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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 : anomalous_completeness WorkflowRun : anomalous_multiplicity WorkflowRun : cc_anomalous WorkflowRun : cc_half WorkflowRun : clashscore WorkflowRun : completed_at WorkflowRun : completeness_percent WorkflowRun : compute_resources WorkflowRun --> "0..1" ComputeResources : compute_resources click ComputeResources href "../ComputeResources/" WorkflowRun : ctf_estimation_params WorkflowRun --> "0..1" CTFEstimationParameters : ctf_estimation_params click CTFEstimationParameters href "../CTFEstimationParameters/" WorkflowRun : deposited_to_pdb WorkflowRun : description WorkflowRun : experiment_id WorkflowRun : fsc_curve WorkflowRun --> "0..1" FSCCurve : fsc_curve click FSCCurve href "../FSCCurve/" WorkflowRun : i_over_sigma WorkflowRun : id WorkflowRun : indexer_module WorkflowRun : integrator_module WorkflowRun : ispyb_auto_proc_program_id WorkflowRun : ispyb_auto_proc_scaling_id WorkflowRun : ligands_cofactors WorkflowRun : motion_correction_params WorkflowRun --> "0..1" MotionCorrectionParameters : motion_correction_params click MotionCorrectionParameters href "../MotionCorrectionParameters/" WorkflowRun : multiplicity WorkflowRun : n_total_observations WorkflowRun : n_total_unique 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 : particle_picking_params WorkflowRun --> "0..1" ParticlePickingParameters : particle_picking_params click ParticlePickingParameters href "../ParticlePickingParameters/" 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 : r_anomalous WorkflowRun : ramachandran_favored WorkflowRun : ramachandran_outliers WorkflowRun : refinement_params WorkflowRun --> "0..1" RefinementParameters : refinement_params click RefinementParameters href "../RefinementParameters/" WorkflowRun : refinement_resolution_a WorkflowRun : resolution_high WorkflowRun : resolution_low WorkflowRun : restraints_other WorkflowRun : rfree WorkflowRun : rmerge WorkflowRun : rmsd_angles WorkflowRun : rmsd_bonds WorkflowRun : rpim WorkflowRun : rwork WorkflowRun : scaler_module WorkflowRun : search_model_pdb_id WorkflowRun : sig_anomalous WorkflowRun : software_name WorkflowRun : software_version WorkflowRun : space_group WorkflowRun : started_at WorkflowRun : title WorkflowRun : tls_used WorkflowRun : unit_cell_a WorkflowRun : unit_cell_alpha WorkflowRun : unit_cell_b WorkflowRun : unit_cell_beta WorkflowRun : unit_cell_c WorkflowRun : unit_cell_gamma WorkflowRun : validation_report_path WorkflowRun : wilson_b_factor 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
space_group 0..1
String		 Crystallographic space group direct
unit_cell_a 0..1
Float		 Unit cell parameter a direct
unit_cell_b 0..1
Float		 Unit cell parameter b direct
unit_cell_c 0..1
Float		 Unit cell parameter c direct
unit_cell_alpha 0..1
Float		 Unit cell angle alpha direct
unit_cell_beta 0..1
Float		 Unit cell angle beta direct
unit_cell_gamma 0..1
Float		 Unit cell angle gamma direct
resolution_high 0..1
Float		 High resolution limit direct
resolution_low 0..1
Float		 Low resolution limit direct
rmerge 0..1
Float		 Rmerge - merge R-factor direct
rpim 0..1
Float		 Rpim - precision-indicating merging R-factor direct
cc_half 0..1
Float		 Half-set correlation coefficient CC(1/2) direct
completeness_percent 0..1
Float		 Data completeness percentage direct
i_over_sigma 0..1
Float		 Mean I/sigma(I) - signal to noise ratio direct
wilson_b_factor 0..1
Float		 Wilson B-factor direct
multiplicity 0..1
Float		 Data multiplicity (redundancy) direct
anomalous_completeness 0..1
Float		 Completeness of anomalous data as percentage direct
anomalous_multiplicity 0..1
Float		 Multiplicity of anomalous data direct
cc_anomalous 0..1
Float		 Anomalous correlation coefficient direct
r_anomalous 0..1
Float		 Anomalous R-factor direct
sig_anomalous 0..1
Float		 Mean anomalous difference signal direct
n_total_observations 0..1
Integer		 Total number of observations (before merging) direct
n_total_unique 0..1
Integer		 Total number of unique reflections direct
ispyb_auto_proc_program_id 0..1
Integer		 ISPyB AutoProcProgram direct
ispyb_auto_proc_scaling_id 0..1
Integer		 ISPyB AutoProcScaling direct
rwork 0..1
Float		 Refinement R-factor (working set) direct
rfree 0..1
Float		 R-free (test set) direct
rmsd_bonds 0..1
Float		 RMSD from ideal bond lengths direct
rmsd_angles 0..1
Float		 RMSD from ideal bond angles direct
ramachandran_favored 0..1
Float		 Percentage of residues in favored Ramachandran regions direct
ramachandran_outliers 0..1
Float		 Percentage of Ramachandran outliers direct
clashscore 0..1
Float		 MolProbity clashscore 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
motion_correction_params 0..1
MotionCorrectionParameters		 Motion correction specific parameters direct
ctf_estimation_params 0..1
CTFEstimationParameters		 CTF estimation specific parameters direct
particle_picking_params 0..1
ParticlePickingParameters		 Particle picking specific parameters direct
refinement_params 0..1
RefinementParameters		 3D refinement specific parameters direct
fsc_curve 0..1
FSCCurve		 Fourier Shell Correlation curve data 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		 A human-readable name or title for this entity NamedThing
