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Class: ExperimentRun

An experimental data collection session

URI: lambdaber:ExperimentRun

classDiagram class ExperimentRun click ExperimentRun href "../ExperimentRun/" NamedThing <|-- ExperimentRun click NamedThing href "../NamedThing/" ExperimentRun : acquisition_software ExperimentRun : acquisition_software_version ExperimentRun : astigmatism_target ExperimentRun : autoloader_slot ExperimentRun : beam_center_x ExperimentRun : beam_center_y ExperimentRun : beamline ExperimentRun : calibrated_pixel_size ExperimentRun : camera_binning ExperimentRun : coma ExperimentRun : data_collection_strategy ExperimentRun --> "0..1" DataCollectionStrategy : data_collection_strategy click DataCollectionStrategy href "../DataCollectionStrategy/" ExperimentRun : defocus_range_increment ExperimentRun : defocus_range_max ExperimentRun : defocus_range_min ExperimentRun : defocus_target ExperimentRun : description ExperimentRun : detector_distance ExperimentRun : dose_rate ExperimentRun : end_time ExperimentRun : experiment_code ExperimentRun : experiment_date ExperimentRun : experimental_conditions ExperimentRun --> "0..1" ExperimentalConditions : experimental_conditions click ExperimentalConditions href "../ExperimentalConditions/" ExperimentRun : experimental_method ExperimentRun --> "0..1" ExperimentalMethodEnum : experimental_method click ExperimentalMethodEnum href "../ExperimentalMethodEnum/" ExperimentRun : exposure_time ExperimentRun : exposure_time_per_frame ExperimentRun : flux ExperimentRun : flux_end ExperimentRun : frames_per_movie ExperimentRun : holes_per_group ExperimentRun : id ExperimentRun : instrument_id ExperimentRun --> "1" Instrument : instrument_id click Instrument href "../Instrument/" ExperimentRun : ispyb_data_collection_id ExperimentRun : ispyb_session_id ExperimentRun : magnification ExperimentRun : number_of_images ExperimentRun : operator_id ExperimentRun : oscillation_angle ExperimentRun : pixel_size_x ExperimentRun : pixel_size_y ExperimentRun : processing_status ExperimentRun --> "0..1" ProcessingStatusEnum : processing_status click ProcessingStatusEnum href "../ProcessingStatusEnum/" ExperimentRun : quality_metrics ExperimentRun --> "0..1" QualityMetrics : quality_metrics click QualityMetrics href "../QualityMetrics/" ExperimentRun : raw_data_location ExperimentRun : resolution ExperimentRun : resolution_at_corner ExperimentRun : sample_id ExperimentRun : shots_per_hole ExperimentRun : slit_gap_horizontal ExperimentRun : slit_gap_vertical ExperimentRun : stage_tilt ExperimentRun : start_angle ExperimentRun : start_time ExperimentRun : synchrotron_mode ExperimentRun : technique ExperimentRun --> "1" TechniqueEnum : technique click TechniqueEnum href "../TechniqueEnum/" ExperimentRun : title ExperimentRun : total_dose ExperimentRun : total_exposure_time ExperimentRun : total_rotation ExperimentRun : transmission ExperimentRun : undulator_gap ExperimentRun : wavelength

Inheritance

Slots

Name Cardinality and Range Description Inheritance
experiment_code 1
String		 Human-friendly laboratory or facility identifier for the experiment (e direct
sample_id 1
String		 Reference to the sample being analyzed direct
instrument_id 1
Instrument		 Reference to the instrument used direct
experiment_date 0..1
String		 Date of the experiment direct
operator_id 0..1
String		 Identifier or name of the person who performed the experiment data collection... direct
technique 1
TechniqueEnum		 Technique used for data collection direct
experimental_method 0..1
ExperimentalMethodEnum		 Specific experimental method for structure determination (particularly for di... direct
experimental_conditions 0..1
ExperimentalConditions		 Environmental and experimental conditions direct
data_collection_strategy 0..1
DataCollectionStrategy		 Strategy for data collection direct
quality_metrics 0..1
QualityMetrics		 Quality metrics for the experiment direct
raw_data_location 0..1
String		 Location of raw data files direct
processing_status 0..1
ProcessingStatusEnum		 Current processing status direct
magnification 0..1
Integer		 Magnification used during data collection direct
calibrated_pixel_size 0..1
Float		 Calibrated pixel size in Angstroms per pixel direct
camera_binning 0..1
Float		 Camera binning factor direct
exposure_time_per_frame 0..1
Float		 Exposure time per frame in milliseconds direct
frames_per_movie 0..1
Integer		 Number of frames per movie direct
total_exposure_time 0..1
Float		 Total exposure time in milliseconds direct
total_dose 0..1
Float		 Total electron dose in e-/Angstrom^2 direct
dose_rate 0..1
Float		 Dose rate in e-/pixel/s or e-/Angstrom^2/s direct
defocus_target 0..1
Float		 Target defocus value in micrometers direct
defocus_range_min 0..1
Float		 Minimum defocus range in micrometers direct
defocus_range_max 0..1
Float		 Maximum defocus range in micrometers direct
defocus_range_increment 0..1
