URI: https://w3id.org/osc-em/oscem-schemas/:Acquisition
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| nominal_defocus | +0..1 Range |
+Target defocus set, min and max values in µm | +direct | +
| calibrated_defocus | +0..1 Range |
+Machine estimated defocus, min and max values in µm | +direct | +
| nominal_magnification | +0..1 Integer |
+Magnification level as indicated by the instrument, no unit | +direct | +
| calibrated_magnification | +0..1 Integer |
+Calculated magnification, no unit | +direct | +
| holder | +0..1 String |
+Speciman holder model | +direct | +
| holder_cryogen | +0..1 String |
+Type of cryogen used in the holder - if the holder is cooled seperately | +direct | +
| temperature_range | +0..1 Range |
+Temperature during data collection, in K with min and max values | +direct | +
| microscope_software | +0..1 String |
+Software used for instrument control, | +direct | +
| detector | +1 String |
+Make and model of the detector used | +direct | +
| detector_mode | +0..1 String |
+Operating mode of the detector | +direct | +
| dose_per_movie | +1 QuantityValue |
+Average dose per image/movie/tilt - given in electrons per square Angstrom | +direct | +
| energy_filter | +0..1 EnergyFilter |
+Wether an energy filter was used and its specifics | +direct | +
| image_size | +0..1 ImageSize |
+The size of the image in pixels, height and width given | +direct | +
| date_time | +1 Any or Datetime or Date |
+Time and date of the data acquisition | +direct | +
| exposure_time | +0..1 QuantityValue |
+Time of data acquisition per movie/tilt - in s | +direct | +
| cryogen | +0..1 String |
+Cryogen used in cooling the instrument and sample, usually nitrogen | +direct | +
| frames_per_movie | +0..1 Integer |
+Number of frames that on average constitute a full movie, can be a bit hard t... | +direct | +
| grids_imaged | +0..1 Integer |
+Number of grids imaged for this project - here with qualifier during this dat... | +direct | +
| images_generated | +0..1 Integer |
+Number of images generated total for this data collection - might need a qual... | +direct | +
| binning_camera | +1 Float |
+Level of binning on the images applied during data collection | +direct | +
| pixel_size | +1 QuantityValue |
+Pixel size, in Angstrom | +direct | +
| specialist_optics | +0..1 SpecialistOptics |
+Any type of special optics, such as a phaseplate | +direct | +
| beamshift | +0..1 BoundingBox2D |
+Movement of the beam above the sample for data collection purposes that does ... | +direct | +
| beamtilt | +0..1 BoundingBox2D |
+Another way to move the beam above the sample for data collection purposes th... | +direct | +
| imageshift | +0..1 BoundingBox2D |
+Movement of the Beam below the image in order to shift the image on the detec... | +direct | +
| beamtiltgroups | +0..1 Integer |
+Number of Beamtilt groups present in this dataset - for optimized processing ... | +direct | +
| gainref_flip_rotate | +0..1 String |
+Whether and how you have to flip or rotate the gainref in order to align with... | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| EMDataset | +acquisition | +range | +Acquisition | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Acquisition | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Acquisition | +
name: Acquisition
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- nominal_defocus
+- calibrated_defocus
+- nominal_magnification
+- calibrated_magnification
+- holder
+- holder_cryogen
+- temperature_range
+- microscope_software
+- detector
+- detector_mode
+- dose_per_movie
+- energy_filter
+- image_size
+- date_time
+- exposure_time
+- cryogen
+- frames_per_movie
+- grids_imaged
+- images_generated
+- binning_camera
+- pixel_size
+- specialist_optics
+- beamshift
+- beamtilt
+- imageshift
+- beamtiltgroups
+- gainref_flip_rotate
+slot_usage:
+ detector:
+ name: detector
+ required: true
+ dose_per_movie:
+ name: dose_per_movie
+ required: true
+ date_time:
+ name: date_time
+ required: true
+ binning_camera:
+ name: binning_camera
+ required: true
+ pixel_size:
+ name: pixel_size
+ required: true
+
+name: Acquisition
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ detector:
+ name: detector
+ required: true
+ dose_per_movie:
+ name: dose_per_movie
+ required: true
+ date_time:
+ name: date_time
+ required: true
+ binning_camera:
+ name: binning_camera
+ required: true
+ pixel_size:
+ name: pixel_size
+ required: true
+attributes:
+ nominal_defocus:
+ name: nominal_defocus
+ description: Target defocus set, min and max values in µm.
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: nominal_defocus
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: Range
+ calibrated_defocus:
+ name: calibrated_defocus
+ description: Machine estimated defocus, min and max values in µm. Has a tendency
+ to be off.
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: calibrated_defocus
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: Range
+ nominal_magnification:
+ name: nominal_magnification
+ description: Magnification level as indicated by the instrument, no unit
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: nominal_magnification
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: integer
+ calibrated_magnification:
+ name: calibrated_magnification
+ description: Calculated magnification, no unit
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: calibrated_magnification
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: integer
+ holder:
+ name: holder
+ description: Speciman holder model
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: holder
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: string
+ holder_cryogen:
+ name: holder_cryogen
+ description: Type of cryogen used in the holder - if the holder is cooled seperately
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: holder_cryogen
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: string
+ temperature_range:
+ name: temperature_range
+ description: Temperature during data collection, in K with min and max values.
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: temperature
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: Range
+ microscope_software:
+ name: microscope_software
+ description: Software used for instrument control,
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: microscope_software
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: string
+ detector:
+ name: detector
+ description: Make and model of the detector used
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: detector
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: string
+ required: true
+ detector_mode:
+ name: detector_mode
+ description: Operating mode of the detector
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: detector_mode
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: string
+ dose_per_movie:
+ name: dose_per_movie
+ description: Average dose per image/movie/tilt - given in electrons per square
+ Angstrom
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: dose_per_movie
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: QuantityValue
+ required: true
+ energy_filter:
+ name: energy_filter
+ description: Wether an energy filter was used and its specifics.
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: energy_filter
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: EnergyFilter
+ image_size:
+ name: image_size
+ description: The size of the image in pixels, height and width given.
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: image_size
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: ImageSize
+ date_time:
+ name: date_time
+ description: Time and date of the data acquisition
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: date_time
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: Any
+ required: true
+ any_of:
+ - range: datetime
+ - range: date
+ exposure_time:
+ name: exposure_time
+ description: Time of data acquisition per movie/tilt - in s
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: exposure_time
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: QuantityValue
+ cryogen:
+ name: cryogen
+ description: Cryogen used in cooling the instrument and sample, usually nitrogen
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: cryogen
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: string
+ frames_per_movie:
+ name: frames_per_movie
+ description: Number of frames that on average constitute a full movie, can be
+ a bit hard to define for some detectors
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: frames_per_movie
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: integer
+ grids_imaged:
+ name: grids_imaged
+ description: Number of grids imaged for this project - here with qualifier during
+ this data acquisition
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: grids_imaged
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: integer
+ images_generated:
+ name: images_generated
+ description: Number of images generated total for this data collection - might
+ need a qualifier for tilt series to determine whether full series or individual
+ tilts are counted
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: images_generated
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: integer
+ binning_camera:
+ name: binning_camera
+ description: Level of binning on the images applied during data collection
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: binning_camera
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: float
+ required: true
+ pixel_size:
+ name: pixel_size
+ description: Pixel size, in Angstrom
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: pixel_size
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: QuantityValue
+ required: true
+ specialist_optics:
+ name: specialist_optics
+ description: Any type of special optics, such as a phaseplate
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: specialist_optics
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: SpecialistOptics
+ beamshift:
+ name: beamshift
+ description: Movement of the beam above the sample for data collection purposes
+ that does not require movement of the stage. Given in mrad.
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: beamshift
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: BoundingBox2D
+ beamtilt:
+ name: beamtilt
+ description: Another way to move the beam above the sample for data collection
+ purposes that does not require movement of the stage. Given in mrad.
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: beamtilt
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: BoundingBox2D
+ imageshift:
+ name: imageshift
+ description: Movement of the Beam below the image in order to shift the image
+ on the detector. Given in µm.