description 0..1
String		 A detailed textual description of this entity 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
  space_group:
    name: space_group
    description: Crystallographic space group
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Space_Group
    - mmCIF:_symmetry.space_group_name_H-M
    - ispyb:AutoProcScaling.spaceGroup
    rank: 1000
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: string
  unit_cell_a:
    name: unit_cell_a
    description: Unit cell parameter a
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_a
    - mmCIF:_cell.length_a
    rank: 1000
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: Ao
  unit_cell_b:
    name: unit_cell_b
    description: Unit cell parameter b
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_b
    - mmCIF:_cell.length_b
    rank: 1000
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: Ao
  unit_cell_c:
    name: unit_cell_c
    description: Unit cell parameter c
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_c
    - mmCIF:_cell.length_c
    rank: 1000
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: Ao
  unit_cell_alpha:
    name: unit_cell_alpha
    description: Unit cell angle alpha
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_alpha
    - mmCIF:_cell.angle_alpha
    rank: 1000
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: deg
  unit_cell_beta:
    name: unit_cell_beta
    description: Unit cell angle beta
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_beta
    - mmCIF:_cell.angle_beta
    rank: 1000
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: deg
  unit_cell_gamma:
    name: unit_cell_gamma
    description: Unit cell angle gamma
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_gamma
    - mmCIF:_cell.angle_gamma
    rank: 1000
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: deg
  resolution_high:
    name: resolution_high
    description: High resolution limit
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Resolution_High_A
    - mmCIF:_reflns.d_resolution_high
    - ispyb:AutoProcScalingStatistics.resolutionLimitHigh
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: Ao
  resolution_low:
    name: resolution_low
    description: Low resolution limit
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Resolution_Low_A
    - mmCIF:_reflns.d_resolution_low
    - ispyb:AutoProcScalingStatistics.resolutionLimitLow
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: Ao
  rmerge:
    name: rmerge
    description: Rmerge - merge R-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Rmerge
    - mmCIF:_reflns.pdbx_Rmerge_I_obs
    - ispyb:AutoProcScalingStatistics.rMerge
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
  rpim:
    name: rpim
    description: Rpim - precision-indicating merging R-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Rpim
    - mmCIF:_reflns.pdbx_Rpim_I_all
    - ispyb:AutoProcScalingStatistics.rPim
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
  cc_half:
    name: cc_half
    description: Half-set correlation coefficient CC(1/2)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:CC_half
    - mmCIF:_reflns.pdbx_CC_half
    - ispyb:AutoProcScalingStatistics.ccHalf
    rank: 1000
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
  completeness_percent:
    name: completeness_percent
    description: Data completeness percentage
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Completeness
    - mmCIF:_reflns.percent_possible_obs
    - ispyb:AutoProcScalingStatistics.completeness
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: '%'
  i_over_sigma:
    name: i_over_sigma
    description: Mean I/sigma(I) - signal to noise ratio
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:I_over_sigma
    - mmCIF:_reflns.pdbx_netI_over_sigmaI
    - ispyb:AutoProcScalingStatistics.meanIOverSigI
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
  wilson_b_factor:
    name: wilson_b_factor
    description: Wilson B-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Wilson_B
    - mmCIF:_reflns.B_iso_Wilson_estimate
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: Ao2
  multiplicity:
    name: multiplicity
    description: Data multiplicity (redundancy)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Multiplicity
    - mmCIF:_reflns.pdbx_redundancy
    - ispyb:AutoProcScalingStatistics.multiplicity
    rank: 1000
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
  anomalous_completeness:
    name: anomalous_completeness
    description: Completeness of anomalous data as percentage
    comments:
    - Completeness of Bijvoet pairs
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.anomalousCompleteness
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: '%'
  anomalous_multiplicity:
    name: anomalous_multiplicity
    description: Multiplicity of anomalous data
    comments:
    - Redundancy of Bijvoet pairs
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.anomalousMultiplicity
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
  cc_anomalous:
    name: cc_anomalous
    description: Anomalous correlation coefficient
    comments:
    - Correlation coefficient between Bijvoet pairs