Float		 Defocus range increment in micrometers direct
astigmatism_target 0..1
Float		 Target astigmatism in Angstroms direct
coma 0..1
Float		 Coma aberration in nanometers direct
stage_tilt 0..1
Float		 Stage tilt angle in degrees direct
autoloader_slot 0..1
String		 Autoloader slot identifier direct
shots_per_hole 0..1
Integer		 Number of shots taken per hole direct
holes_per_group 0..1
Integer		 Number of holes per group direct
acquisition_software 0..1
String		 Acquisition software used (e direct
acquisition_software_version 0..1
String		 Version of acquisition software direct
wavelength 0..1
Float		 X-ray wavelength direct
oscillation_angle 0..1
Float		 Oscillation angle per image direct
start_angle 0..1
Float		 Starting rotation angle direct
number_of_images 0..1
Integer		 Total number of diffraction images collected direct
beam_center_x 0..1
Float		 Beam center X coordinate direct
beam_center_y 0..1
Float		 Beam center Y coordinate direct
detector_distance 0..1
Float		 Distance from sample to detector direct
pixel_size_x 0..1
Float		 Pixel size X dimension direct
pixel_size_y 0..1
Float		 Pixel size Y dimension direct
total_rotation 0..1
Float		 Total rotation range collected direct
beamline 0..1
String		 Beamline identifier (e direct
transmission 0..1
Float		 X-ray beam transmission as percentage (0-100) direct
flux 0..1
Float		 Photon flux at sample position in photons/second direct
flux_end 0..1
Float		 Photon flux at end of data collection in photons/second direct
slit_gap_horizontal 0..1
Float		 Horizontal slit gap aperture in micrometers direct
slit_gap_vertical 0..1
Float		 Vertical slit gap aperture in micrometers direct
undulator_gap 0..1
Float		 Undulator gap setting in millimeters direct
synchrotron_mode 0..1
String		 Synchrotron storage ring fill mode direct
exposure_time 0..1
Float		 Exposure time per image in seconds direct
start_time 0..1
String		 Data collection start timestamp direct
end_time 0..1
String		 Data collection end timestamp direct
resolution 0..1
Float		 Resolution at edge of detector in Angstroms direct
resolution_at_corner 0..1
Float		 Resolution at corner of detector in Angstroms direct
ispyb_data_collection_id 0..1
Integer		 ISPyB DataCollection direct
ispyb_session_id 0..1
Integer		 ISPyB BLSession 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 instrument_runs range ExperimentRun

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ExperimentRun
description: An experimental data collection session
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  experiment_code:
    name: experiment_code
    description: Human-friendly laboratory or facility identifier for the experiment
      (e.g., 'SIBYLS-2024-02-01-hetBGL', 'CRYOEM-RUN-240815-001'). Used for local
      tracking and cross-referencing within laboratory systems.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    required: true
  sample_id:
    name: sample_id
    description: Reference to the sample being analyzed
    from_schema: https://w3id.org/lambda-ber-schema/
    domain_of:
    - SamplePreparation
    - ExperimentRun
    range: string
    required: true
  instrument_id:
    name: instrument_id
    description: Reference to the instrument used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: Instrument
    required: true
  experiment_date:
    name: experiment_date
    description: Date of the experiment
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: string
  operator_id:
    name: operator_id
    description: Identifier or name of the person who performed the experiment data
      collection (e.g., 'jsmith', 'John Smith', or personnel ID)
    from_schema: https://w3id.org/lambda-ber-schema/
    domain_of:
    - SamplePreparation
    - ExperimentRun
    range: string
  technique:
    name: technique
    description: Technique used for data collection
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: TechniqueEnum
    required: true
  experimental_method:
    name: experimental_method
    description: Specific experimental method for structure determination (particularly
      for diffraction techniques)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    - BiophysicalProperty
    range: ExperimentalMethodEnum
  experimental_conditions:
    name: experimental_conditions
    description: Environmental and experimental conditions
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: ExperimentalConditions
  data_collection_strategy:
    name: data_collection_strategy
    description: Strategy for data collection
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: DataCollectionStrategy
  quality_metrics:
    name: quality_metrics
    description: Quality metrics for the experiment
    from_schema: https://w3id.org/lambda-ber-schema/
    domain_of:
    - Sample
    - ExperimentRun
    range: QualityMetrics
  raw_data_location:
    name: raw_data_location
    description: Location of raw data files
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