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: imageshift
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: BoundingBox2D
+ beamtiltgroups:
+ name: beamtiltgroups
+ description: Number of Beamtilt groups present in this dataset - for optimized
+ processing split dataset into groups of same tilt angle. Despite its name Beamshift
+ is often used to achive this result.
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: beamtiltgroups
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: integer
+ gainref_flip_rotate:
+ name: gainref_flip_rotate
+ description: Whether and how you have to flip or rotate the gainref in order to
+ align with your acquired images
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: gainref_flip_rotate
+ owner: Acquisition
+ domain_of:
+ - Acquisition
+ range: string
+
+Any type, used as the base for type-narrowing.
+__
+See https://linkml.io/linkml/schemas/advanced.html
+URI: linkml:Any
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| + | + | + | + |
| used by | +used in | +type | +used | +
|---|---|---|---|
| Acquisition | +date_time | +range | +Any | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +linkml:Any | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Any | +
name: Any
+description: 'Any type, used as the base for type-narrowing.
+
+
+ See https://linkml.io/linkml/schemas/advanced.html'
+from_schema: https://w3id.org/osc-em/oscem-schemas
+class_uri: linkml:Any
+
+name: Any
+description: 'Any type, used as the base for type-narrowing.
+
+
+ See https://linkml.io/linkml/schemas/advanced.html'
+from_schema: https://w3id.org/osc-em/oscem-schemas
+class_uri: linkml:Any
+
+URI: https://w3id.org/osc-em/oscem-schemas/:Author
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| orcid | +1 String |
+ORCID of the author, a type of unique identifier | +direct | +
| country | +1 String |
+Country of the institution | +direct | +
| role | +0..1 String |
+Role of the author, i | +direct | +
| name_org | +1 String |
+Name of the organization | +direct | +
| type_org | +1 OrganizationTypeEnum |
+Type of organization, academic, commercial, governmental, etc | +direct | +
| name | +1 String |
+name | +Person | +
| first_name | +0..1 String |
+first name | +Person | +
| work_status | +0..1 Boolean |
+work status | +Person | +
| 1 String |
+Person | +||
| work_phone | +1 String |
+work phone | +Person | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| EMDataset | +authors | +range | +Author | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Author | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Author | +
name: Author
+from_schema: https://w3id.org/osc-em/oscem-schemas
+is_a: Person
+slots:
+- orcid
+- country
+- role
+- name_org
+- type_org
+slot_usage:
+ name:
+ name: name
+ required: true
+ email:
+ name: email
+ required: true
+ work_phone:
+ name: work_phone
+ required: true
+ orcid:
+ name: orcid
+ required: true
+ country:
+ name: country
+ required: true
+ type_org:
+ name: type_org
+ required: true
+ name_org:
+ name: name_org
+ required: true
+
+name: Author
+from_schema: https://w3id.org/osc-em/oscem-schemas
+is_a: Person
+slot_usage:
+ name:
+ name: name
+ required: true
+ email:
+ name: email
+ required: true
+ work_phone:
+ name: work_phone
+ required: true
+ orcid:
+ name: orcid
+ required: true
+ country:
+ name: country
+ required: true
+ type_org:
+ name: type_org
+ required: true
+ name_org:
+ name: name_org
+ required: true
+attributes:
+ orcid:
+ name: orcid
+ description: ORCID of the author, a type of unique identifier
+ title: ORCID
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: orcid
+ owner: Author
+ domain_of:
+ - Author
+ range: string
+ required: true
+ country:
+ name: country
+ description: Country of the institution
+ title: Country
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: country
+ owner: Author
+ domain_of:
+ - Author
+ - Grant
+ range: string
+ required: true
+ role:
+ name: role
+ description: Role of the author, i.e., principal investigator
+ title: Role
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: role
+ owner: Author
+ domain_of:
+ - Author
+ range: string
+ name_org:
+ name: name_org
+ description: Name of the organization
+ title: Name_org
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: name_org
+ owner: Author
+ domain_of:
+ - Author
+ range: string
+ required: true
+ type_org:
+ name: type_org
+ description: Type of organization, academic, commercial, governmental, etc.
+ title: Type_org
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: type_org
+ owner: Author
+ domain_of:
+ - Author
+ range: OrganizationTypeEnum
+ required: true
+ name:
+ name: name
+ description: name
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ slot_uri: schema:name
+ alias: name
+ owner: Author
+ domain_of:
+ - Person
+ - Grant
+ range: string
+ required: true
+ first_name:
+ name: first_name
+ description: first name
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: first_name
+ owner: Author
+ domain_of:
+ - Person
+ range: string
+ work_status:
+ name: work_status
+ description: work status
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: work_status
+ owner: Author
+ domain_of:
+ - Person
+ range: boolean
+ email:
+ name: email
+ description: email
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ slot_uri: schema:email
+ alias: email
+ owner: Author
+ domain_of:
+ - Person
+ range: string
+ required: true
+ pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$
+ work_phone:
+ name: work_phone
+ description: work phone
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ slot_uri: schema:telephone
+ alias: work_phone
+ owner: Author
+ domain_of:
+ - Person
+ range: string
+ required: true
+
+A binary (true or false) value
+URI: xsd:boolean
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:boolean | +
| native | +https://w3id.org/osc-em/oscem-schemas/:boolean | +
| exact | +schema:Boolean | +
an axis-aligned 2D bounding box (float units)
+URI: https://w3id.org/osc-em/oscem-schemas/:BoundingBox2D
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| x_min | +0..1 QuantityValue |
+minimum x | +direct | +
| x_max | +0..1 QuantityValue |
+maximum x | +direct | +
| y_min | +0..1 QuantityValue |
+minimum y | +direct | +
| y_max | +0..1 QuantityValue |
+maximum y | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Acquisition | +beamshift | +range | +BoundingBox2D | +
| Acquisition | +beamtilt | +range | +BoundingBox2D | +
| Acquisition | +imageshift | +range | +BoundingBox2D | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:BoundingBox2D | +
| native | +https://w3id.org/osc-em/oscem-schemas/:BoundingBox2D | +
name: BoundingBox2D
+description: an axis-aligned 2D bounding box (float units)
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- x_min
+- x_max
+- y_min
+- y_max
+
+name: BoundingBox2D
+description: an axis-aligned 2D bounding box (float units)
+from_schema: https://w3id.org/osc-em/oscem-schemas
+attributes:
+ x_min:
+ name: x_min
+ description: minimum x
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: x_min
+ owner: BoundingBox2D
+ domain_of:
+ - BoundingBox2D
+ range: QuantityValue
+ x_max:
+ name: x_max
+ description: maximum x
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: x_max
+ owner: BoundingBox2D
+ domain_of:
+ - BoundingBox2D
+ range: QuantityValue
+ y_min:
+ name: y_min
+ description: minimum y
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: y_min
+ owner: BoundingBox2D
+ domain_of:
+ - BoundingBox2D
+ range: QuantityValue
+ y_max:
+ name: y_max
+ description: maximum y
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: y_max
+ owner: BoundingBox2D
+ domain_of:
+ - BoundingBox2D
+ range: QuantityValue
+
+URI: https://w3id.org/osc-em/oscem-schemas/:ChromaticAberrationCorrector
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +1 Boolean |
+whether a specific instrument was used during data acquisition | +direct | +
| instrument_type | +1 String |
+Details of a given specialist instrument | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| SpecialistOptics | +chromatic_aberration_corrector | +range | +ChromaticAberrationCorrector | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:ChromaticAberrationCorrector | +
| native | +https://w3id.org/osc-em/oscem-schemas/:ChromaticAberrationCorrector | +
name: ChromaticAberrationCorrector
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- used
+- instrument_type
+slot_usage:
+ used:
+ name: used
+ required: true
+ instrument_type:
+ name: instrument_type
+ required: true
+
+name: ChromaticAberrationCorrector
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ used:
