
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  phasing_method:
    name: phasing_method
    description: Phasing method used for X-ray crystallography structure determination
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: PhasingMethodEnum
  search_model_pdb_id:
    name: search_model_pdb_id
    description: PDB ID of search model for molecular replacement
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  tls_used:
    name: tls_used
    description: Whether TLS (Translation/Libration/Screw) refinement was used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: boolean
  ncs_used:
    name: ncs_used
    description: Whether Non-Crystallographic Symmetry restraints were used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: boolean
  restraints_other:
    name: restraints_other
    description: Other restraints applied during refinement
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  ligands_cofactors:
    name: ligands_cofactors
    description: Ligands or cofactors modeled in the structure
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  number_of_waters:
    name: number_of_waters
    description: Number of water molecules modeled
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: integer
  refinement_resolution_a:
    name: refinement_resolution_a
    description: Resolution cutoff used for refinement in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
  deposited_to_pdb:
    name: deposited_to_pdb
    description: Whether structure was deposited to PDB
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: boolean
  pdb_id:
    name: pdb_id
    description: PDB accession code if deposited
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  validation_report_path:
    name: validation_report_path
    description: Path to validation report
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  processing_notes:
    name: processing_notes
    description: Additional notes about processing
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
  compute_resources:
    name: compute_resources
    description: Computational resources used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: ComputeResources
  started_at:
    name: started_at
    description: Workflow start time
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: string
  completed_at:
    name: completed_at
    description: Workflow completion time
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: string
  output_files:
    name: output_files
    description: Output files generated
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: DataFile
    multivalued: true

Induced

name: WorkflowRun
description: A computational processing workflow execution
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  workflow_code:
    name: workflow_code
    description: Human-friendly identifier for the computational workflow run (e.g.,
      'MOTION-CORR-RUN-001', 'RELION-REFINE-240815'). Used for tracking processing
      pipelines and computational provenance.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: workflow_code
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
    required: true
  workflow_type:
    name: workflow_type
    description: Type of processing workflow
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: workflow_type
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: WorkflowTypeEnum
    required: true
  experiment_id:
    name: experiment_id
    description: Reference to the source experiment
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: experiment_id
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
    required: true
  processing_level:
    name: processing_level
    description: Processing level (0=raw, 1=corrected, 2=derived, 3=model)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: processing_level
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: integer
    minimum_value: 0
    maximum_value: 4
  software_name:
    name: software_name
    description: Software used for processing
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: software_name
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
    required: true
  software_version:
    name: software_version
    description: Software version
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: software_version
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  additional_software:
    name: additional_software
    description: Additional software used in pipeline
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: additional_software
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  processing_parameters:
    name: processing_parameters
    description: Parameters used in processing
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: processing_parameters
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  parameters_file_path:
    name: parameters_file_path
    description: Path to parameters file or text of key parameters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: parameters_file_path
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  indexer_module:
    name: indexer_module
    description: Indexing module used (e.g., MOSFLM, XDS)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: indexer_module
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  integrator_module:
    name: integrator_module
    description: Integration module used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: integrator_module
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  scaler_module:
    name: scaler_module
    description: Scaling module used (e.g., AIMLESS, SCALA)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: scaler_module
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  outlier_rejection_method:
    name: outlier_rejection_method
    description: Method for rejecting outlier reflections
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: outlier_rejection_method
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  phasing_method:
    name: phasing_method
    description: Phasing method used for X-ray crystallography structure determination
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: phasing_method
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: PhasingMethodEnum
  search_model_pdb_id:
    name: search_model_pdb_id
    description: PDB ID of search model for molecular replacement
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: search_model_pdb_id
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  tls_used:
    name: tls_used
    description: Whether TLS (Translation/Libration/Screw) refinement was used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: tls_used
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: boolean
  ncs_used:
    name: ncs_used
    description: Whether Non-Crystallographic Symmetry restraints were used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: ncs_used
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: boolean
  restraints_other:
    name: restraints_other
    description: Other restraints applied during refinement
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: restraints_other
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  ligands_cofactors:
    name: ligands_cofactors
    description: Ligands or cofactors modeled in the structure
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: ligands_cofactors
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  number_of_waters:
    name: number_of_waters
    description: Number of water molecules modeled
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: number_of_waters
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: integer
  refinement_resolution_a:
    name: refinement_resolution_a
    description: Resolution cutoff used for refinement in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: refinement_resolution_a
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
  deposited_to_pdb:
    name: deposited_to_pdb
    description: Whether structure was deposited to PDB
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: deposited_to_pdb
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: boolean
  pdb_id:
    name: pdb_id
    description: PDB accession code if deposited
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: pdb_id
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  validation_report_path:
    name: validation_report_path
    description: Path to validation report
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: validation_report_path
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  processing_notes:
    name: processing_notes
    description: Additional notes about processing
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: processing_notes
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  compute_resources:
    name: compute_resources
    description: Computational resources used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: compute_resources
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: ComputeResources
  started_at:
    name: started_at
    description: Workflow start time
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: started_at
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  completed_at:
    name: completed_at
    description: Workflow completion time
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: completed_at
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: string
  output_files:
    name: output_files
    description: Output files generated
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: output_files
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: DataFile
    multivalued: true
  id:
    name: id
    description: Globally unique identifier as an IRI or CURIE for machine processing
      and external references. Used for linking data across systems and semantic web
      integration.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    identifier: true
    alias: id
    owner: WorkflowRun
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
  title:
    name: title
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: WorkflowRun
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: WorkflowRun
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string