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.ccAno
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
  r_anomalous:
    name: r_anomalous
    description: Anomalous R-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.rAnom
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
  sig_anomalous:
    name: sig_anomalous
    description: Mean anomalous difference signal
    comments:
    - Mean |F(+) - F(-)|/sigma
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.sigAno
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
  n_total_observations:
    name: n_total_observations
    description: Total number of observations (before merging)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.nTotalObservations
    rank: 1000
    domain_of:
    - WorkflowRun
    range: integer
  n_total_unique:
    name: n_total_unique
    description: Total number of unique reflections
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.nTotalUniqueObservations
    rank: 1000
    domain_of:
    - WorkflowRun
    range: integer
  ispyb_auto_proc_program_id:
    name: ispyb_auto_proc_program_id
    description: ISPyB AutoProcProgram.autoProcProgramId
    comments:
    - Links to ISPyB processing program record
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcProgram.autoProcProgramId
    rank: 1000
    domain_of:
    - WorkflowRun
    range: integer
  ispyb_auto_proc_scaling_id:
    name: ispyb_auto_proc_scaling_id
    description: ISPyB AutoProcScaling.autoProcScalingId
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScaling.autoProcScalingId
    rank: 1000
    domain_of:
    - WorkflowRun
    range: integer
  rwork:
    name: rwork
    description: Refinement R-factor (working set)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Rwork
    - mmCIF:_refine.ls_R_factor_R_work
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
  rfree:
    name: rfree
    description: R-free (test set)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Rfree
    - mmCIF:_refine.ls_R_factor_R_free
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
  rmsd_bonds:
    name: rmsd_bonds
    description: RMSD from ideal bond lengths
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:RMSD_bonds
    - mmCIF:_refine.ls_d_res_high
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: Ao
  rmsd_angles:
    name: rmsd_angles
    description: RMSD from ideal bond angles
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:RMSD_angles
    - mmCIF:_refine.ls_d_res_low
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: deg
  ramachandran_favored:
    name: ramachandran_favored
    description: Percentage of residues in favored Ramachandran regions
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Ramachandran_Favored
    - mmCIF:_refine.pdbx_overall_ESU_R
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: '%'
  ramachandran_outliers:
    name: ramachandran_outliers
    description: Percentage of Ramachandran outliers
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Ramachandran_Outliers
    - mmCIF:_refine.pdbx_overall_ESU_R_Free
    rank: 1000
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: '%'
  clashscore:
    name: clashscore
    description: MolProbity clashscore
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Clashscore
    rank: 1000
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
  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
  motion_correction_params:
    name: motion_correction_params
    description: Motion correction specific parameters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: MotionCorrectionParameters
  ctf_estimation_params:
    name: ctf_estimation_params
    description: CTF estimation specific parameters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: CTFEstimationParameters
  particle_picking_params:
    name: particle_picking_params
    description: Particle picking specific parameters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: ParticlePickingParameters
  refinement_params:
    name: refinement_params
    description: 3D refinement specific parameters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: RefinementParameters
  fsc_curve:
    name: fsc_curve
    description: Fourier Shell Correlation curve data
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - WorkflowRun
    range: FSCCurve
  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
  space_group:
    name: space_group
    description: Crystallographic space group
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Space_Group
    - mmCIF:_symmetry.space_group_name_H-M
    - ispyb:AutoProcScaling.spaceGroup
    rank: 1000
    alias: space_group
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: string
  unit_cell_a:
    name: unit_cell_a
    description: Unit cell parameter a
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_a
    - mmCIF:_cell.length_a
    rank: 1000
    alias: unit_cell_a
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: Ao
  unit_cell_b:
    name: unit_cell_b
    description: Unit cell parameter b
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_b
    - mmCIF:_cell.length_b
    rank: 1000
    alias: unit_cell_b
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: Ao
  unit_cell_c:
    name: unit_cell_c