+ name: used
+ required: true
+ instrument_type:
+ name: instrument_type
+ required: true
+attributes:
+ used:
+ name: used
+ description: whether a specific instrument was used during data acquisition
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: used
+ owner: ChromaticAberrationCorrector
+ domain_of:
+ - EnergyFilter
+ - Phaseplate
+ - SphericalAberrationCorrector
+ - ChromaticAberrationCorrector
+ range: boolean
+ required: true
+ instrument_type:
+ name: instrument_type
+ description: Details of a given specialist instrument
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: instrument_type
+ owner: ChromaticAberrationCorrector
+ domain_of:
+ - Phaseplate
+ - SphericalAberrationCorrector
+ - ChromaticAberrationCorrector
+ range: string
+ required: true
+
+a compact URI
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +https://w3id.org/osc-em/oscem-schemas/:curie | +
a date (year, month and day) in an idealized calendar
+URI: xsd:date
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:date | +
| native | +https://w3id.org/osc-em/oscem-schemas/:date | +
| exact | +schema:Date | +
Either a date or a datetime
+ + +| Mapping Type | +Mapped Value | +
|---|---|
| self | +linkml:DateOrDatetime | +
| native | +https://w3id.org/osc-em/oscem-schemas/:date_or_datetime | +
The combination of a date and time
+URI: xsd:dateTime
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:dateTime | +
| native | +https://w3id.org/osc-em/oscem-schemas/:datetime | +
| exact | +schema:DateTime | +
A real number with arbitrary precision that conforms to the xsd:decimal specification
+URI: xsd:decimal
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:decimal | +
| native | +https://w3id.org/osc-em/oscem-schemas/:decimal | +
| broad | +schema:Number | +
A real number that conforms to the xsd:double specification
+URI: xsd:double
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:double | +
| native | +https://w3id.org/osc-em/oscem-schemas/:double | +
| close | +schema:Float | +
OSC-EM Metadata for a dataset
+URI: https://w3id.org/osc-em/oscem-schemas/:EMDataset
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| acquisition | +1 Acquisition |
+Describe the data acquisition parameters | +direct | +
| instrument | +1 Instrument |
+Describe the instrument used to acquire the data | +direct | +
| sample | +1 Sample |
+Sample information | +direct | +
| grants | +1..* Grant |
+List of grants associated with the project | +direct | +
| authors | +1..* Author |
+List of authors associated with the project | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:EMDataset | +
| native | +https://w3id.org/osc-em/oscem-schemas/:EMDataset | +
name: EMDataset
+description: OSC-EM Metadata for a dataset
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- acquisition
+- instrument
+- sample
+- grants
+- authors
+slot_usage:
+ acquisition:
+ name: acquisition
+ required: true
+ instrument:
+ name: instrument
+ required: true
+ sample:
+ name: sample
+ required: true
+ grants:
+ name: grants
+ required: true
+ authors:
+ name: authors
+ required: true
+tree_root: true
+
+name: EMDataset
+description: OSC-EM Metadata for a dataset
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ acquisition:
+ name: acquisition
+ required: true
+ instrument:
+ name: instrument
+ required: true
+ sample:
+ name: sample
+ required: true
+ grants:
+ name: grants
+ required: true
+ authors:
+ name: authors
+ required: true
+attributes:
+ acquisition:
+ name: acquisition
+ description: Describe the data acquisition parameters
+ title: Acquisition
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: acquisition
+ owner: EMDataset
+ domain_of:
+ - EMDataset
+ range: Acquisition
+ required: true
+ instrument:
+ name: instrument
+ description: Describe the instrument used to acquire the data
+ title: Instrument
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: instrument
+ owner: EMDataset
+ domain_of:
+ - EMDataset
+ range: Instrument
+ required: true
+ sample:
+ name: sample
+ description: Sample information
+ title: Sample
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: sample
+ owner: EMDataset
+ domain_of:
+ - EMDataset
+ range: Sample
+ required: true
+ grants:
+ name: grants
+ description: List of grants associated with the project
+ title: Grants
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: grants
+ owner: EMDataset
+ domain_of:
+ - EMDataset
+ range: Grant
+ required: true
+ multivalued: true
+ authors:
+ name: authors
+ description: List of authors associated with the project
+ title: Authors
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: authors
+ owner: EMDataset
+ domain_of:
+ - EMDataset
+ range: Author
+ required: true
+ multivalued: true
+tree_root: true
+
+URI: https://w3id.org/osc-em/oscem-schemas/:EnergyFilter
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +1 Boolean |
+whether a specific instrument was used during data acquisition | +direct | +
| model | +0..1 String |
+Make and model of a specilized device | +direct | +
| width | +1 Integer |
+The width of a given item - unit depends on item | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Acquisition | +energy_filter | +range | +EnergyFilter | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:EnergyFilter | +
| native | +https://w3id.org/osc-em/oscem-schemas/:EnergyFilter | +
name: EnergyFilter
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- used
+- model
+- width
+slot_usage:
+ used:
+ name: used
+ required: true
+ width:
+ name: width
+ required: true
+
+name: EnergyFilter
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ used:
+ name: used
+ required: true
+ width:
+ name: width
+ required: true
+attributes:
+ used:
+ name: used
+ description: whether a specific instrument was used during data acquisition
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: used
+ owner: EnergyFilter
+ domain_of:
+ - EnergyFilter
+ - Phaseplate
+ - SphericalAberrationCorrector
+ - ChromaticAberrationCorrector
+ range: boolean
+ required: true
+ model:
+ name: model
+ description: Make and model of a specilized device
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: model
+ owner: EnergyFilter
+ domain_of:
+ - EnergyFilter
+ range: string
+ width:
+ name: width
+ description: The width of a given item - unit depends on item
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: width
+ owner: EnergyFilter
+ domain_of:
+ - ImageSize
+ - EnergyFilter
+ range: integer
+ required: true
+
+A real number that conforms to the xsd:float specification
+URI: xsd:float
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:float | +
| native | +https://w3id.org/osc-em/oscem-schemas/:float | +
| exact | +schema:Float | +
Grant
+URI: schema:Grant
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| name | +0..1 String |
+name | +direct | +
| funder | +0..1 String |
+funder | +direct | +
| start_date | +0..1 Date |
+start date | +direct | +
| end_date | +0..1 Date |
+end date | +direct | +
| budget | +0..1 QuantityValue |
+budget | +direct | +
| project_id | +0..1 String |
+project id | +direct | +
| country | +0..1 String |
+Country of the institution | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| EMDataset | +grants | +range | +Grant | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +schema:Grant | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Grant | +
name: Grant
+description: Grant
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- name
+- funder
+- start_date
+- end_date
+- budget
+- project_id
+- country
+class_uri: schema:Grant
+
+name: Grant
+description: Grant
+from_schema: https://w3id.org/osc-em/oscem-schemas
+attributes:
+ name:
+ name: name
+ description: name
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ slot_uri: schema:name
+ alias: name
+ owner: Grant
+ domain_of:
+ - Person
+ - Grant
+ range: string
+ funder:
+ name: funder
+ description: funder
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: funder
+ owner: Grant
+ domain_of:
+ - Grant
+ range: string
+ start_date:
+ name: start_date
+ description: start date
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: start_date
+ owner: Grant
+ domain_of:
+ - Grant
+ range: date
+ end_date:
+ name: end_date
+ description: end date
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: end_date
+ owner: Grant
+ domain_of:
+ - Grant
+ range: date
+ budget:
+ name: budget
+ description: budget
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: budget
+ owner: Grant
+ domain_of:
+ - Grant
+ range: QuantityValue
+ project_id:
+ name: project_id
+ description: project id
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ slot_uri: schema:identifier