  processing_status:
    name: processing_status
    description: Current processing status
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: ProcessingStatusEnum
  magnification:
    name: magnification
    description: Magnification used during data collection
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    - OpticalImage
    range: integer
  calibrated_pixel_size:
    name: calibrated_pixel_size
    description: Calibrated pixel size in Angstroms per pixel
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  camera_binning:
    name: camera_binning
    description: Camera binning factor. This must be a positive float value (e.g.,
      1, 1.5, 2, 3).
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    minimum_value: 0.01
  exposure_time_per_frame:
    name: exposure_time_per_frame
    description: Exposure time per frame in milliseconds
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  frames_per_movie:
    name: frames_per_movie
    description: Number of frames per movie
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: integer
  total_exposure_time:
    name: total_exposure_time
    description: Total exposure time in milliseconds
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  total_dose:
    name: total_dose
    description: Total electron dose in e-/Angstrom^2
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    - DataCollectionStrategy
    range: float
  dose_rate:
    name: dose_rate
    description: Dose rate in e-/pixel/s or e-/Angstrom^2/s
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  defocus_target:
    name: defocus_target
    description: Target defocus value in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  defocus_range_min:
    name: defocus_range_min
    description: Minimum defocus range in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  defocus_range_max:
    name: defocus_range_max
    description: Maximum defocus range in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  defocus_range_increment:
    name: defocus_range_increment
    description: Defocus range increment in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  astigmatism_target:
    name: astigmatism_target
    description: Target astigmatism in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  coma:
    name: coma
    description: Coma aberration in nanometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  stage_tilt:
    name: stage_tilt
    description: Stage tilt angle in degrees
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
  autoloader_slot:
    name: autoloader_slot
    description: Autoloader slot identifier
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: string
  shots_per_hole:
    name: shots_per_hole
    description: Number of shots taken per hole
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: integer
  holes_per_group:
    name: holes_per_group
    description: Number of holes per group
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: integer
  acquisition_software:
    name: acquisition_software
    description: Acquisition software used (e.g., SerialEM, EPU, Leginon)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: string
  acquisition_software_version:
    name: acquisition_software_version
    description: Version of acquisition software
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ExperimentRun
    range: string
  wavelength:
    name: wavelength
    description: X-ray wavelength
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Wavelength
    - imgCIF:_diffrn_radiation_wavelength.wavelength
    - mmCIF:_diffrn_radiation_wavelength.wavelength
    - ispyb:DataCollection.wavelength
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: Ao
  oscillation_angle:
    name: oscillation_angle
    description: Oscillation angle per image
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Angle_increment
    - imgCIF:_diffrn_scan_axis.angle_increment
    - mmCIF:_diffrn_scan.angle_increment
    - ispyb:DataCollection.axisRange
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: deg
  start_angle:
    name: start_angle
    description: Starting rotation angle
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Start_angle
    - imgCIF:_diffrn_scan_axis.angle_start
    - ispyb:DataCollection.axisStart
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: deg
  number_of_images:
    name: number_of_images
    description: Total number of diffraction images collected
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Number_of_images
    - imgCIF:_diffrn_scan.frames
    - ispyb:DataCollection.numberOfImages
    rank: 1000
    domain_of:
    - ExperimentRun
    range: integer
  beam_center_x:
    name: beam_center_x
    description: Beam center X coordinate
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Beam_xy_x
    - imgCIF:_diffrn_detector.beam_centre_x
    - mmCIF:_diffrn_detector.beam_center_x