    description: Unit cell parameter c
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_c
    - mmCIF:_cell.length_c
    rank: 1000
    alias: unit_cell_c
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: Ao
  unit_cell_alpha:
    name: unit_cell_alpha
    description: Unit cell angle alpha
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_alpha
    - mmCIF:_cell.angle_alpha
    rank: 1000
    alias: unit_cell_alpha
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: deg
  unit_cell_beta:
    name: unit_cell_beta
    description: Unit cell angle beta
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_beta
    - mmCIF:_cell.angle_beta
    rank: 1000
    alias: unit_cell_beta
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: deg
  unit_cell_gamma:
    name: unit_cell_gamma
    description: Unit cell angle gamma
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Unit_Cell_gamma
    - mmCIF:_cell.angle_gamma
    rank: 1000
    alias: unit_cell_gamma
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: deg
  resolution_high:
    name: resolution_high
    description: High resolution limit
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Resolution_High_A
    - mmCIF:_reflns.d_resolution_high
    - ispyb:AutoProcScalingStatistics.resolutionLimitHigh
    rank: 1000
    alias: resolution_high
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: Ao
  resolution_low:
    name: resolution_low
    description: Low resolution limit
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Resolution_Low_A
    - mmCIF:_reflns.d_resolution_low
    - ispyb:AutoProcScalingStatistics.resolutionLimitLow
    rank: 1000
    alias: resolution_low
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: Ao
  rmerge:
    name: rmerge
    description: Rmerge - merge R-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Rmerge
    - mmCIF:_reflns.pdbx_Rmerge_I_obs
    - ispyb:AutoProcScalingStatistics.rMerge
    rank: 1000
    alias: rmerge
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
  rpim:
    name: rpim
    description: Rpim - precision-indicating merging R-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Rpim
    - mmCIF:_reflns.pdbx_Rpim_I_all
    - ispyb:AutoProcScalingStatistics.rPim
    rank: 1000
    alias: rpim
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
  cc_half:
    name: cc_half
    description: Half-set correlation coefficient CC(1/2)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:CC_half
    - mmCIF:_reflns.pdbx_CC_half
    - ispyb:AutoProcScalingStatistics.ccHalf
    rank: 1000
    alias: cc_half
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
  completeness_percent:
    name: completeness_percent
    description: Data completeness percentage
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Completeness
    - mmCIF:_reflns.percent_possible_obs
    - ispyb:AutoProcScalingStatistics.completeness
    rank: 1000
    alias: completeness_percent
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: '%'
  i_over_sigma:
    name: i_over_sigma
    description: Mean I/sigma(I) - signal to noise ratio
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:I_over_sigma
    - mmCIF:_reflns.pdbx_netI_over_sigmaI
    - ispyb:AutoProcScalingStatistics.meanIOverSigI
    rank: 1000
    alias: i_over_sigma
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
  wilson_b_factor:
    name: wilson_b_factor
    description: Wilson B-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Wilson_B
    - mmCIF:_reflns.B_iso_Wilson_estimate
    rank: 1000
    alias: wilson_b_factor
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: Ao2
  multiplicity:
    name: multiplicity
    description: Data multiplicity (redundancy)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Multiplicity
    - mmCIF:_reflns.pdbx_redundancy
    - ispyb:AutoProcScalingStatistics.multiplicity
    rank: 1000
    alias: multiplicity
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
  anomalous_completeness:
    name: anomalous_completeness
    description: Completeness of anomalous data as percentage
    comments:
    - Completeness of Bijvoet pairs
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.anomalousCompleteness
    rank: 1000
    alias: anomalous_completeness
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: '%'
  anomalous_multiplicity:
    name: anomalous_multiplicity
    description: Multiplicity of anomalous data
    comments:
    - Redundancy of Bijvoet pairs
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.anomalousMultiplicity
    rank: 1000
    alias: anomalous_multiplicity
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
  cc_anomalous:
    name: cc_anomalous
    description: Anomalous correlation coefficient
    comments:
    - Correlation coefficient between Bijvoet pairs
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.ccAno
    rank: 1000
    alias: cc_anomalous
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
  r_anomalous:
    name: r_anomalous
    description: Anomalous R-factor
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.rAnom
    rank: 1000
    alias: r_anomalous
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
  sig_anomalous:
    name: sig_anomalous
    description: Mean anomalous difference signal