+ alias: project_id
+ owner: Grant
+ domain_of:
+ - Grant
+ range: string
+ country:
+ name: country
+ description: Country of the institution
+ title: Country
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: country
+ owner: Grant
+ domain_of:
+ - Author
+ - Grant
+ range: string
+class_uri: schema:Grant
+
+A class representing a grid
+URI: https://w3id.org/osc-em/oscem-schemas/:Grid
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| manufacturer | +0..1 String |
+Grid manufacturer | +direct | +
| material | +0..1 String |
+Material out of which the grid is made | +direct | +
| mesh | +0..1 Float |
+Grid mesh in lines per inch | +direct | +
| film_support | +0..1 Boolean |
+Whether a support film was used | +direct | +
| film_material | +0..1 String |
+Type of material the support film is made of | +direct | +
| film_topology | +0..1 String |
+Topology of the support film | +direct | +
| film_thickness | +0..1 String |
+Thickness of the support film | +direct | +
| pretreatment_type | +0..1 String |
+Type of pretreatment of the grid, i | +direct | +
| pretreatment_time | +0..1 QuantityValue |
+Length of time of the pretreatment in s | +direct | +
| pretreatment_pressure | +0..1 QuantityValue |
+Pressure of the chamber during pretreatment, in Pa | +direct | +
| pretreatment_atmosphere | +0..1 String |
+Atmospheric conditions in the chamber during pretreatment, i | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Sample | +grid | +range | +Grid | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Grid | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Grid | +
name: Grid
+description: A class representing a grid
+title: Grid
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- manufacturer
+- material
+- mesh
+- film_support
+- film_material
+- film_topology
+- film_thickness
+- pretreatment_type
+- pretreatment_time
+- pretreatment_pressure
+- pretreatment_atmosphere
+slot_usage:
+ manufacturer:
+ name: manufacturer
+ material:
+ name: material
+ mesh:
+ name: mesh
+ film_support:
+ name: film_support
+ film_material:
+ name: film_material
+ film_topology:
+ name: film_topology
+ film_thickness:
+ name: film_thickness
+ pretreatment_type:
+ name: pretreatment_type
+ pretreatment_time:
+ name: pretreatment_time
+ pretreatment_pressure:
+ name: pretreatment_pressure
+ pretreatment_atmosphere:
+ name: pretreatment_atmosphere
+
+name: Grid
+description: A class representing a grid
+title: Grid
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ manufacturer:
+ name: manufacturer
+ material:
+ name: material
+ mesh:
+ name: mesh
+ film_support:
+ name: film_support
+ film_material:
+ name: film_material
+ film_topology:
+ name: film_topology
+ film_thickness:
+ name: film_thickness
+ pretreatment_type:
+ name: pretreatment_type
+ pretreatment_time:
+ name: pretreatment_time
+ pretreatment_pressure:
+ name: pretreatment_pressure
+ pretreatment_atmosphere:
+ name: pretreatment_atmosphere
+attributes:
+ manufacturer:
+ name: manufacturer
+ description: Grid manufacturer
+ title: Manufacturer
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: manufacturer
+ owner: Grid
+ domain_of:
+ - Grid
+ range: string
+ material:
+ name: material
+ description: Material out of which the grid is made
+ title: Material
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: material
+ owner: Grid
+ domain_of:
+ - Grid
+ range: string
+ mesh:
+ name: mesh
+ description: Grid mesh in lines per inch
+ title: Mesh
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: mesh
+ owner: Grid
+ domain_of:
+ - Grid
+ range: float
+ film_support:
+ name: film_support
+ description: Whether a support film was used
+ title: Film_support
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: film_support
+ owner: Grid
+ domain_of:
+ - Grid
+ range: boolean
+ film_material:
+ name: film_material
+ description: Type of material the support film is made of
+ title: Film_material
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: film_material
+ owner: Grid
+ domain_of:
+ - Grid
+ range: string
+ film_topology:
+ name: film_topology
+ description: Topology of the support film
+ title: Film_topology
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: film_topology
+ owner: Grid
+ domain_of:
+ - Grid
+ range: string
+ film_thickness:
+ name: film_thickness
+ description: Thickness of the support film
+ title: Film_thickness
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: film_thickness
+ owner: Grid
+ domain_of:
+ - Grid
+ range: string
+ pretreatment_type:
+ name: pretreatment_type
+ description: Type of pretreatment of the grid, i.e., glow discharge
+ title: Pretreatment_type
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: pretreatment_type
+ owner: Grid
+ domain_of:
+ - Grid
+ range: string
+ pretreatment_time:
+ name: pretreatment_time
+ description: Length of time of the pretreatment in s
+ title: Pretreatment_time
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: pretreatment_time
+ owner: Grid
+ domain_of:
+ - Grid
+ range: QuantityValue
+ pretreatment_pressure:
+ name: pretreatment_pressure
+ description: Pressure of the chamber during pretreatment, in Pa
+ title: Pretreatment_pressure
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: pretreatment_pressure
+ owner: Grid
+ domain_of:
+ - Grid
+ range: QuantityValue
+ pretreatment_atmosphere:
+ name: pretreatment_atmosphere
+ description: Atmospheric conditions in the chamber during pretreatment, i.e.,
+ addition of specific gases, etc.
+ title: Pretreatment_atmosphere
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: pretreatment_atmosphere
+ owner: Grid
+ domain_of:
+ - Grid
+ range: string
+
+size of a 2D image (in integer units)
+URI: https://w3id.org/osc-em/oscem-schemas/:ImageSize
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| height | +0..1 Integer |
+The height of a given item - unit depends on item | +direct | +
| width | +0..1 Integer |
+The width of a given item - unit depends on item | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Acquisition | +image_size | +range | +ImageSize | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:ImageSize | +
| native | +https://w3id.org/osc-em/oscem-schemas/:ImageSize | +
name: ImageSize
+description: size of a 2D image (in integer units)
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- height
+- width
+
+name: ImageSize
+description: size of a 2D image (in integer units)
+from_schema: https://w3id.org/osc-em/oscem-schemas
+attributes:
+ height:
+ name: height
+ description: The height of a given item - unit depends on item
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: height
+ owner: ImageSize
+ domain_of:
+ - ImageSize
+ range: integer
+ width:
+ name: width
+ description: The width of a given item - unit depends on item
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: width
+ owner: ImageSize
+ domain_of:
+ - ImageSize
+ - EnergyFilter
+ range: integer
+
+Instrument values, mostly constant across a data collection.
+URI: https://w3id.org/osc-em/oscem-schemas/:Instrument
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| microscope | +1 String |
+Name/Type of the Microscope | +direct | +
| illumination | +1 String |
+Mode of illumination used during data collection | +direct | +
| imaging | +1 String |
+Mode of imaging used during data collection | +direct | +
| electron_source | +1 String |
+Type of electron source used in the microscope, such as FEG | +direct | +
| acceleration_voltage | +1 QuantityValue |
+Voltage used for the electron acceleration, in kV | +direct | +
| c2_aperture | +0..1 QuantityValue |
+C2 aperture size used in data acquisition, in µm | +direct | +
| cs | +1 QuantityValue |
+Spherical aberration of the instrument, in mm | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| EMDataset | +instrument | +range | +Instrument | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Instrument | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Instrument | +
name: Instrument
+description: Instrument values, mostly constant across a data collection.
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- microscope
+- illumination
+- imaging
+- electron_source
+- acceleration_voltage
+- c2_aperture
+- cs
+slot_usage:
+ microscope:
+ name: microscope
+ required: true
+ illumination:
+ name: illumination
+ required: true
+ imaging:
+ name: imaging
+ required: true
+ electron_source:
+ name: electron_source
+ required: true
+ acceleration_voltage:
+ name: acceleration_voltage
+ required: true
+ cs:
+ name: cs
+ required: true
+
+name: Instrument
+description: Instrument values, mostly constant across a data collection.