    - ispyb:DataCollection.xBeam
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: '[px]'
  beam_center_y:
    name: beam_center_y
    description: Beam center Y coordinate
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Beam_xy_y
    - imgCIF:_diffrn_detector.beam_centre_y
    - mmCIF:_diffrn_detector.beam_center_y
    - ispyb:DataCollection.yBeam
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: '[px]'
  detector_distance:
    name: detector_distance
    description: Distance from sample to detector
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Detector_distance
    - imgCIF:_diffrn_measurement.sample_detector_distance
    - mmCIF:_diffrn_detector.distance
    - ispyb:DataCollection.detectorDistance
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: mm
  pixel_size_x:
    name: pixel_size_x
    description: Pixel size X dimension
    comments:
    - 'imgCIF: _array_element_size.size[1]'
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Pixel_size_x
    - imgCIF:_array_element_size.size
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: um
  pixel_size_y:
    name: pixel_size_y
    description: Pixel size Y dimension
    comments:
    - 'imgCIF: _array_element_size.size[2]'
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Pixel_size_y
    - imgCIF:_array_element_size.size
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: um
  total_rotation:
    name: total_rotation
    description: Total rotation range collected
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Total_rotation_deg
    - imgCIF:_diffrn_scan_axis.angle_range
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: deg
  beamline:
    name: beamline
    description: Beamline identifier (e.g., FMX, AMX, 12.3.1)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Beamline
    - mmCIF:_diffrn_source.pdbx_synchrotron_beamline
    - ispyb:BLSession.beamLineName
    rank: 1000
    domain_of:
    - ExperimentRun
    range: string
  transmission:
    name: transmission
    description: X-ray beam transmission as percentage (0-100)
    comments:
    - Percentage of full beam intensity used
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.transmission
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    minimum_value: 0
    maximum_value: 100
    unit:
      ucum_code: '%'
  flux:
    name: flux
    description: Photon flux at sample position in photons/second
    comments:
    - Measured or calculated photon flux
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.flux
    rank: 1000
    domain_of:
    - ExperimentRun
    - XRFImage
    range: float
    unit:
      ucum_code: '{photons}/s'
  flux_end:
    name: flux_end
    description: Photon flux at end of data collection in photons/second
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.flux_end
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: '{photons}/s'
  slit_gap_horizontal:
    name: slit_gap_horizontal
    description: Horizontal slit gap aperture in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.slitGapHorizontal
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: um
  slit_gap_vertical:
    name: slit_gap_vertical
    description: Vertical slit gap aperture in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.slitGapVertical
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: um
  undulator_gap:
    name: undulator_gap
    description: Undulator gap setting in millimeters
    comments:
    - Primary undulator gap for beamlines with insertion devices
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.undulatorGap1
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: mm
  synchrotron_mode:
    name: synchrotron_mode
    description: Synchrotron storage ring fill mode
    comments:
    - e.g., 'Top-up', 'Decay', 'Hybrid'
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.synchrotronMode
    rank: 1000
    domain_of:
    - ExperimentRun
    range: string
  exposure_time:
    name: exposure_time
    description: Exposure time per image in seconds
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.exposureTime
    rank: 1000
    domain_of:
    - ExperimentRun
    - Image
    - ExperimentalConditions
    range: float
    unit:
      ucum_code: s
  start_time:
    name: start_time
    description: Data collection start timestamp
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.startTime
    rank: 1000
    domain_of:
    - ExperimentRun
    range: string
  end_time:
    name: end_time
    description: Data collection end timestamp
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.endTime
    rank: 1000
    domain_of:
    - ExperimentRun
    range: string
  resolution:
    name: resolution
    description: Resolution at edge of detector in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.resolution
    rank: 1000
    domain_of:
    - ExperimentRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: Ao
  resolution_at_corner:
    name: resolution_at_corner
