From 659b35bbbf9362df62887bdb6aa48d10c36d6d4a Mon Sep 17 00:00:00 2001 From: <> Date: Tue, 27 Aug 2024 14:18:17 +0000 Subject: [PATCH] Deployed c700158 with MkDocs version: 1.6.0 --- model/index.html | 4 ++-- name/index.html | 10 +++++----- search/search_index.json | 2 +- used/index.html | 4 ++-- width/index.html | 10 +++++----- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/model/index.html b/model/index.html index 9ead61f..705c191 100644 --- a/model/index.html +++ b/model/index.html @@ -344,7 +344,7 @@

Applicable Classes

no -SphericalAberrationCorrector +ChromaticAberrationCorrector yes @@ -354,7 +354,7 @@

Applicable Classes

yes -ChromaticAberrationCorrector +SphericalAberrationCorrector yes diff --git a/name/index.html b/name/index.html index 626d3e0..7d28986 100644 --- a/name/index.html +++ b/name/index.html @@ -339,16 +339,16 @@

Applicable Classes

-Grant -Grant -no - - Author yes +Grant +Grant +no + + Person no diff --git a/search/search_index.json b/search/search_index.json index 33b56c0..27d88cb 100644 --- a/search/search_index.json +++ b/search/search_index.json @@ -1 +1 @@ -{"config":{"indexing":"full","lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"oscem-schemas Schema for the Open Standards Community for Electron Microscopy (OSC-EM) URI: https://w3id.org/osc-em/oscem-schemas Name: oscem-schemas Classes Class Description Acquisition None Any Any type, used as the base for type-narrowing. See https://linkml.io/linkml/schemas/advanced.html | | BoundingBox2D | an axis-aligned 2D bounding box (float units) | | ChromaticAberrationCorrector | None | | EMDataset | OSC-EM Metadata for a dataset | | EnergyFilter | None | | Grant | Grant | | Grid | A class representing a grid | | ImageSize | size of a 2D image (in integer units) | | Instrument | Instrument values, mostly constant across a data collection. | | Ligand | A class representing a ligand | | Molecule | A class representing a molecule | | OverallMolecule | A class representing the overall molecule | | Person | None | | Author | None | | Phaseplate | None | | QuantityValue | Value together with unit | | Range | A range constructed from min and max | | Series | A series of numbers constructed from min, max, and increment | | TiltAngle | The min, max and increment of the tilt angle in a tomography session. Unit is degree. | | Sample | A class representing a sample | | SpecialistOptics | None | | Specimen | A class representing a specimen | | SphericalAberrationCorrector | None | Slots Slot Description acceleration_voltage Voltage used for the electron acceleration, in kV acquisition Describe the data acquisition parameters authors List of authors associated with the project beamshift Movement of the beam above the sample for data collection purposes that does ... beamtilt Another way to move the beam above the sample for data collection purposes th... beamtiltgroups Number of Beamtilt groups present in this dataset - for optimized processing ... binning_camera Level of binning on the images applied during data collection budget budget buffer Name/composition of the (chemical) sample buffer during grid preparation c2_aperture C2 aperture size used in data acquisition, in \u00b5m calibrated_defocus Machine estimated defocus, min and max values in \u00b5m calibrated_magnification Calculated magnification, no unit chromatic_aberration_corrector Specialist device to correct for chromatic aberration of the microscope lense... concentration Concentration of the (supra)molecule in the sample, in M country Country of the author's institution cryogen Cryogen used in cooling the instrument and sample, usually nitrogen cs Spherical aberration of the instrument, in mm date_time Time and date of the data acquisition detector Make and model of the detector used detector_mode Operating mode of the detector dose_per_movie Average dose per image/movie/tilt - given in electrons per square Angstrom electron_source Type of electron source used in the microscope, such as FEG email email embedding Whether the sample was embedded end_date end date energy_filter Wether an energy filter was used and its specifics exposure_time Time of data acquisition per movie/tilt - in s expression_system Scientific name of the organism used to produce the molecule of interest film_material Type of material the support film is made of film_support Whether a support film was used film_thickness Thickness of the support film film_topology Topology of the support film first_name first name frames_per_movie Number of frames that on average constitute a full movie, can be a bit hard t... funder funder gainref_flip_rotate Whether and how you have to flip or rotate the gainref in order to align with... gene_name Name of the gene of interest grants List of grants associated with the project grid Description of the grid used grids_imaged Number of grids imaged for this project - here with qualifier during this dat... has_unit Unit has_value Value height The height of a given item - unit depends on item holder Speciman holder model holder_cryogen Type of cryogen used in the holder - if the holder is cooled seperately humidity Environmental humidity just before vitrification, in % illumination Mode of illumination used during data collection image_size The size of the image in pixels, height and width given images_generated Number of images generated total for this data collection - might need a qual... imageshift Movement of the Beam below the image in order to shift the image on the detec... imaging Mode of imaging used during data collection increment Increment between elements of a series instrument Describe the instrument used to acquire the data ligands List of ligands associated with the sample manufacturer Grid manufacturer material Material out of which the grid is made maximal Maximal value of a given dataset property mesh Grid mesh in lines per inch microscope Name/Type of the Microscope microscope_software Software used for instrument control, minimal Minimal value of a given dataset property model Make and model of a specialized device molecular_class Class of the molecule molecular_type Description of the overall supramolecular type, i molecular_weight Molecular weight in Da molecule List of molecule associated with the sample name name name_mol Name of an individual molecule (often protein) in the sample name_org Name of the organization name_sample Name of the full sample natural_source Scientific name of the natural host organism nominal_defocus Target defocus set, min and max values in \u00b5m nominal_magnification Magnification level as indicated by the instrument, no unit orcid ORCID of the author, a type of unique identifier overall_molecule Description of the overall molecule person person ph pH of the sample buffer phaseplate Phaseplate is a special optics device that can be used to enhance contrast pixel_size Pixel size, in Angstrom present Whether the model contains any ligands pretreatment_atmosphere Atmospheric conditions in the chamber during pretreatment, i pretreatment_pressure Pressure of the chamber during pretreatment, in Pa pretreatment_time Length of time of the pretreatment in s pretreatment_type Type of pretreatment of the grid, i project_id project id reference Link to a reference of your ligand, i role Role of the author, i sample Sample information sequence Full sequence of the sample as in the data, i shadowing Whether the sample was shadowed smile Provide a valid SMILE string of your ligand source Where the sample was taken from, i specialist_optics Any type of special optics, such as a phaseplate specimen Description of the specimen spherical_aberration_corrector Specialist device to correct for spherical aberration of the microscope lense... staining Whether the sample was stained start_date start date taxonomy_id_expression Taxonomy ID of the expression system organism taxonomy_id_source Taxonomy ID of the natural source organism temperature Environmental temperature just before vitrification, in K temperature_range Temperature during data collection, in K with min and max values tilt_angle The min, max and increment of the tilt angle in a tomography session tilt_axis_angle The tilt axis angle of a tomography series type_org Type of organization, academic, commercial, governmental, etc used whether a specific instrument was used during data acquisition vitrification Whether the sample was vitrified vitrification_cryogen Which cryogen was used for vitrification width The width of a given item - unit depends on item work_phone work phone work_status work status x_max maximum x x_min minimum x y_max maximum y y_min minimum y Enumerations Enumeration Description MoleculeClassEnum OrganizationTypeEnum Types Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE Subsets Subset Description","title":"Index"},{"location":"#oscem-schemas","text":"Schema for the Open Standards Community for Electron Microscopy (OSC-EM) URI: https://w3id.org/osc-em/oscem-schemas Name: oscem-schemas","title":"oscem-schemas"},{"location":"#classes","text":"Class Description Acquisition