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ microscope:
+ name: microscope
+ required: true
+ illumination:
+ name: illumination
+ required: true
+ imaging:
+ name: imaging
+ required: true
+ electron_source:
+ name: electron_source
+ required: true
+ acceleration_voltage:
+ name: acceleration_voltage
+ required: true
+ cs:
+ name: cs
+ required: true
+attributes:
+ microscope:
+ name: microscope
+ description: Name/Type of the Microscope
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: microscope
+ owner: Instrument
+ domain_of:
+ - Instrument
+ range: string
+ required: true
+ illumination:
+ name: illumination
+ description: Mode of illumination used during data collection
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: illumination
+ owner: Instrument
+ domain_of:
+ - Instrument
+ range: string
+ required: true
+ imaging:
+ name: imaging
+ description: Mode of imaging used during data collection
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: imaging
+ owner: Instrument
+ domain_of:
+ - Instrument
+ range: string
+ required: true
+ electron_source:
+ name: electron_source
+ description: Type of electron source used in the microscope, such as FEG
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: electron_source
+ owner: Instrument
+ domain_of:
+ - Instrument
+ range: string
+ required: true
+ acceleration_voltage:
+ name: acceleration_voltage
+ description: Voltage used for the electron acceleration, in kV
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: acceleration_voltage
+ owner: Instrument
+ domain_of:
+ - Instrument
+ range: QuantityValue
+ required: true
+ c2_aperture:
+ name: c2_aperture
+ description: C2 aperture size used in data acquisition, in µm
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: c2_aperture
+ owner: Instrument
+ domain_of:
+ - Instrument
+ range: QuantityValue
+ cs:
+ name: cs
+ description: Spherical aberration of the instrument, in mm
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: cs
+ owner: Instrument
+ domain_of:
+ - Instrument
+ range: QuantityValue
+ required: true
+
+An integer
+URI: xsd:integer
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:integer | +
| native | +https://w3id.org/osc-em/oscem-schemas/:integer | +
| exact | +schema:Integer | +
A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +https://w3id.org/osc-em/oscem-schemas/:jsonpath | +
A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +https://w3id.org/osc-em/oscem-schemas/:jsonpointer | +
A class representing a ligand
+URI: https://w3id.org/osc-em/oscem-schemas/:Ligand
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| present | +1 Boolean |
+Whether the model contains any ligands | +direct | +
| smiles | +0..1 String |
+Provide a valid SMILES string of your ligand | +direct | +
| reference | +0..1 String |
+Link to a reference of your ligand, i | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Sample | +ligands | +range | +Ligand | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Ligand | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Ligand | +
name: Ligand
+description: A class representing a ligand
+title: Ligand
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- present
+- smiles
+- reference
+slot_usage:
+ present:
+ name: present
+ required: true
+
+name: Ligand
+description: A class representing a ligand
+title: Ligand
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ present:
+ name: present
+ required: true
+attributes:
+ present:
+ name: present
+ description: Whether the model contains any ligands
+ title: Present
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: present
+ owner: Ligand
+ domain_of:
+ - Ligand
+ range: boolean
+ required: true
+ smiles:
+ name: smiles
+ description: Provide a valid SMILES string of your ligand
+ title: SMILES
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: smiles
+ owner: Ligand
+ domain_of:
+ - Ligand
+ range: string
+ reference:
+ name: reference
+ description: Link to a reference of your ligand, i.e., CCD, PubChem, etc.
+ title: Reference
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: reference
+ owner: Ligand
+ domain_of:
+ - Ligand
+ range: string
+
+A class representing a molecule
+URI: https://w3id.org/osc-em/oscem-schemas/:Molecule
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| name_mol | +1 String |
+Name of an individual molecule (often protein) in the sample | +direct | +
| molecular_type | +1 String |
+Description of the overall molecular type, i | +direct | +
| molecular_class | +1 MoleculeClassEnum |
+Class of the molecule | +direct | +
| sequence | +1 String |
+Full sequence of the sample as in the data, i | +direct | +
| natural_source | +1 String |
+Scientific name of the natural host organism | +direct | +
| taxonomy_id_source | +1 String |
+Taxonomy ID of the natural source organism | +direct | +
| expression_system | +1 String |
+Scientific name of the organism used to produce the molecule of interest | +direct | +
| taxonomy_id_expression | +1 String |
+Taxonomy ID of the expression system organism | +direct | +
| gene_name | +0..1 String |
+Name of the gene of interest | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Sample | +molecule | +range | +Molecule | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Molecule | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Molecule | +
name: Molecule
+description: A class representing a molecule
+title: Molecule
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- name_mol
+- molecular_type
+- molecular_class
+- sequence
+- natural_source
+- taxonomy_id_source
+- expression_system
+- taxonomy_id_expression
+- gene_name
+slot_usage:
+ name_mol:
+ name: name_mol
+ required: true
+ molecular_type:
+ name: molecular_type
+ required: true
+ molecular_class:
+ name: molecular_class
+ required: true
+ sequence:
+ name: sequence
+ required: true
+ natural_source:
+ name: natural_source
+ required: true
+ taxonomy_id_source:
+ name: taxonomy_id_source
+ required: true
+ expression_system:
+ name: expression_system
+ required: true
+ taxonomy_id_expression:
+ name: taxonomy_id_expression
+ required: true
+ gene_name:
+ name: gene_name
+
+name: Molecule
+description: A class representing a molecule
+title: Molecule
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ name_mol:
+ name: name_mol
+ required: true
+ molecular_type:
+ name: molecular_type
+ required: true
+ molecular_class:
+ name: molecular_class
+ required: true
+ sequence:
+ name: sequence
+ required: true
+ natural_source:
+ name: natural_source
+ required: true
+ taxonomy_id_source:
+ name: taxonomy_id_source
+ required: true
+ expression_system:
+ name: expression_system
+ required: true
+ taxonomy_id_expression:
+ name: taxonomy_id_expression
+ required: true
+ gene_name:
+ name: gene_name
+attributes:
+ name_mol:
+ name: name_mol
+ description: Name of an individual molecule (often protein) in the sample
+ title: Name
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: name_mol
+ owner: Molecule
+ domain_of:
+ - Molecule
+ range: string
+ required: true
+ molecular_type:
+ name: molecular_type
+ description: Description of the overall molecular type, i.e., a complex
+ title: Type
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: molecular_type
+ owner: Molecule
+ domain_of:
+ - OverallMolecule
+ - Molecule
+ range: string
+ required: true
+ molecular_class:
+ name: molecular_class
+ description: Class of the molecule
+ title: Class
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: molecular_class
+ owner: Molecule
+ domain_of:
+ - Molecule
+ range: MoleculeClassEnum
+ required: true
+ sequence:
+ name: sequence
+ description: Full sequence of the sample as in the data, i.e., cleaved tags should
+ also be removed from sequence here
+ title: Sequence
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: sequence
+ owner: Molecule
+ domain_of:
+ - Molecule
+ range: string
+ required: true
+ natural_source:
+ name: natural_source
+ description: Scientific name of the natural host organism
+ title: Natural_source
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: natural_source
+ owner: Molecule
+ domain_of:
+ - Molecule
+ range: string
+ required: true
+ taxonomy_id_source:
+ name: taxonomy_id_source
+ description: Taxonomy ID of the natural source organism
+ title: Taxonomy_ID_source
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: taxonomy_id_source
+ owner: Molecule
+ domain_of:
+ - Molecule
+ range: string
+ required: true
+ expression_system:
+ name: expression_system
+ description: Scientific name of the organism used to produce the molecule of interest
+ title: Expression_system
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: expression_system
+ owner: Molecule
+ domain_of:
+ - Molecule
+ range: string
+ required: true
+ taxonomy_id_expression:
+ name: taxonomy_id_expression
+ description: Taxonomy ID of the expression system organism
+ title: Taxonomy_ID_expression
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: taxonomy_id_expression
+ owner: Molecule
+ domain_of:
+ - Molecule
+ range: string
+ required: true
+ gene_name:
+ name: gene_name
+ description: Name of the gene of interest
+ title: Gene_name
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: gene_name
+ owner: Molecule
+ domain_of:
+ - Molecule
+ range: string
+
+URI: MoleculeClassEnum
+| Value | +Meaning | +Description | +
|---|---|---|
| Antibiotic | +None | +Antibiotic | +
| Carbohydrate | +None | +Carbohydrate | +
| Chimera | +None | +Chimera | +
| None of these | +None | +None of these | +
| Name | +Description | +
|---|---|
| molecular_class | +Class of the molecule | +
name: MoleculeClassEnum
+title: MoleculeClassEnum
+from_schema: https://w3id.org/osc-em/oscem-schemas
+rank: 1000
+permissible_values:
+ Antibiotic:
+ text: Antibiotic
+ description: Antibiotic
+ Carbohydrate:
+ text: Carbohydrate
+ description: Carbohydrate
+ Chimera:
+ text: Chimera
+ description: Chimera
+ None of these:
+ text: None of these
+ description: None of these
+
+Prefix part of CURIE
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +https://w3id.org/osc-em/oscem-schemas/:ncname | +
A URI, CURIE or BNODE that represents a node in a model.