    description: Resolution at corner of detector in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.resolutionAtCorner
    rank: 1000
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: Ao
  ispyb_data_collection_id:
    name: ispyb_data_collection_id
    description: ISPyB DataCollection.dataCollectionId for traceability
    comments:
    - Use to link back to ISPyB records
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.dataCollectionId
    rank: 1000
    domain_of:
    - ExperimentRun
    range: integer
  ispyb_session_id:
    name: ispyb_session_id
    description: ISPyB BLSession.sessionId
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:BLSession.sessionId
    rank: 1000
    domain_of:
    - ExperimentRun
    range: integer

Induced

name: ExperimentRun
description: An experimental data collection session
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  experiment_code:
    name: experiment_code
    description: Human-friendly laboratory or facility identifier for the experiment
      (e.g., 'SIBYLS-2024-02-01-hetBGL', 'CRYOEM-RUN-240815-001'). Used for local
      tracking and cross-referencing within laboratory systems.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: experiment_code
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: string
    required: true
  sample_id:
    name: sample_id
    description: Reference to the sample being analyzed
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: sample_id
    owner: ExperimentRun
    domain_of:
    - SamplePreparation
    - ExperimentRun
    range: string
    required: true
  instrument_id:
    name: instrument_id
    description: Reference to the instrument used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: instrument_id
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: Instrument
    required: true
  experiment_date:
    name: experiment_date
    description: Date of the experiment
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: experiment_date
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: string
  operator_id:
    name: operator_id
    description: Identifier or name of the person who performed the experiment data
      collection (e.g., 'jsmith', 'John Smith', or personnel ID)
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: operator_id
    owner: ExperimentRun
    domain_of:
    - SamplePreparation
    - ExperimentRun
    range: string
  technique:
    name: technique
    description: Technique used for data collection
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: technique
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: TechniqueEnum
    required: true
  experimental_method:
    name: experimental_method
    description: Specific experimental method for structure determination (particularly
      for diffraction techniques)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: experimental_method
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    - BiophysicalProperty
    range: ExperimentalMethodEnum
  experimental_conditions:
    name: experimental_conditions
    description: Environmental and experimental conditions
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: experimental_conditions
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: ExperimentalConditions
  data_collection_strategy:
    name: data_collection_strategy
    description: Strategy for data collection
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: data_collection_strategy
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: DataCollectionStrategy
  quality_metrics:
    name: quality_metrics
    description: Quality metrics for the experiment
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: quality_metrics
    owner: ExperimentRun
    domain_of:
    - Sample
    - ExperimentRun
    range: QualityMetrics
  raw_data_location:
    name: raw_data_location
    description: Location of raw data files
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: raw_data_location
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: string
  processing_status:
    name: processing_status
    description: Current processing status
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: processing_status
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: ProcessingStatusEnum
  magnification:
    name: magnification
    description: Magnification used during data collection
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: magnification
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    - OpticalImage
    range: integer
  calibrated_pixel_size:
    name: calibrated_pixel_size
    description: Calibrated pixel size in Angstroms per pixel
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: calibrated_pixel_size
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  camera_binning:
    name: camera_binning
    description: Camera binning factor. This must be a positive float value (e.g.,
      1, 1.5, 2, 3).