None Any Any type, used as the base for type-narrowing. See https://linkml.io/linkml/schemas/advanced.html | | BoundingBox2D | an axis-aligned 2D bounding box (float units) | | ChromaticAberrationCorrector | None | | EMDataset | OSC-EM Metadata for a dataset | | EnergyFilter | None | | Grant | Grant | | Grid | A class representing a grid | | ImageSize | size of a 2D image (in integer units) | | Instrument | Instrument values, mostly constant across a data collection. | | Ligand | A class representing a ligand | | Molecule | A class representing a molecule | | OverallMolecule | A class representing the overall molecule | | Person | None | | Author | None | | Phaseplate | None | | QuantityValue | Value together with unit | | Range | A range constructed from min and max | | Series | A series of numbers constructed from min, max, and increment | | TiltAngle | The min, max and increment of the tilt angle in a tomography session. Unit is degree. | | Sample | A class representing a sample | | SpecialistOptics | None | | Specimen | A class representing a specimen | | SphericalAberrationCorrector | None |","title":"Classes"},{"location":"#slots","text":"Slot Description acceleration_voltage Voltage used for the electron acceleration, in kV acquisition Describe the data acquisition parameters authors List of authors associated with the project beamshift Movement of the beam above the sample for data collection purposes that does ... beamtilt Another way to move the beam above the sample for data collection purposes th... beamtiltgroups Number of Beamtilt groups present in this dataset - for optimized processing ... binning_camera Level of binning on the images applied during data collection budget budget buffer Name/composition of the (chemical) sample buffer during grid preparation c2_aperture C2 aperture size used in data acquisition, in \u00b5m calibrated_defocus Machine estimated defocus, min and max values in \u00b5m calibrated_magnification Calculated magnification, no unit chromatic_aberration_corrector Specialist device to correct for chromatic aberration of the microscope lense... concentration Concentration of the (supra)molecule in the sample, in M country Country of the author's institution cryogen Cryogen used in cooling the instrument and sample, usually nitrogen cs Spherical aberration of the instrument, in mm date_time Time and date of the data acquisition detector Make and model of the detector used detector_mode Operating mode of the detector dose_per_movie Average dose per image/movie/tilt - given in electrons per square Angstrom electron_source Type of electron source used in the microscope, such as FEG email email embedding Whether the sample was embedded end_date end date energy_filter Wether an energy filter was used and its specifics exposure_time Time of data acquisition per movie/tilt - in s expression_system Scientific name of the organism used to produce the molecule of interest film_material Type of material the support film is made of film_support Whether a support film was used film_thickness Thickness of the support film film_topology Topology of the support film first_name first name frames_per_movie Number of frames that on average constitute a full movie, can be a bit hard t... funder funder gainref_flip_rotate Whether and how you have to flip or rotate the gainref in order to align with... gene_name Name of the gene of interest grants List of grants associated with the project grid Description of the grid used grids_imaged Number of grids imaged for this project - here with qualifier during this dat... has_unit Unit has_value Value height The height of a given item - unit depends on item holder Speciman holder model holder_cryogen Type of cryogen used in the holder - if the holder is cooled seperately humidity Environmental humidity just before vitrification, in % illumination Mode of illumination used during data collection image_size The size of the image in pixels, height and width given images_generated Number of images generated total for this data collection - might need a qual... imageshift Movement of the Beam below the image in order to shift the image on the detec... imaging Mode of imaging used during data collection increment Increment between elements of a series instrument Describe the instrument used to acquire the data ligands List of ligands associated with the sample manufacturer Grid manufacturer material Material out of which the grid is made maximal Maximal value of a given dataset property mesh Grid mesh in lines per inch microscope Name/Type of the Microscope microscope_software Software used for instrument control, minimal Minimal value of a given dataset property model Make and model of a specialized device molecular_class Class of the molecule molecular_type Description of the overall supramolecular type, i molecular_weight Molecular weight in Da molecule List of molecule associated with the sample name name name_mol Name of an individual molecule (often protein) in the sample name_org Name of the organization name_sample Name of the full sample natural_source Scientific name of the natural host organism nominal_defocus Target defocus set, min and max values in \u00b5m nominal_magnification Magnification level as indicated by the instrument, no unit orcid ORCID of the author, a type of unique identifier overall_molecule Description of the overall molecule person person ph pH of the sample buffer phaseplate Phaseplate is a special optics device that can be used to enhance contrast pixel_size Pixel size, in Angstrom present Whether the model contains any ligands pretreatment_atmosphere Atmospheric conditions in the chamber during pretreatment, i pretreatment_pressure Pressure of the chamber during pretreatment, in Pa pretreatment_time Length of time of the pretreatment in s pretreatment_type Type of pretreatment of the grid, i project_id project id reference Link to a reference of your ligand, i role Role of the author, i sample Sample information sequence Full sequence of the sample as in the data, i shadowing Whether the sample was shadowed smile Provide a valid SMILE string of your ligand source Where the sample was taken from, i specialist_optics Any type of special optics, such as a phaseplate specimen Description of the specimen spherical_aberration_corrector Specialist device to correct for spherical aberration of the microscope lense... staining Whether the sample was stained start_date start date taxonomy_id_expression Taxonomy ID of the expression system organism taxonomy_id_source Taxonomy ID of the natural source organism temperature Environmental temperature just before vitrification, in K temperature_range Temperature during data collection, in K with min and max values tilt_angle The min, max and increment of the tilt angle in a tomography session tilt_axis_angle The tilt axis angle of a tomography series type_org Type of organization, academic, commercial, governmental, etc used whether a specific instrument was used during data acquisition vitrification Whether the sample was vitrified vitrification_cryogen Which cryogen was used for vitrification width The width of a given item - unit depends on item work_phone work phone work_status work status x_max maximum x x_min minimum x y_max maximum y y_min minimum y","title":"Slots"},{"location":"#enumerations","text":"Enumeration Description MoleculeClassEnum OrganizationTypeEnum","title":"Enumerations"},{"location":"#types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE","title":"Types"},{"location":"#subsets","text":"Subset Description","title":"Subsets"},{"location":"Acquisition/","text":"Class: Acquisition URI: https://w3id.org/osc-em/oscem-schemas/:Acquisition classDiagram class Acquisition click Acquisition href \"../Acquisition\" Acquisition : beamshift Acquisition --> \"0..1\" BoundingBox2D : beamshift click BoundingBox2D href \"../BoundingBox2D\" Acquisition : beamtilt Acquisition --> \"0..1\" BoundingBox2D : beamtilt click BoundingBox2D href \"../BoundingBox2D\" Acquisition : beamtiltgroups Acquisition : binning_camera Acquisition : calibrated_defocus Acquisition --> \"0..1\" Range : calibrated_defocus click Range href \"../Range\" Acquisition : calibrated_magnification Acquisition : cryogen Acquisition : date_time Acquisition --> \"1\" Any : date_time click Any href \"../Any\" Acquisition : detector Acquisition : detector_mode Acquisition : dose_per_movie Acquisition : energy_filter Acquisition --> \"0..1\" EnergyFilter : energy_filter click EnergyFilter href \"../EnergyFilter\" Acquisition : exposure_time Acquisition : frames_per_movie Acquisition : gainref_flip_rotate Acquisition : grids_imaged Acquisition : holder Acquisition : holder_cryogen Acquisition : image_size Acquisition --> \"0..1\" ImageSize : image_size click ImageSize href \"../ImageSize\" Acquisition : images_generated Acquisition : imageshift Acquisition --> \"0..1\" BoundingBox2D : imageshift click BoundingBox2D href \"../BoundingBox2D\" Acquisition : microscope_software Acquisition : nominal_defocus Acquisition --> \"0..1\" Range : nominal_defocus click Range href \"../Range\" Acquisition : nominal_magnification Acquisition : pixel_size Acquisition : specialist_optics Acquisition --> \"0..1\" SpecialistOptics : specialist_optics click SpecialistOptics href \"../SpecialistOptics\" Acquisition : temperature_range Acquisition --> \"0..1\" Range : temperature_range click Range href \"../Range\" Slots Name Cardinality and Range Description Inheritance nominal_defocus 0..1 Range Target defocus set, min and max values in \u00b5m direct calibrated_defocus 0..1 Range Machine estimated defocus, min and max values in \u00b5m 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 Float 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 Float 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 Float 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 Usages used by used in type used EMDataset acquisition range Acquisition Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Acquisition native https://w3id.org/osc-em/oscem-schemas/:Acquisition LinkML Source Direct 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 Induced 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 \u00b5m. 