+URI: shex:nonLiteral
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +shex:nonLiteral | +
| native | +https://w3id.org/osc-em/oscem-schemas/:nodeidentifier | +
A URI or CURIE that represents an object in the model.
+URI: shex:iri
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +shex:iri | +
| native | +https://w3id.org/osc-em/oscem-schemas/:objectidentifier | +
URI: OrganizationTypeEnum
+| Value | +Meaning | +Description | +
|---|---|---|
| Academic | +None | +Academic institution | +
| Commercial | +None | +Commercial entity | +
| Government | +None | +Government organization | +
| Other | +None | +Other types of organizations | +
| Name | +Description | +
|---|---|
| type_org | +Type of organization, academic, commercial, governmental, etc | +
name: OrganizationTypeEnum
+title: OrganizationTypeEnum
+from_schema: https://w3id.org/osc-em/oscem-schemas
+rank: 1000
+permissible_values:
+ Academic:
+ text: Academic
+ description: Academic institution
+ Commercial:
+ text: Commercial
+ description: Commercial entity
+ Government:
+ text: Government
+ description: Government organization
+ Other:
+ text: Other
+ description: Other types of organizations
+
+A class representing the overall molecule
+URI: https://w3id.org/osc-em/oscem-schemas/:OverallMolecule
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| molecular_type | +1 String |
+Description of the overall molecular type, i | +direct | +
| name_sample | +1 String |
+Name of the full sample | +direct | +
| source | +1 String |
+Where the sample was taken from, i | +direct | +
| molecular_weight | +0..1 QuantityValue |
+Molecular weight in Da | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Sample | +overall_molecule | +range | +OverallMolecule | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:OverallMolecule | +
| native | +https://w3id.org/osc-em/oscem-schemas/:OverallMolecule | +
name: OverallMolecule
+description: A class representing the overall molecule
+title: OverallMolecule
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- molecular_type
+- name_sample
+- source
+- molecular_weight
+slot_usage:
+ molecular_type:
+ name: molecular_type
+ required: true
+ name_sample:
+ name: name_sample
+ required: true
+ source:
+ name: source
+ required: true
+ molecular_weight:
+ name: molecular_weight
+
+name: OverallMolecule
+description: A class representing the overall molecule
+title: OverallMolecule
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ molecular_type:
+ name: molecular_type
+ required: true
+ name_sample:
+ name: name_sample
+ required: true
+ source:
+ name: source
+ required: true
+ molecular_weight:
+ name: molecular_weight
+attributes:
+ molecular_type:
+ name: molecular_type
+ description: Description of the overall molecular type, i.e., a complex
+ title: Type
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: molecular_type
+ owner: OverallMolecule
+ domain_of:
+ - OverallMolecule
+ - Molecule
+ range: string
+ required: true
+ name_sample:
+ name: name_sample
+ description: Name of the full sample
+ title: Name
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: name_sample
+ owner: OverallMolecule
+ domain_of:
+ - OverallMolecule
+ range: string
+ required: true
+ source:
+ name: source
+ description: Where the sample was taken from, i.e., natural host, recombinantly
+ expressed, etc.
+ title: Source
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: source
+ owner: OverallMolecule
+ domain_of:
+ - OverallMolecule
+ range: string
+ required: true
+ molecular_weight:
+ name: molecular_weight
+ description: Molecular weight in Da
+ title: Molecular_weight
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: molecular_weight
+ owner: OverallMolecule
+ domain_of:
+ - OverallMolecule
+ range: QuantityValue
+
+URI: schema:Person
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| name | +0..1 String |
+name | +direct | +
| first_name | +0..1 String |
+first name | +direct | +
| work_status | +0..1 Boolean |
+work status | +direct | +
| 0..1 String |
+direct | +||
| work_phone | +0..1 String |
+work phone | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +schema:Person | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Person | +
name: Person
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- name
+- first_name
+- work_status
+- email
+- work_phone
+class_uri: schema:Person
+
+name: Person
+from_schema: https://w3id.org/osc-em/oscem-schemas
+attributes:
+ name:
+ name: name
+ description: name
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ slot_uri: schema:name
+ alias: name
+ owner: Person
+ domain_of:
+ - Person
+ - Grant
+ range: string
+ first_name:
+ name: first_name
+ description: first name
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: first_name
+ owner: Person
+ domain_of:
+ - Person
+ range: string
+ work_status:
+ name: work_status
+ description: work status
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: work_status
+ owner: Person
+ domain_of:
+ - Person
+ range: boolean
+ email:
+ name: email
+ description: email
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ slot_uri: schema:email
+ alias: email
+ owner: Person
+ domain_of:
+ - Person
+ range: string
+ pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\.[a-zA-Z0-9-.]+$
+ work_phone:
+ name: work_phone
+ description: work phone
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ slot_uri: schema:telephone
+ alias: work_phone
+ owner: Person
+ domain_of:
+ - Person
+ range: string
+class_uri: schema:Person
+
+URI: https://w3id.org/osc-em/oscem-schemas/:Phaseplate
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +1 Boolean |
+whether a specific instrument was used during data acquisition | +direct | +
| instrument_type | +1 String |
+Type of phaseplate | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| SpecialistOptics | +phaseplate | +range | +Phaseplate | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Phaseplate | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Phaseplate | +
name: Phaseplate
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- used
+- instrument_type
+slot_usage:
+ used:
+ name: used
+ required: true
+ instrument_type:
+ name: instrument_type
+ description: Type of phaseplate
+ required: true
+
+name: Phaseplate
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ used:
+ name: used
+ required: true
+ instrument_type:
+ name: instrument_type
+ description: Type of phaseplate
+ required: true
+attributes:
+ used:
+ name: used
+ description: whether a specific instrument was used during data acquisition
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: used
+ owner: Phaseplate
+ domain_of:
+ - EnergyFilter
+ - Phaseplate
+ - SphericalAberrationCorrector
+ - ChromaticAberrationCorrector
+ range: boolean
+ required: true
+ instrument_type:
+ name: instrument_type
+ description: Type of phaseplate
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: instrument_type
+ owner: Phaseplate
+ domain_of:
+ - Phaseplate
+ - SphericalAberrationCorrector
+ - ChromaticAberrationCorrector
+ range: string
+ required: true
+
+if a value has a unit, it should be given as a unit value pair.
+URI: qudt:quantityValue
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| unit | +1 String |
+the unit of a given value | +direct | +
| value | +1 Float |
+the value of a field with a unit | +direct | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +qudt:quantityValue | +
| native | +https://w3id.org/osc-em/oscem-schemas/:QuantityValue | +
name: QuantityValue
+description: if a value has a unit, it should be given as a unit value pair.
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- unit
+- value
+slot_usage:
+ unit:
+ name: unit
+ required: true
+ value:
+ name: value
+ required: true
+class_uri: qudt:quantityValue
+
+name: QuantityValue
+description: if a value has a unit, it should be given as a unit value pair.