    comments:
    - Mean |F(+) - F(-)|/sigma
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.sigAno
    rank: 1000
    alias: sig_anomalous
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
  n_total_observations:
    name: n_total_observations
    description: Total number of observations (before merging)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.nTotalObservations
    rank: 1000
    alias: n_total_observations
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: integer
  n_total_unique:
    name: n_total_unique
    description: Total number of unique reflections
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScalingStatistics.nTotalUniqueObservations
    rank: 1000
    alias: n_total_unique
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: integer
  ispyb_auto_proc_program_id:
    name: ispyb_auto_proc_program_id
    description: ISPyB AutoProcProgram.autoProcProgramId
    comments:
    - Links to ISPyB processing program record
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcProgram.autoProcProgramId
    rank: 1000
    alias: ispyb_auto_proc_program_id
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: integer
  ispyb_auto_proc_scaling_id:
    name: ispyb_auto_proc_scaling_id
    description: ISPyB AutoProcScaling.autoProcScalingId
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:AutoProcScaling.autoProcScalingId
    rank: 1000
    alias: ispyb_auto_proc_scaling_id
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: integer
  rwork:
    name: rwork
    description: Refinement R-factor (working set)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Rwork
    - mmCIF:_refine.ls_R_factor_R_work
    rank: 1000
    alias: rwork
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
  rfree:
    name: rfree
    description: R-free (test set)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Rfree
    - mmCIF:_refine.ls_R_factor_R_free
    rank: 1000
    alias: rfree
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
  rmsd_bonds:
    name: rmsd_bonds
    description: RMSD from ideal bond lengths
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:RMSD_bonds
    - mmCIF:_refine.ls_d_res_high
    rank: 1000
    alias: rmsd_bonds
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: Ao
  rmsd_angles:
    name: rmsd_angles
    description: RMSD from ideal bond angles
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:RMSD_angles
    - mmCIF:_refine.ls_d_res_low
    rank: 1000
    alias: rmsd_angles
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: deg
  ramachandran_favored:
    name: ramachandran_favored
    description: Percentage of residues in favored Ramachandran regions
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Ramachandran_Favored
    - mmCIF:_refine.pdbx_overall_ESU_R
    rank: 1000
    alias: ramachandran_favored
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: '%'
  ramachandran_outliers:
    name: ramachandran_outliers
    description: Percentage of Ramachandran outliers
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Ramachandran_Outliers
    - mmCIF:_refine.pdbx_overall_ESU_R_Free
    rank: 1000
    alias: ramachandran_outliers
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: float
    unit:
      ucum_code: '%'
  clashscore:
    name: clashscore
    description: MolProbity clashscore
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Clashscore
    rank: 1000
    alias: clashscore
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    - QualityMetrics
    range: float
  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
  motion_correction_params:
    name: motion_correction_params
    description: Motion correction specific parameters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: motion_correction_params
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: MotionCorrectionParameters
  ctf_estimation_params:
    name: ctf_estimation_params
    description: CTF estimation specific parameters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: ctf_estimation_params
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: CTFEstimationParameters
  particle_picking_params:
    name: particle_picking_params
    description: Particle picking specific parameters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: particle_picking_params
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: ParticlePickingParameters
  refinement_params:
    name: refinement_params
    description: 3D refinement specific parameters
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: refinement_params
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: RefinementParameters
  fsc_curve:
    name: fsc_curve
    description: Fourier Shell Correlation curve data
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: fsc_curve
    owner: WorkflowRun
    domain_of:
    - WorkflowRun
    range: FSCCurve
  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
    description: A human-readable name or title for this entity
    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
    description: A detailed textual description of this entity
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: WorkflowRun
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string