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 \u00b5m. 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: float 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: float 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: float 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 \u00b5m. 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","title":"Class: Acquisition"},{"location":"Acquisition/#class-acquisition","text":"URI: https://w3id.org/osc-em/oscem-schemas/:Acquisition classDiagram class Acquisition click Acquisition href \"../Acquisition\" Acquisition : beamshift Acquisition --> \"0..1\" BoundingBox2D : beamshift click BoundingBox2D href \"../BoundingBox2D\" Acquisition : beamtilt Acquisition --> \"0..1\" BoundingBox2D : beamtilt click BoundingBox2D href \"../BoundingBox2D\" Acquisition : beamtiltgroups Acquisition : binning_camera Acquisition : calibrated_defocus Acquisition --> \"0..1\" Range : calibrated_defocus click Range href \"../Range\" Acquisition : calibrated_magnification Acquisition : cryogen Acquisition : date_time Acquisition --> \"1\" Any : date_time click Any href \"../Any\" Acquisition : detector Acquisition : detector_mode Acquisition : dose_per_movie Acquisition : energy_filter Acquisition --> \"0..1\" EnergyFilter : energy_filter click EnergyFilter href \"../EnergyFilter\" Acquisition : exposure_time Acquisition : frames_per_movie Acquisition : gainref_flip_rotate Acquisition : grids_imaged Acquisition : holder Acquisition : holder_cryogen Acquisition : image_size Acquisition --> \"0..1\" ImageSize : image_size click ImageSize href \"../ImageSize\" Acquisition : images_generated Acquisition : imageshift Acquisition --> \"0..1\" BoundingBox2D : imageshift click BoundingBox2D href \"../BoundingBox2D\" Acquisition : microscope_software Acquisition : nominal_defocus Acquisition --> \"0..1\" Range : nominal_defocus click Range href \"../Range\" Acquisition : nominal_magnification Acquisition : pixel_size Acquisition : specialist_optics Acquisition --> \"0..1\" SpecialistOptics : specialist_optics click SpecialistOptics href \"../SpecialistOptics\" Acquisition : temperature_range Acquisition --> \"0..1\" Range : temperature_range click Range href \"../Range\"","title":"Class: Acquisition"},{"location":"Acquisition/#slots","text":"Name Cardinality and Range Description Inheritance nominal_defocus 0..1 Range Target defocus set, min and max values in \u00b5m direct calibrated_defocus 0..1 Range Machine estimated defocus, min and max values in \u00b5m 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 Float 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 Float 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 - 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Acquisition range: Range calibrated_defocus: name: calibrated_defocus description: Machine estimated defocus, min and max values in \u00b5m. 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: float 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: float 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: float 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 \u00b5m. 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. 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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 name_org: name: name_org required: true type_org: name: type_org required: true country: name: country required: true attributes: 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 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 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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","title":"Class: EMDataset"},{"location":"EMDataset/#class-emdataset","text":"OSC-EM Metadata for a dataset URI: https://w3id.org/osc-em/oscem-schemas/:EMDataset classDiagram class EMDataset click EMDataset href \"../EMDataset\" EMDataset : acquisition EMDataset --> \"1\" Acquisition : acquisition click Acquisition href \"../Acquisition\" 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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 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- SphericalAberrationCorrector - ChromaticAberrationCorrector range: boolean required: true model: name: model description: Make and model of a specialized device from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: model owner: EnergyFilter domain_of: - EnergyFilter - Phaseplate - SphericalAberrationCorrector - ChromaticAberrationCorrector 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","title":"Class: EnergyFilter"},{"location":"EnergyFilter/#class-energyfilter","text":"URI: https://w3id.org/osc-em/oscem-schemas/:EnergyFilter classDiagram class EnergyFilter click EnergyFilter href \"../EnergyFilter\" EnergyFilter : model EnergyFilter : used EnergyFilter : width","title":"Class: EnergyFilter"},{"location":"EnergyFilter/#slots","text":"Name Cardinality and Range 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Instrument range: integer required: true c2_aperture: name: c2_aperture description: C2 aperture size used in data acquisition, in \u00b5m from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: c2_aperture owner: Instrument domain_of: - Instrument range: integer 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: float required: true","title":"Induced"},{"location":"Integer/","text":"Type: Integer An integer URI: xsd:integer base : int uri : xsd:integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:integer native https://w3id.org/osc-em/oscem-schemas/:integer exact schema:Integer","title":"Type: Integer"},{"location":"Integer/#type-integer","text":"An integer URI: xsd:integer base : int uri : xsd:integer","title":"Type: Integer"},{"location":"Integer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Integer/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Integer/#mappings","text":"Mapping Type Mapped Value self xsd:integer native https://w3id.org/osc-em/oscem-schemas/:integer exact schema:Integer","title":"Mappings"},{"location":"Jsonpath/","text":"Type: Jsonpath 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 base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:jsonpath","title":"Type: Jsonpath"},{"location":"Jsonpath/#type-jsonpath","text":"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 base : str uri : xsd:string repr : str","title":"Type: Jsonpath"},{"location":"Jsonpath/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Jsonpath/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Jsonpath/#mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:jsonpath","title":"Mappings"},{"location":"Jsonpointer/","text":"Type: Jsonpointer 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 base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:jsonpointer","title":"Type: Jsonpointer"},{"location":"Jsonpointer/#type-jsonpointer","text":"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 base : str uri : xsd:string repr : str","title":"Type: Jsonpointer"},{"location":"Jsonpointer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Jsonpointer/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Jsonpointer/#mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:jsonpointer","title":"Mappings"},{"location":"Ligand/","text":"Class: Ligand (Ligand) A class representing a ligand URI: https://w3id.org/osc-em/oscem-schemas/:Ligand classDiagram class Ligand click Ligand href \"../Ligand\" Ligand : present Ligand : reference Ligand : smile Slots Name Cardinality and Range Description Inheritance present 1 Boolean Whether the model contains any ligands direct smile 0..1 String Provide a valid SMILE string of your ligand direct reference 0..1 String Link to a reference of your ligand, i direct Usages used by used in type used Sample ligands range Ligand Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Ligand native