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ unit:
+ name: unit
+ required: true
+ value:
+ name: value
+ required: true
+attributes:
+ unit:
+ name: unit
+ description: the unit of a given value
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ slot_uri: qudt:hasUnit
+ alias: unit
+ owner: QuantityValue
+ domain_of:
+ - QuantityValue
+ range: string
+ required: true
+ value:
+ name: value
+ description: the value of a field with a unit
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ slot_uri: qudt:hasQuantityKind
+ alias: value
+ owner: QuantityValue
+ domain_of:
+ - QuantityValue
+ range: float
+ required: true
+class_uri: qudt:quantityValue
+
+A range constructed from min and max
+URI: https://w3id.org/osc-em/oscem-schemas/:Range
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| minimal | +0..1 QuantityValue |
+Minimal value of a given dataset property | +direct | +
| maximal | +0..1 QuantityValue |
+Maximal value of a given dataset property | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Acquisition | +nominal_defocus | +range | +Range | +
| Acquisition | +calibrated_defocus | +range | +Range | +
| Acquisition | +temperature_range | +range | +Range | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Range | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Range | +
name: Range
+description: A range constructed from min and max
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- minimal
+- maximal
+
+name: Range
+description: A range constructed from min and max
+from_schema: https://w3id.org/osc-em/oscem-schemas
+attributes:
+ minimal:
+ name: minimal
+ description: Minimal value of a given dataset property
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: minimal
+ owner: Range
+ domain_of:
+ - Range
+ range: QuantityValue
+ maximal:
+ name: maximal
+ description: Maximal value of a given dataset property
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: maximal
+ owner: Range
+ domain_of:
+ - Range
+ range: QuantityValue
+
+A class representing a sample
+URI: https://w3id.org/osc-em/oscem-schemas/:Sample
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| overall_molecule | +1 OverallMolecule |
+Description of the overall molecule | +direct | +
| molecule | +1..* Molecule |
+List of molecule associated with the sample | +direct | +
| ligands | +* Ligand |
+List of ligands associated with the sample | +direct | +
| specimen | +1 Specimen |
+Description of the specimen | +direct | +
| grid | +0..1 Grid |
+Description of the grid used | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| EMDataset | +sample | +range | +Sample | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Sample | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Sample | +
name: Sample
+description: A class representing a sample
+title: Sample
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- overall_molecule
+- molecule
+- ligands
+- specimen
+- grid
+slot_usage:
+ overall_molecule:
+ name: overall_molecule
+ required: true
+ molecule:
+ name: molecule
+ required: true
+ ligands:
+ name: ligands
+ specimen:
+ name: specimen
+ required: true
+ grid:
+ name: grid
+
+name: Sample
+description: A class representing a sample
+title: Sample
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ overall_molecule:
+ name: overall_molecule
+ required: true
+ molecule:
+ name: molecule
+ required: true
+ ligands:
+ name: ligands
+ specimen:
+ name: specimen
+ required: true
+ grid:
+ name: grid
+attributes:
+ overall_molecule:
+ name: overall_molecule
+ description: Description of the overall molecule
+ title: Overall_Molecule
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: overall_molecule
+ owner: Sample
+ domain_of:
+ - Sample
+ range: OverallMolecule
+ required: true
+ molecule:
+ name: molecule
+ description: List of molecule associated with the sample
+ title: Molecule
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: molecule
+ owner: Sample
+ domain_of:
+ - Sample
+ range: Molecule
+ required: true
+ multivalued: true
+ ligands:
+ name: ligands
+ description: List of ligands associated with the sample
+ title: Ligands
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: ligands
+ owner: Sample
+ domain_of:
+ - Sample
+ range: Ligand
+ multivalued: true
+ specimen:
+ name: specimen
+ description: Description of the specimen
+ title: Specimen
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: specimen
+ owner: Sample
+ domain_of:
+ - Sample
+ range: Specimen
+ required: true
+ grid:
+ name: grid
+ description: Description of the grid used
+ title: Grid
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: grid
+ owner: Sample
+ domain_of:
+ - Sample
+ range: Grid
+
+A series of numbers constructed from min, max, and increment
+URI: https://w3id.org/osc-em/oscem-schemas/:Series
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| increment | +0..1 QuantityValue |
+Increment between elements of a series | +direct | +
| minimal | +0..1 QuantityValue |
+Minimal value of a given dataset property | +Range | +
| maximal | +0..1 QuantityValue |
+Maximal value of a given dataset property | +Range | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Series | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Series | +
name: Series
+description: A series of numbers constructed from min, max, and increment
+from_schema: https://w3id.org/osc-em/oscem-schemas
+is_a: Range
+slots:
+- increment
+
+name: Series
+description: A series of numbers constructed from min, max, and increment
+from_schema: https://w3id.org/osc-em/oscem-schemas
+is_a: Range
+attributes:
+ increment:
+ name: increment
+ description: Increment between elements of a series
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: increment
+ owner: Series
+ domain_of:
+ - Series
+ range: QuantityValue
+ minimal:
+ name: minimal
+ description: Minimal value of a given dataset property
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: minimal
+ owner: Series
+ domain_of:
+ - Range
+ range: QuantityValue
+ maximal:
+ name: maximal
+ description: Maximal value of a given dataset property
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: maximal
+ owner: Series
+ domain_of:
+ - Range
+ range: QuantityValue
+
+A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +https://w3id.org/osc-em/oscem-schemas/:sparqlpath | +
URI: https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| phaseplate | +0..1 Phaseplate |
+Phaseplate is a special optics device that can be used to enhance contrast | +direct | +
| spherical_aberration_corrector | +0..1 SphericalAberrationCorrector |
+Specialist device to correct for spherical aberration of the microscope lense... | +direct | +
| chromatic_aberration_corrector | +0..1 ChromaticAberrationCorrector |
+Specialist device to correct for chromatic aberration of the microscope lense... | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Acquisition | +specialist_optics | +range | +SpecialistOptics | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics | +
| native | +https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics | +
name: SpecialistOptics
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- phaseplate
+- spherical_aberration_corrector
+- chromatic_aberration_corrector
+
+name: SpecialistOptics
+from_schema: https://w3id.org/osc-em/oscem-schemas
+attributes:
+ phaseplate:
+ name: phaseplate
+ description: Phaseplate is a special optics device that can be used to enhance
+ contrast
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: phaseplate
+ owner: SpecialistOptics
+ domain_of:
+ - SpecialistOptics
+ range: Phaseplate
+ spherical_aberration_corrector:
+ name: spherical_aberration_corrector
+ description: Specialist device to correct for spherical aberration of the microscope
+ lenses
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: spherical_aberration_corrector
+ owner: SpecialistOptics
+ domain_of:
+ - SpecialistOptics
+ range: SphericalAberrationCorrector
+ chromatic_aberration_corrector:
+ name: chromatic_aberration_corrector
+ description: Specialist device to correct for chromatic aberration of the microscope
+ lenses
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: chromatic_aberration_corrector
+ owner: SpecialistOptics
+ domain_of:
+ - SpecialistOptics
+ range: ChromaticAberrationCorrector
+
+A class representing a specimen
+URI: https://w3id.org/osc-em/oscem-schemas/:Specimen
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| buffer | +0..1 String |
+Name/composition of the (chemical) sample buffer during grid preparation | +direct | +
| concentration | +0..1 QuantityValue |
+Concentration of the (supra)molecule in the sample, in mg/ml | +direct | +
| ph | +1 Float |
+pH of the sample buffer | +direct | +
| vitrification | +1 Boolean |
+Whether the sample was vitrified | +direct | +
| vitrification_cryogen | +1 String |
+Which cryogen was used for vitrification | +direct | +
| humidity | +0..1 QuantityValue |
+Environmental humidity just before vitrification, in % | +direct | +
| temperature | +0..1 QuantityValue |
+Environmental temperature just before vitrification, in K | +direct | +
| staining | +1 Boolean |
+Whether the sample was stained | +direct | +
| embedding | +1 Boolean |
+Whether the sample was embedded | +direct | +
| shadowing | +1 Boolean |
+Whether the sample was shadowed | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| Sample | +specimen | +range | +Specimen | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:Specimen | +