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: camera_binning
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    minimum_value: 0.01
  exposure_time_per_frame:
    name: exposure_time_per_frame
    description: Exposure time per frame in milliseconds
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: exposure_time_per_frame
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  frames_per_movie:
    name: frames_per_movie
    description: Number of frames per movie
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: frames_per_movie
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: integer
  total_exposure_time:
    name: total_exposure_time
    description: Total exposure time in milliseconds
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: total_exposure_time
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  total_dose:
    name: total_dose
    description: Total electron dose in e-/Angstrom^2
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: total_dose
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    - DataCollectionStrategy
    range: float
  dose_rate:
    name: dose_rate
    description: Dose rate in e-/pixel/s or e-/Angstrom^2/s
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: dose_rate
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  defocus_target:
    name: defocus_target
    description: Target defocus value in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: defocus_target
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  defocus_range_min:
    name: defocus_range_min
    description: Minimum defocus range in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: defocus_range_min
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  defocus_range_max:
    name: defocus_range_max
    description: Maximum defocus range in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: defocus_range_max
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  defocus_range_increment:
    name: defocus_range_increment
    description: Defocus range increment in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: defocus_range_increment
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  astigmatism_target:
    name: astigmatism_target
    description: Target astigmatism in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: astigmatism_target
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  coma:
    name: coma
    description: Coma aberration in nanometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: coma
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  stage_tilt:
    name: stage_tilt
    description: Stage tilt angle in degrees
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: stage_tilt
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
  autoloader_slot:
    name: autoloader_slot
    description: Autoloader slot identifier
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: autoloader_slot
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: string
  shots_per_hole:
    name: shots_per_hole
    description: Number of shots taken per hole
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: shots_per_hole
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: integer
  holes_per_group:
    name: holes_per_group
    description: Number of holes per group
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: holes_per_group
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: integer
  acquisition_software:
    name: acquisition_software
    description: Acquisition software used (e.g., SerialEM, EPU, Leginon)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: acquisition_software
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: string
  acquisition_software_version:
    name: acquisition_software_version
    description: Version of acquisition software
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: acquisition_software_version
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: string
  wavelength:
    name: wavelength
    description: X-ray wavelength
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Wavelength
    - imgCIF:_diffrn_radiation_wavelength.wavelength
    - mmCIF:_diffrn_radiation_wavelength.wavelength
    - ispyb:DataCollection.wavelength
    rank: 1000
    alias: wavelength
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: Ao
  oscillation_angle:
    name: oscillation_angle
    description: Oscillation angle per image
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Angle_increment
    - imgCIF:_diffrn_scan_axis.angle_increment
    - mmCIF:_diffrn_scan.angle_increment
    - ispyb:DataCollection.axisRange
    rank: 1000
    alias: oscillation_angle
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: deg
  start_angle:
    name: start_angle
    description: Starting rotation angle
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Start_angle
    - imgCIF:_diffrn_scan_axis.angle_start
    - ispyb:DataCollection.axisStart
    rank: 1000
    alias: start_angle
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: deg
  number_of_images:
    name: number_of_images
    description: Total number of diffraction images collected
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Number_of_images
    - imgCIF:_diffrn_scan.frames
    - ispyb:DataCollection.numberOfImages
    rank: 1000
    alias: number_of_images
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: integer
  beam_center_x:
    name: beam_center_x
    description: Beam center X coordinate
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Beam_xy_x
    - imgCIF:_diffrn_detector.beam_centre_x
    - mmCIF:_diffrn_detector.beam_center_x
    - ispyb:DataCollection.xBeam
    rank: 1000
    alias: beam_center_x
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: '[px]'
  beam_center_y:
    name: beam_center_y
    description: Beam center Y coordinate
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Beam_xy_y
    - imgCIF:_diffrn_detector.beam_centre_y
    - mmCIF:_diffrn_detector.beam_center_y
    - ispyb:DataCollection.yBeam
    rank: 1000
    alias: beam_center_y
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: '[px]'
  detector_distance:
    name: detector_distance
    description: Distance from sample to detector