https://w3id.org/osc-em/oscem-schemas/:Ligand LinkML Source Direct name: Ligand description: A class representing a ligand title: Ligand from_schema: https://w3id.org/osc-em/oscem-schemas slots: - present - smile - reference slot_usage: present: name: present required: true Induced 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 smile: name: smile description: Provide a valid SMILE string of your ligand title: SMILE from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: smile 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","title":"Class: Ligand (Ligand)"},{"location":"Ligand/#class-ligand-ligand","text":"A class representing a ligand URI: https://w3id.org/osc-em/oscem-schemas/:Ligand classDiagram class Ligand click Ligand href \"../Ligand\" Ligand : present Ligand : reference Ligand : smile","title":"Class: Ligand (Ligand)"},{"location":"Ligand/#slots","text":"Name Cardinality and Range Description Inheritance present 1 Boolean Whether the model contains any ligands direct smile 0..1 String Provide a valid SMILE string of your ligand direct reference 0..1 String Link to a reference of your ligand, i direct","title":"Slots"},{"location":"Ligand/#usages","text":"used by used in type used Sample ligands range Ligand","title":"Usages"},{"location":"Ligand/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Ligand/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Ligand/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Ligand native https://w3id.org/osc-em/oscem-schemas/:Ligand","title":"Mappings"},{"location":"Ligand/#linkml-source","text":"","title":"LinkML Source"},{"location":"Ligand/#direct","text":"name: Ligand description: A class representing a ligand title: Ligand from_schema: https://w3id.org/osc-em/oscem-schemas slots: - present - smile - reference slot_usage: present: name: present required: true","title":"Direct"},{"location":"Ligand/#induced","text":"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 smile: name: smile description: Provide a valid SMILE string of your ligand title: SMILE from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: smile 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","title":"Induced"},{"location":"Molecule/","text":"Class: Molecule (Molecule) A class representing a molecule URI: https://w3id.org/osc-em/oscem-schemas/:Molecule classDiagram class Molecule click Molecule href \"../Molecule\" Molecule : expression_system Molecule : gene_name Molecule : molecular_class Molecule --> \"1\" MoleculeClassEnum : molecular_class click MoleculeClassEnum href \"../MoleculeClassEnum\" Molecule : molecular_type Molecule : name_mol Molecule : natural_source Molecule : sequence Molecule : taxonomy_id_expression Molecule : taxonomy_id_source Slots 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 supramolecular 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 Usages used by used in type used Sample molecule range Molecule Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Molecule native https://w3id.org/osc-em/oscem-schemas/:Molecule LinkML Source Direct 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 Induced 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 supramolecular 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","title":"Class: Molecule (Molecule)"},{"location":"Molecule/#class-molecule-molecule","text":"A class representing a molecule URI: https://w3id.org/osc-em/oscem-schemas/:Molecule classDiagram class Molecule click Molecule href \"../Molecule\" Molecule : expression_system Molecule : gene_name Molecule : molecular_class Molecule --> \"1\" MoleculeClassEnum : molecular_class click MoleculeClassEnum href \"../MoleculeClassEnum\" Molecule : molecular_type Molecule : name_mol Molecule : natural_source Molecule : sequence Molecule : taxonomy_id_expression Molecule : taxonomy_id_source","title":"Class: Molecule (Molecule)"},{"location":"Molecule/#slots","text":"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 supramolecular 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","title":"Slots"},{"location":"Molecule/#usages","text":"used by used in type used Sample molecule range Molecule","title":"Usages"},{"location":"Molecule/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Molecule/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Molecule/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Molecule native https://w3id.org/osc-em/oscem-schemas/:Molecule","title":"Mappings"},{"location":"Molecule/#linkml-source","text":"","title":"LinkML Source"},{"location":"Molecule/#direct","text":"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","title":"Direct"},{"location":"Molecule/#induced","text":"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 supramolecular 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","title":"Induced"},{"location":"MoleculeClassEnum/","text":"Enum: MoleculeClassEnum URI: MoleculeClassEnum Permissible Values Value Meaning Description Antibiotic None Antibiotic Carbohydrate None Carbohydrate Chimera None Chimera None of these None None of these Slots Name Description molecular_class Class of the molecule Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas LinkML Source 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","title":"Enum: MoleculeClassEnum"},{"location":"MoleculeClassEnum/#enum-moleculeclassenum","text":"URI: MoleculeClassEnum","title":"Enum: MoleculeClassEnum"},{"location":"MoleculeClassEnum/#permissible-values","text":"Value Meaning Description Antibiotic None Antibiotic Carbohydrate None Carbohydrate Chimera None Chimera None of these None None of these","title":"Permissible Values"},{"location":"MoleculeClassEnum/#slots","text":"Name Description molecular_class Class of the molecule","title":"Slots"},{"location":"MoleculeClassEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"MoleculeClassEnum/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"MoleculeClassEnum/#linkml-source","text":"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","title":"LinkML Source"},{"location":"Ncname/","text":"Type: Ncname Prefix part of CURIE URI: xsd:string base : NCName uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:ncname","title":"Type: Ncname"},{"location":"Ncname/#type-ncname","text":"Prefix part of CURIE URI: xsd:string base : NCName uri : xsd:string repr : str","title":"Type: Ncname"},{"location":"Ncname/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Ncname/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Ncname/#mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:ncname","title":"Mappings"},{"location":"Nodeidentifier/","text":"Type: Nodeidentifier A URI, CURIE or BNODE that represents a node in a model. URI: shex:nonLiteral base : NodeIdentifier uri : shex:nonLiteral repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self shex:nonLiteral native https://w3id.org/osc-em/oscem-schemas/:nodeidentifier","title":"Type: Nodeidentifier"},{"location":"Nodeidentifier/#type-nodeidentifier","text":"A URI, CURIE or BNODE that represents a node in a model. URI: shex:nonLiteral base : NodeIdentifier uri : shex:nonLiteral repr : str","title":"Type: Nodeidentifier"},{"location":"Nodeidentifier/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Nodeidentifier/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Nodeidentifier/#mappings","text":"Mapping Type Mapped Value self shex:nonLiteral native https://w3id.org/osc-em/oscem-schemas/:nodeidentifier","title":"Mappings"},{"location":"Objectidentifier/","text":"Type: Objectidentifier A URI or CURIE that represents an object in the model. 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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","title":"Direct"},{"location":"Sample/#induced","text":"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","title":"Induced"},{"location":"Series/","text":"Class: Series A series of numbers constructed from min, max, and increment URI: https://w3id.org/osc-em/oscem-schemas/:Series classDiagram class Series click Series href \"../Series\" Range <|-- Series click Range href \"../Range\" Series <|-- TiltAngle click TiltAngle href \"../TiltAngle\" Series : increment Series : maximal Series : minimal Inheritance Range Series TiltAngle Slots Name Cardinality and Range Description Inheritance increment 0..1 Float Increment between elements of a series direct minimal 0..1 Float Minimal value of a given dataset property Range maximal 0..1 Float Maximal value of a given dataset property Range Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Series native https://w3id.org/osc-em/oscem-schemas/:Series LinkML Source Direct 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 Induced 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: float 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: float 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: float","title":"Class: Series"},{"location":"Series/#class-series","text":"A series of numbers constructed from min, max, and increment URI: https://w3id.org/osc-em/oscem-schemas/:Series classDiagram class Series click Series