| native | +https://w3id.org/osc-em/oscem-schemas/:Specimen | +
name: Specimen
+description: A class representing a specimen
+title: Specimen
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- buffer
+- concentration
+- ph
+- vitrification
+- vitrification_cryogen
+- humidity
+- temperature
+- staining
+- embedding
+- shadowing
+slot_usage:
+ buffer:
+ name: buffer
+ concentration:
+ name: concentration
+ ph:
+ name: ph
+ required: true
+ vitrification:
+ name: vitrification
+ required: true
+ vitrification_cryogen:
+ name: vitrification_cryogen
+ required: true
+ humidity:
+ name: humidity
+ temperature:
+ name: temperature
+ staining:
+ name: staining
+ required: true
+ embedding:
+ name: embedding
+ required: true
+ shadowing:
+ name: shadowing
+ required: true
+
+name: Specimen
+description: A class representing a specimen
+title: Specimen
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ buffer:
+ name: buffer
+ concentration:
+ name: concentration
+ ph:
+ name: ph
+ required: true
+ vitrification:
+ name: vitrification
+ required: true
+ vitrification_cryogen:
+ name: vitrification_cryogen
+ required: true
+ humidity:
+ name: humidity
+ temperature:
+ name: temperature
+ staining:
+ name: staining
+ required: true
+ embedding:
+ name: embedding
+ required: true
+ shadowing:
+ name: shadowing
+ required: true
+attributes:
+ buffer:
+ name: buffer
+ description: Name/composition of the (chemical) sample buffer during grid preparation
+ title: Buffer
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: buffer
+ owner: Specimen
+ domain_of:
+ - Specimen
+ range: string
+ concentration:
+ name: concentration
+ description: Concentration of the (supra)molecule in the sample, in mg/ml
+ title: Concentration
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: concentration
+ owner: Specimen
+ domain_of:
+ - Specimen
+ range: QuantityValue
+ ph:
+ name: ph
+ description: pH of the sample buffer
+ title: pH
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: ph
+ owner: Specimen
+ domain_of:
+ - Specimen
+ range: float
+ required: true
+ vitrification:
+ name: vitrification
+ description: Whether the sample was vitrified
+ title: Vitrification
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: vitrification
+ owner: Specimen
+ domain_of:
+ - Specimen
+ range: boolean
+ required: true
+ vitrification_cryogen:
+ name: vitrification_cryogen
+ description: Which cryogen was used for vitrification
+ title: Vitrification_cryogen
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: vitrification_cryogen
+ owner: Specimen
+ domain_of:
+ - Specimen
+ range: string
+ required: true
+ humidity:
+ name: humidity
+ description: Environmental humidity just before vitrification, in %
+ title: Humidity
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: humidity
+ owner: Specimen
+ domain_of:
+ - Specimen
+ range: QuantityValue
+ temperature:
+ name: temperature
+ description: Environmental temperature just before vitrification, in K
+ title: Temperature
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: temperature
+ owner: Specimen
+ domain_of:
+ - Specimen
+ range: QuantityValue
+ minimum_value: 0.0
+ staining:
+ name: staining
+ description: Whether the sample was stained
+ title: Staining
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: staining
+ owner: Specimen
+ domain_of:
+ - Specimen
+ range: boolean
+ required: true
+ embedding:
+ name: embedding
+ description: Whether the sample was embedded
+ title: Embedding
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: embedding
+ owner: Specimen
+ domain_of:
+ - Specimen
+ range: boolean
+ required: true
+ shadowing:
+ name: shadowing
+ description: Whether the sample was shadowed
+ title: Shadowing
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: shadowing
+ owner: Specimen
+ domain_of:
+ - Specimen
+ range: boolean
+ required: true
+
+URI: https://w3id.org/osc-em/oscem-schemas/:SphericalAberrationCorrector
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| used | +1 Boolean |
+whether a specific instrument was used during data acquisition | +direct | +
| instrument_type | +1 String |
+Details of a given specialist instrument | +direct | +
| used by | +used in | +type | +used | +
|---|---|---|---|
| SpecialistOptics | +spherical_aberration_corrector | +range | +SphericalAberrationCorrector | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:SphericalAberrationCorrector | +
| native | +https://w3id.org/osc-em/oscem-schemas/:SphericalAberrationCorrector | +
name: SphericalAberrationCorrector
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slots:
+- used
+- instrument_type
+slot_usage:
+ used:
+ name: used
+ required: true
+ instrument_type:
+ name: instrument_type
+ required: true
+
+name: SphericalAberrationCorrector
+from_schema: https://w3id.org/osc-em/oscem-schemas
+slot_usage:
+ used:
+ name: used
+ required: true
+ instrument_type:
+ name: instrument_type
+ required: true
+attributes:
+ used:
+ name: used
+ description: whether a specific instrument was used during data acquisition
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: used
+ owner: SphericalAberrationCorrector
+ domain_of:
+ - EnergyFilter
+ - Phaseplate
+ - SphericalAberrationCorrector
+ - ChromaticAberrationCorrector
+ range: boolean
+ required: true
+ instrument_type:
+ name: instrument_type
+ description: Details of a given specialist instrument
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: instrument_type
+ owner: SphericalAberrationCorrector
+ domain_of:
+ - Phaseplate
+ - SphericalAberrationCorrector
+ - ChromaticAberrationCorrector
+ range: string
+ required: true
+
+A character string
+URI: xsd:string
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:string | +
| native | +https://w3id.org/osc-em/oscem-schemas/:string | +
| exact | +schema:Text | +
The min, max and increment of the tilt angle in a tomography session. Unit is degree.
+URI: https://w3id.org/osc-em/oscem-schemas/:TiltAngle
+| Name | +Cardinality and Range | +Description | +Inheritance | +
|---|---|---|---|
| increment | +0..1 QuantityValue |
+Increment between elements of a series | +Series | +
| minimal | +0..1 QuantityValue |
+Minimal value of a given dataset property | +Range | +
| maximal | +0..1 QuantityValue |
+Maximal value of a given dataset property | +Range | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:TiltAngle | +
| native | +https://w3id.org/osc-em/oscem-schemas/:TiltAngle | +
name: TiltAngle
+description: The min, max and increment of the tilt angle in a tomography session.
+ Unit is degree.
+from_schema: https://w3id.org/osc-em/oscem-schemas
+is_a: Series
+
+name: TiltAngle
+description: The min, max and increment of the tilt angle in a tomography session.
+ Unit is degree.
+from_schema: https://w3id.org/osc-em/oscem-schemas
+is_a: Series
+attributes:
+ increment:
+ name: increment
+ description: Increment between elements of a series
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: increment
+ owner: TiltAngle
+ domain_of:
+ - Series
+ range: QuantityValue
+ minimal:
+ name: minimal
+ description: Minimal value of a given dataset property
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: minimal
+ owner: TiltAngle
+ domain_of:
+ - Range
+ range: QuantityValue
+ maximal:
+ name: maximal
+ description: Maximal value of a given dataset property
+ from_schema: https://w3id.org/osc-em/oscem-schemas
+ rank: 1000
+ alias: maximal
+ owner: TiltAngle
+ domain_of:
+ - Range
+ range: QuantityValue
+
+A time object represents a (local) time of day, independent of any particular day
+URI: xsd:time
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:time | +
| native | +https://w3id.org/osc-em/oscem-schemas/:time | +
| exact | +schema:Time | +
a complete URI
+URI: xsd:anyURI
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:anyURI | +
| native | +https://w3id.org/osc-em/oscem-schemas/:uri | +
| close | +schema:URL | +
a URI or a CURIE
+URI: xsd:anyURI
+ +| Mapping Type | +Mapped Value | +
|---|---|
| self | +xsd:anyURI | +
| native | +https://w3id.org/osc-em/oscem-schemas/:uriorcurie | +
Schema for the Open Standards Community for Electron Microscopy (OSC-EM)
+ + + + + + +Voltage used for the electron acceleration, in kV
+URI: https://w3id.org/osc-em/oscem-schemas/:acceleration_voltage
+ + +| Name | +Description | +Modifies Slot | +
|---|---|---|
| Instrument | +Instrument values, mostly constant across a data collection | +yes | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:acceleration_voltage | +
| native | +https://w3id.org/osc-em/oscem-schemas/:acceleration_voltage | +
name: acceleration_voltage
+description: Voltage used for the electron acceleration, in kV
+from_schema: https://w3id.org/osc-em/oscem-schemas
+rank: 1000
+alias: acceleration_voltage
+domain_of:
+- Instrument
+range: QuantityValue
+
+Describe the data acquisition parameters
+URI: https://w3id.org/osc-em/oscem-schemas/:acquisition
+ + +| Name | +Description | +Modifies Slot | +
|---|---|---|
| EMDataset | +OSC-EM Metadata for a dataset | +yes | +
| Mapping Type | +Mapped Value | +
|---|---|
| self | +https://w3id.org/osc-em/oscem-schemas/:acquisition | +
| native | +https://w3id.org/osc-em/oscem-schemas/:acquisition | +
name: acquisition
+description: Describe the data acquisition parameters
+title: Acquisition
+from_schema: https://w3id.org/osc-em/oscem-schemas
+rank: 1000
+alias: acquisition
+domain_of:
+- EMDataset
+range: Acquisition
+
+\n {translation(\"search.result.term.missing\")}: {...missing}\n
\n }\n \n