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Detector_distance
    - imgCIF:_diffrn_measurement.sample_detector_distance
    - mmCIF:_diffrn_detector.distance
    - ispyb:DataCollection.detectorDistance
    rank: 1000
    alias: detector_distance
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: mm
  pixel_size_x:
    name: pixel_size_x
    description: Pixel size X dimension
    comments:
    - 'imgCIF: _array_element_size.size[1]'
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Pixel_size_x
    - imgCIF:_array_element_size.size
    rank: 1000
    alias: pixel_size_x
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: um
  pixel_size_y:
    name: pixel_size_y
    description: Pixel size Y dimension
    comments:
    - 'imgCIF: _array_element_size.size[2]'
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Pixel_size_y
    - imgCIF:_array_element_size.size
    rank: 1000
    alias: pixel_size_y
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: um
  total_rotation:
    name: total_rotation
    description: Total rotation range collected
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Total_rotation_deg
    - imgCIF:_diffrn_scan_axis.angle_range
    rank: 1000
    alias: total_rotation
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: deg
  beamline:
    name: beamline
    description: Beamline identifier (e.g., FMX, AMX, 12.3.1)
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - nsls2:Beamline
    - mmCIF:_diffrn_source.pdbx_synchrotron_beamline
    - ispyb:BLSession.beamLineName
    rank: 1000
    alias: beamline
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: string
  transmission:
    name: transmission
    description: X-ray beam transmission as percentage (0-100)
    comments:
    - Percentage of full beam intensity used
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.transmission
    rank: 1000
    alias: transmission
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    minimum_value: 0
    maximum_value: 100
    unit:
      ucum_code: '%'
  flux:
    name: flux
    description: Photon flux at sample position in photons/second
    comments:
    - Measured or calculated photon flux
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.flux
    rank: 1000
    alias: flux
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    - XRFImage
    range: float
    unit:
      ucum_code: '{photons}/s'
  flux_end:
    name: flux_end
    description: Photon flux at end of data collection in photons/second
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.flux_end
    rank: 1000
    alias: flux_end
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: '{photons}/s'
  slit_gap_horizontal:
    name: slit_gap_horizontal
    description: Horizontal slit gap aperture in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.slitGapHorizontal
    rank: 1000
    alias: slit_gap_horizontal
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: um
  slit_gap_vertical:
    name: slit_gap_vertical
    description: Vertical slit gap aperture in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.slitGapVertical
    rank: 1000
    alias: slit_gap_vertical
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: um
  undulator_gap:
    name: undulator_gap
    description: Undulator gap setting in millimeters
    comments:
    - Primary undulator gap for beamlines with insertion devices
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.undulatorGap1
    rank: 1000
    alias: undulator_gap
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: mm
  synchrotron_mode:
    name: synchrotron_mode
    description: Synchrotron storage ring fill mode
    comments:
    - e.g., 'Top-up', 'Decay', 'Hybrid'
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.synchrotronMode
    rank: 1000
    alias: synchrotron_mode
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: string
  exposure_time:
    name: exposure_time
    description: Exposure time per image in seconds
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.exposureTime
    rank: 1000
    alias: exposure_time
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    - Image
    - ExperimentalConditions
    range: float
    unit:
      ucum_code: s
  start_time:
    name: start_time
    description: Data collection start timestamp
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.startTime
    rank: 1000
    alias: start_time
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: string
  end_time:
    name: end_time
    description: Data collection end timestamp
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.endTime
    rank: 1000
    alias: end_time
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: string
  resolution:
    name: resolution
    description: Resolution at edge of detector in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.resolution
    rank: 1000
    alias: resolution
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    - QualityMetrics
    range: float
    unit:
      ucum_code: Ao
  resolution_at_corner:
    name: resolution_at_corner
    description: Resolution at corner of detector in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.resolutionAtCorner
    rank: 1000
    alias: resolution_at_corner
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: float
    unit:
      ucum_code: Ao
  ispyb_data_collection_id:
    name: ispyb_data_collection_id
    description: ISPyB DataCollection.dataCollectionId for traceability
    comments:
    - Use to link back to ISPyB records
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:DataCollection.dataCollectionId
    rank: 1000
    alias: ispyb_data_collection_id
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: integer
  ispyb_session_id:
    name: ispyb_session_id
    description: ISPyB BLSession.sessionId
    from_schema: https://w3id.org/lambda-ber-schema/
    exact_mappings:
    - ispyb:BLSession.sessionId
    rank: 1000
    alias: ispyb_session_id
    owner: ExperimentRun
    domain_of:
    - ExperimentRun
    range: integer
  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: ExperimentRun
    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: ExperimentRun
    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: ExperimentRun
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string