href \"../Series\" Range <|-- Series click Range href \"../Range\" Series <|-- TiltAngle click TiltAngle href \"../TiltAngle\" Series : increment Series : maximal Series : minimal","title":"Class: Series"},{"location":"Series/#inheritance","text":"Range Series TiltAngle","title":"Inheritance"},{"location":"Series/#slots","text":"Name Cardinality and Range Description Inheritance increment 0..1 Float Increment between elements of a series direct minimal 0..1 Float Minimal value of a given dataset property Range maximal 0..1 Float Maximal value of a given dataset property Range","title":"Slots"},{"location":"Series/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Series/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Series/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Series native https://w3id.org/osc-em/oscem-schemas/:Series","title":"Mappings"},{"location":"Series/#linkml-source","text":"","title":"LinkML Source"},{"location":"Series/#direct","text":"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","title":"Direct"},{"location":"Series/#induced","text":"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: float 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: float 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: float","title":"Induced"},{"location":"Sparqlpath/","text":"Type: Sparqlpath 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 base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:sparqlpath","title":"Type: Sparqlpath"},{"location":"Sparqlpath/#type-sparqlpath","text":"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 base : str uri : xsd:string repr : str","title":"Type: Sparqlpath"},{"location":"Sparqlpath/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Sparqlpath/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Sparqlpath/#mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:sparqlpath","title":"Mappings"},{"location":"SpecialistOptics/","text":"Class: SpecialistOptics URI: https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics classDiagram class SpecialistOptics click SpecialistOptics href \"../SpecialistOptics\" SpecialistOptics : chromatic_aberration_corrector SpecialistOptics --> \"0..1\" ChromaticAberrationCorrector : chromatic_aberration_corrector click ChromaticAberrationCorrector href \"../ChromaticAberrationCorrector\" SpecialistOptics : phaseplate SpecialistOptics --> \"0..1\" Phaseplate : phaseplate click Phaseplate href \"../Phaseplate\" SpecialistOptics : spherical_aberration_corrector SpecialistOptics --> \"0..1\" SphericalAberrationCorrector : spherical_aberration_corrector click SphericalAberrationCorrector href \"../SphericalAberrationCorrector\" Slots 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 Usages used by used in type used Acquisition specialist_optics range SpecialistOptics Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics native https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics LinkML Source Direct name: SpecialistOptics from_schema: https://w3id.org/osc-em/oscem-schemas slots: - phaseplate - spherical_aberration_corrector - chromatic_aberration_corrector Induced 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","title":"Class: SpecialistOptics"},{"location":"SpecialistOptics/#class-specialistoptics","text":"URI: https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics classDiagram class SpecialistOptics click SpecialistOptics href \"../SpecialistOptics\" SpecialistOptics : chromatic_aberration_corrector SpecialistOptics --> \"0..1\" ChromaticAberrationCorrector : chromatic_aberration_corrector click ChromaticAberrationCorrector href \"../ChromaticAberrationCorrector\" SpecialistOptics : phaseplate SpecialistOptics --> \"0..1\" Phaseplate : phaseplate click Phaseplate href \"../Phaseplate\" SpecialistOptics : spherical_aberration_corrector SpecialistOptics --> \"0..1\" SphericalAberrationCorrector : spherical_aberration_corrector click SphericalAberrationCorrector href \"../SphericalAberrationCorrector\"","title":"Class: SpecialistOptics"},{"location":"SpecialistOptics/#slots","text":"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","title":"Slots"},{"location":"SpecialistOptics/#usages","text":"used by used in type used Acquisition specialist_optics range SpecialistOptics","title":"Usages"},{"location":"SpecialistOptics/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecialistOptics/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"SpecialistOptics/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics native https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics","title":"Mappings"},{"location":"SpecialistOptics/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecialistOptics/#direct","text":"name: SpecialistOptics from_schema: https://w3id.org/osc-em/oscem-schemas slots: - phaseplate - spherical_aberration_corrector - chromatic_aberration_corrector","title":"Direct"},{"location":"SpecialistOptics/#induced","text":"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","title":"Induced"},{"location":"Specimen/","text":"Class: Specimen (Specimen) A class representing a specimen URI: https://w3id.org/osc-em/oscem-schemas/:Specimen classDiagram class Specimen click Specimen href \"../Specimen\" Specimen : buffer Specimen : concentration Specimen : embedding Specimen : humidity Specimen : ph Specimen : shadowing Specimen : staining Specimen : temperature Specimen : vitrification Specimen : vitrification_cryogen Slots Name Cardinality and Range Description Inheritance buffer 0..1 String Name/composition of the (chemical) sample buffer during grid preparation direct concentration 0..1 Float Concentration of the (supra)molecule in the sample, in M 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 Float Environmental humidity just before vitrification, in % direct temperature 0..1 Float 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 Usages used by used in type used Sample specimen range Specimen Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Specimen native https://w3id.org/osc-em/oscem-schemas/:Specimen LinkML Source Direct 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 Induced 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 M title: Concentration from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: concentration owner: Specimen domain_of: - Specimen range: float 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: float 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: float 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","title":"Class: Specimen (Specimen)"},{"location":"Specimen/#class-specimen-specimen","text":"A class representing a specimen URI: https://w3id.org/osc-em/oscem-schemas/:Specimen classDiagram class Specimen click Specimen href \"../Specimen\" Specimen : buffer Specimen : concentration Specimen : embedding Specimen : humidity Specimen : ph Specimen : shadowing Specimen : staining Specimen : temperature Specimen : vitrification Specimen : vitrification_cryogen","title":"Class: Specimen (Specimen)"},{"location":"Specimen/#slots","text":"Name Cardinality and Range Description Inheritance buffer 0..1 String Name/composition of the (chemical) sample buffer during grid preparation direct concentration 0..1 Float Concentration of the (supra)molecule in the sample, in M 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 Float Environmental humidity just before vitrification, in % direct temperature 0..1 Float 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","title":"Slots"},{"location":"Specimen/#usages","text":"used by used in type used Sample specimen range Specimen","title":"Usages"},{"location":"Specimen/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Specimen/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Specimen/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Specimen native https://w3id.org/osc-em/oscem-schemas/:Specimen","title":"Mappings"},{"location":"Specimen/#linkml-source","text":"","title":"LinkML Source"},{"location":"Specimen/#direct","text":"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","title":"Direct"},{"location":"Specimen/#induced","text":"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: - 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Despite its name Beamshift is often used to achive this result. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: beamtiltgroups domain_of: - Acquisition range: integer","title":"LinkML Source"},{"location":"binning_camera/","text":"Slot: binning_camera Level of binning on the images applied during data collection URI: https://w3id.org/osc-em/oscem-schemas/:binning_camera Applicable Classes Name Description Modifies Slot Acquisition yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:binning_camera native https://w3id.org/osc-em/oscem-schemas/:binning_camera LinkML Source 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 domain_of: - Acquisition range: float","title":"Slot: binning_camera"},{"location":"binning_camera/#slot-binning_camera","text":"Level of binning on the images applied during data collection URI: https://w3id.org/osc-em/oscem-schemas/:binning_camera","title":"Slot: binning_camera"},{"location":"binning_camera/#applicable-classes","text":"Name Description Modifies Slot Acquisition yes","title":"Applicable Classes"},{"location":"binning_camera/#properties","text":"Range: Float","title":"Properties"},{"location":"binning_camera/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"binning_camera/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"binning_camera/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:binning_camera native https://w3id.org/osc-em/oscem-schemas/:binning_camera","title":"Mappings"},{"location":"binning_camera/#linkml-source","text":"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 domain_of: - Acquisition range: float","title":"LinkML Source"},{"location":"budget/","text":"Slot: budget budget URI: https://w3id.org/osc-em/oscem-schemas/:budget Applicable Classes Name Description Modifies Slot Grant Grant no Properties Range: QuantityValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:budget native https://w3id.org/osc-em/oscem-schemas/:budget LinkML Source name: budget description: budget from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: budget domain_of: - Grant range: QuantityValue","title":"Slot: budget"},{"location":"budget/#slot-budget","text":"budget URI: https://w3id.org/osc-em/oscem-schemas/:budget","title":"Slot: budget"},{"location":"budget/#applicable-classes","text":"Name Description Modifies Slot Grant Grant no","title":"Applicable Classes"},{"location":"budget/#properties","text":"Range: QuantityValue","title":"Properties"},{"location":"budget/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"budget/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"budget/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:budget native https://w3id.org/osc-em/oscem-schemas/:budget","title":"Mappings"},{"location":"budget/#linkml-source","text":"name: budget description: budget from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: budget domain_of: - Grant range: QuantityValue","title":"LinkML Source"},{"location":"buffer/","text":"Slot: Buffer (buffer) Name/composition of the (chemical) sample buffer during grid preparation URI: https://w3id.org/osc-em/oscem-schemas/:buffer Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:buffer native https://w3id.org/osc-em/oscem-schemas/:buffer LinkML Source 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 domain_of: - Specimen range: string","title":"Slot: Buffer (buffer)"},{"location":"buffer/#slot-buffer-buffer","text":"Name/composition of the (chemical) sample buffer during grid preparation URI: https://w3id.org/osc-em/oscem-schemas/:buffer","title":"Slot: Buffer (buffer)"},{"location":"buffer/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"buffer/#properties","text":"Range: String","title":"Properties"},{"location":"buffer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"buffer/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"buffer/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:buffer native https://w3id.org/osc-em/oscem-schemas/:buffer","title":"Mappings"},{"location":"buffer/#linkml-source","text":"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 domain_of: - Specimen range: string","title":"LinkML Source"},{"location":"c2_aperture/","text":"Slot: c2_aperture C2 aperture size used in data acquisition, in \u00b5m URI: https://w3id.org/osc-em/oscem-schemas/:c2_aperture Applicable Classes Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:c2_aperture native https://w3id.org/osc-em/oscem-schemas/:c2_aperture LinkML Source name: c2_aperture description: C2 aperture size used in data acquisition, in \u00b5m from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: c2_aperture domain_of: - Instrument range: integer","title":"Slot: c2_aperture"},{"location":"c2_aperture/#slot-c2_aperture","text":"C2 aperture size used in data acquisition, in \u00b5m URI: https://w3id.org/osc-em/oscem-schemas/:c2_aperture","title":"Slot: c2_aperture"},{"location":"c2_aperture/#applicable-classes","text":"Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection no","title":"Applicable Classes"},{"location":"c2_aperture/#properties","text":"Range: Integer","title":"Properties"},{"location":"c2_aperture/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"c2_aperture/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"c2_aperture/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:c2_aperture native https://w3id.org/osc-em/oscem-schemas/:c2_aperture","title":"Mappings"},{"location":"c2_aperture/#linkml-source","text":"name: c2_aperture description: C2 aperture size used in data acquisition, in \u00b5m from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: c2_aperture domain_of: - Instrument range: integer","title":"LinkML Source"},{"location":"calibrated_defocus/","text":"Slot: calibrated_defocus Machine estimated defocus, min and max values in \u00b5m. Has a tendency to be off. URI: https://w3id.org/osc-em/oscem-schemas/:calibrated_defocus Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Range Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:calibrated_defocus native https://w3id.org/osc-em/oscem-schemas/:calibrated_defocus LinkML Source name: calibrated_defocus description: Machine estimated defocus, min and max values in \u00b5m. Has a tendency to be off. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: calibrated_defocus domain_of: - Acquisition range: Range","title":"Slot: calibrated_defocus"},{"location":"calibrated_defocus/#slot-calibrated_defocus","text":"Machine estimated defocus, min and max values in \u00b5m. Has a tendency to be off. URI: https://w3id.org/osc-em/oscem-schemas/:calibrated_defocus","title":"Slot: calibrated_defocus"},{"location":"calibrated_defocus/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"calibrated_defocus/#properties","text":"Range: Range","title":"Properties"},{"location":"calibrated_defocus/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"calibrated_defocus/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"calibrated_defocus/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:calibrated_defocus native https://w3id.org/osc-em/oscem-schemas/:calibrated_defocus","title":"Mappings"},{"location":"calibrated_defocus/#linkml-source","text":"name: calibrated_defocus description: Machine estimated defocus, min and max values in \u00b5m. Has a tendency to be off. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: calibrated_defocus domain_of: - Acquisition range: Range","title":"LinkML Source"},{"location":"calibrated_magnification/","text":"Slot: calibrated_magnification Calculated magnification, no unit URI: https://w3id.org/osc-em/oscem-schemas/:calibrated_magnification Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:calibrated_magnification native https://w3id.org/osc-em/oscem-schemas/:calibrated_magnification LinkML Source name: calibrated_magnification description: Calculated magnification, no unit from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: calibrated_magnification domain_of: - Acquisition range: integer","title":"Slot: calibrated_magnification"},{"location":"calibrated_magnification/#slot-calibrated_magnification","text":"Calculated magnification, no unit URI: https://w3id.org/osc-em/oscem-schemas/:calibrated_magnification","title":"Slot: calibrated_magnification"},{"location":"calibrated_magnification/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"calibrated_magnification/#properties","text":"Range: Integer","title":"Properties"},{"location":"calibrated_magnification/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"calibrated_magnification/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"calibrated_magnification/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:calibrated_magnification native https://w3id.org/osc-em/oscem-schemas/:calibrated_magnification","title":"Mappings"},{"location":"calibrated_magnification/#linkml-source","text":"name: calibrated_magnification description: Calculated magnification, no unit from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: calibrated_magnification domain_of: - Acquisition range: integer","title":"LinkML Source"},{"location":"chromatic_aberration_corrector/","text":"Slot: chromatic_aberration_corrector Specialist device to correct for chromatic aberration of the microscope lenses URI: https://w3id.org/osc-em/oscem-schemas/:chromatic_aberration_corrector Applicable Classes Name Description Modifies Slot SpecialistOptics no Properties Range: ChromaticAberrationCorrector Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:chromatic_aberration_corrector native https://w3id.org/osc-em/oscem-schemas/:chromatic_aberration_corrector LinkML Source 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 domain_of: - SpecialistOptics range: ChromaticAberrationCorrector","title":"Slot: chromatic_aberration_corrector"},{"location":"chromatic_aberration_corrector/#slot-chromatic_aberration_corrector","text":"Specialist device to correct for chromatic aberration of the microscope lenses URI: https://w3id.org/osc-em/oscem-schemas/:chromatic_aberration_corrector","title":"Slot: chromatic_aberration_corrector"},{"location":"chromatic_aberration_corrector/#applicable-classes","text":"Name Description Modifies Slot SpecialistOptics no","title":"Applicable Classes"},{"location":"chromatic_aberration_corrector/#properties","text":"Range: ChromaticAberrationCorrector","title":"Properties"},{"location":"chromatic_aberration_corrector/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"chromatic_aberration_corrector/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"chromatic_aberration_corrector/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:chromatic_aberration_corrector native https://w3id.org/osc-em/oscem-schemas/:chromatic_aberration_corrector","title":"Mappings"},{"location":"chromatic_aberration_corrector/#linkml-source","text":"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 domain_of: - SpecialistOptics range: ChromaticAberrationCorrector","title":"LinkML Source"},{"location":"concentration/","text":"Slot: Concentration (concentration) Concentration of the (supra)molecule in the sample, in M URI: https://w3id.org/osc-em/oscem-schemas/:concentration Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:concentration native https://w3id.org/osc-em/oscem-schemas/:concentration LinkML Source name: concentration description: Concentration of the (supra)molecule in the sample, in M title: Concentration from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: concentration domain_of: - Specimen range: float","title":"Slot: Concentration (concentration)"},{"location":"concentration/#slot-concentration-concentration","text":"Concentration of the (supra)molecule in the sample, in M URI: https://w3id.org/osc-em/oscem-schemas/:concentration","title":"Slot: Concentration (concentration)"},{"location":"concentration/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"concentration/#properties","text":"Range: Float","title":"Properties"},{"location":"concentration/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"concentration/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"concentration/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:concentration native https://w3id.org/osc-em/oscem-schemas/:concentration","title":"Mappings"},{"location":"concentration/#linkml-source","text":"name: concentration description: Concentration of the (supra)molecule in the sample, in M title: Concentration from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: concentration domain_of: - Specimen range: float","title":"LinkML Source"},{"location":"country/","text":"Slot: Country (country) Country of the author's institution URI: https://w3id.org/osc-em/oscem-schemas/:country Applicable Classes Name Description Modifies Slot Author yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:country native https://w3id.org/osc-em/oscem-schemas/:country LinkML Source name: country description: Country of the author's institution title: Country from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: country domain_of: - Author range: string","title":"Slot: Country (country)"},{"location":"country/#slot-country-country","text":"Country of the author's institution URI: https://w3id.org/osc-em/oscem-schemas/:country","title":"Slot: Country (country)"},{"location":"country/#applicable-classes","text":"Name Description Modifies Slot Author yes","title":"Applicable Classes"},{"location":"country/#properties","text":"Range: String","title":"Properties"},{"location":"country/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"country/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"country/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:country native https://w3id.org/osc-em/oscem-schemas/:country","title":"Mappings"},{"location":"country/#linkml-source","text":"name: country description: Country of the author's institution title: Country from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: country domain_of: - Author range: string","title":"LinkML Source"},{"location":"cryogen/","text":"Slot: cryogen Cryogen used in cooling the instrument and sample, usually nitrogen URI: https://w3id.org/osc-em/oscem-schemas/:cryogen Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:cryogen native https://w3id.org/osc-em/oscem-schemas/:cryogen LinkML Source 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 domain_of: - Acquisition range: string","title":"Slot: cryogen"},{"location":"cryogen/#slot-cryogen","text":"Cryogen used in cooling the instrument and sample, usually nitrogen URI: https://w3id.org/osc-em/oscem-schemas/:cryogen","title":"Slot: cryogen"},{"location":"cryogen/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"cryogen/#properties","text":"Range: String","title":"Properties"},{"location":"cryogen/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"cryogen/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"cryogen/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:cryogen native https://w3id.org/osc-em/oscem-schemas/:cryogen","title":"Mappings"},{"location":"cryogen/#linkml-source","text":"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 domain_of: - Acquisition range: string","title":"LinkML Source"},{"location":"cs/","text":"Slot: cs Spherical aberration of the instrument, in mm URI: https://w3id.org/osc-em/oscem-schemas/:cs Applicable Classes Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:cs native https://w3id.org/osc-em/oscem-schemas/:cs LinkML Source name: cs description: Spherical aberration of the instrument, in mm from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: cs domain_of: - Instrument range: float","title":"Slot: cs"},{"location":"cs/#slot-cs","text":"Spherical aberration of the instrument, in mm URI: https://w3id.org/osc-em/oscem-schemas/:cs","title":"Slot: cs"},{"location":"cs/#applicable-classes","text":"Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection yes","title":"Applicable Classes"},{"location":"cs/#properties","text":"Range: Float","title":"Properties"},{"location":"cs/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"cs/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"cs/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:cs native https://w3id.org/osc-em/oscem-schemas/:cs","title":"Mappings"},{"location":"cs/#linkml-source","text":"name: cs description: Spherical aberration of the instrument, in mm from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: cs domain_of: - Instrument range: float","title":"LinkML Source"},{"location":"date_time/","text":"Slot: date_time Time and date of the data acquisition URI: https://w3id.org/osc-em/oscem-schemas/:date_time Applicable Classes Name Description Modifies Slot Acquisition yes Properties Range: Any or Datetime or Date Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:date_time native https://w3id.org/osc-em/oscem-schemas/:date_time LinkML Source 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 domain_of: - Acquisition range: Any any_of: - range: datetime - range: date","title":"Slot: date_time"},{"location":"date_time/#slot-date_time","text":"Time and date of the data acquisition URI: https://w3id.org/osc-em/oscem-schemas/:date_time","title":"Slot: date_time"},{"location":"date_time/#applicable-classes","text":"Name Description Modifies Slot Acquisition yes","title":"Applicable Classes"},{"location":"date_time/#properties","text":"Range: Any or Datetime or Date","title":"Properties"},{"location":"date_time/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"date_time/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"date_time/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:date_time native https://w3id.org/osc-em/oscem-schemas/:date_time","title":"Mappings"},{"location":"date_time/#linkml-source","text":"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 domain_of: - Acquisition range: Any any_of: - range: datetime - range: date","title":"LinkML Source"},{"location":"detector/","text":"Slot: detector Make and model of the detector used URI: https://w3id.org/osc-em/oscem-schemas/:detector Applicable Classes Name Description Modifies Slot Acquisition yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:detector native https://w3id.org/osc-em/oscem-schemas/:detector LinkML Source name: detector description: Make and model of the detector used from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: detector domain_of: - Acquisition range: string","title":"Slot: detector"},{"location":"detector/#slot-detector","text":"Make and model of the detector used URI: https://w3id.org/osc-em/oscem-schemas/:detector","title":"Slot: detector"},{"location":"detector/#applicable-classes","text":"Name Description Modifies Slot Acquisition yes","title":"Applicable Classes"},{"location":"detector/#properties","text":"Range: String","title":"Properties"},{"location":"detector/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"detector/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"detector/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:detector native https://w3id.org/osc-em/oscem-schemas/:detector","title":"Mappings"},{"location":"detector/#linkml-source","text":"name: detector description: Make and model of the detector used from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: detector domain_of: - 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Instrument range: string","title":"LinkML Source"},{"location":"email/","text":"Slot: email email URI: schema:email Applicable Classes Name Description Modifies Slot Author yes Person no Properties Range: String Regex pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\\.[a-zA-Z0-9-.]+$ Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self schema:email native https://w3id.org/osc-em/oscem-schemas/:email LinkML Source name: email description: email from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:email alias: email domain_of: - Person range: string pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\\.[a-zA-Z0-9-.]+$","title":"Slot: email"},{"location":"email/#slot-email","text":"email URI: schema:email","title":"Slot: email"},{"location":"email/#applicable-classes","text":"Name Description Modifies Slot Author yes Person no","title":"Applicable Classes"},{"location":"email/#properties","text":"Range: String Regex pattern: ^[a-zA-Z0-9_.+-]+@[a-zA-Z0-9-]+\\.[a-zA-Z0-9-.]+$","title":"Properties"},{"location":"email/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"email/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"email/#mappings","text":"Mapping Type Mapped Value self schema:email native https://w3id.org/osc-em/oscem-schemas/:email","title":"Mappings"},{"location":"email/#linkml-source","text":"name: email description: email from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:email alias: email domain_of: - 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URI: https://w3id.org/osc-em/oscem-schemas/:energy_filter Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: EnergyFilter Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:energy_filter native https://w3id.org/osc-em/oscem-schemas/:energy_filter LinkML Source 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 domain_of: - Acquisition range: EnergyFilter","title":"Slot: energy_filter"},{"location":"energy_filter/#slot-energy_filter","text":"Wether an energy filter was used and its specifics. URI: https://w3id.org/osc-em/oscem-schemas/:energy_filter","title":"Slot: energy_filter"},{"location":"energy_filter/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"energy_filter/#properties","text":"Range: EnergyFilter","title":"Properties"},{"location":"energy_filter/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"energy_filter/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"energy_filter/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:energy_filter native https://w3id.org/osc-em/oscem-schemas/:energy_filter","title":"Mappings"},{"location":"energy_filter/#linkml-source","text":"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 domain_of: - Acquisition range: EnergyFilter","title":"LinkML Source"},{"location":"exposure_time/","text":"Slot: exposure_time Time of data acquisition per movie/tilt - in s URI: https://w3id.org/osc-em/oscem-schemas/:exposure_time Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:exposure_time native https://w3id.org/osc-em/oscem-schemas/:exposure_time LinkML Source 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 domain_of: - Acquisition range: float","title":"Slot: exposure_time"},{"location":"exposure_time/#slot-exposure_time","text":"Time of data acquisition per movie/tilt - in s URI: https://w3id.org/osc-em/oscem-schemas/:exposure_time","title":"Slot: exposure_time"},{"location":"exposure_time/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"exposure_time/#properties","text":"Range: Float","title":"Properties"},{"location":"exposure_time/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"exposure_time/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"exposure_time/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:exposure_time native https://w3id.org/osc-em/oscem-schemas/:exposure_time","title":"Mappings"},{"location":"exposure_time/#linkml-source","text":"name: exposure_time description: Time of data acquisition per movie/tilt - 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Molecule range: string","title":"Slot: Expression_system (expression_system)"},{"location":"expression_system/#slot-expression_system-expression_system","text":"Scientific name of the organism used to produce the molecule of interest URI: https://w3id.org/osc-em/oscem-schemas/:expression_system","title":"Slot: Expression_system (expression_system)"},{"location":"expression_system/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"expression_system/#properties","text":"Range: String","title":"Properties"},{"location":"expression_system/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"expression_system/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"expression_system/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:expression_system native https://w3id.org/osc-em/oscem-schemas/:expression_system","title":"Mappings"},{"location":"expression_system/#linkml-source","text":"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 domain_of: - Molecule range: string","title":"LinkML Source"},{"location":"film_material/","text":"Slot: Film_material (film_material) Type of material the support film is made of URI: https://w3id.org/osc-em/oscem-schemas/:film_material Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_material native https://w3id.org/osc-em/oscem-schemas/:film_material LinkML Source 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 domain_of: - Grid range: string","title":"Slot: Film_material (film_material)"},{"location":"film_material/#slot-film_material-film_material","text":"Type of material the support film is made of URI: https://w3id.org/osc-em/oscem-schemas/:film_material","title":"Slot: Film_material (film_material)"},{"location":"film_material/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"film_material/#properties","text":"Range: String","title":"Properties"},{"location":"film_material/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"film_material/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"film_material/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_material native https://w3id.org/osc-em/oscem-schemas/:film_material","title":"Mappings"},{"location":"film_material/#linkml-source","text":"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 domain_of: - Grid range: string","title":"LinkML Source"},{"location":"film_support/","text":"Slot: Film_support (film_support) Whether a support film was used URI: https://w3id.org/osc-em/oscem-schemas/:film_support Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: Boolean Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_support native https://w3id.org/osc-em/oscem-schemas/:film_support LinkML Source 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 domain_of: - Grid range: boolean","title":"Slot: Film_support (film_support)"},{"location":"film_support/#slot-film_support-film_support","text":"Whether a support film was used URI: https://w3id.org/osc-em/oscem-schemas/:film_support","title":"Slot: Film_support (film_support)"},{"location":"film_support/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"film_support/#properties","text":"Range: Boolean","title":"Properties"},{"location":"film_support/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"film_support/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"film_support/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_support native https://w3id.org/osc-em/oscem-schemas/:film_support","title":"Mappings"},{"location":"film_support/#linkml-source","text":"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 domain_of: - Grid range: boolean","title":"LinkML Source"},{"location":"film_thickness/","text":"Slot: Film_thickness (film_thickness) Thickness of the support film URI: https://w3id.org/osc-em/oscem-schemas/:film_thickness Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_thickness native https://w3id.org/osc-em/oscem-schemas/:film_thickness LinkML Source 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 domain_of: - Grid range: string","title":"Slot: Film_thickness (film_thickness)"},{"location":"film_thickness/#slot-film_thickness-film_thickness","text":"Thickness of the support film URI: https://w3id.org/osc-em/oscem-schemas/:film_thickness","title":"Slot: Film_thickness (film_thickness)"},{"location":"film_thickness/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"film_thickness/#properties","text":"Range: String","title":"Properties"},{"location":"film_thickness/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"film_thickness/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"film_thickness/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_thickness native https://w3id.org/osc-em/oscem-schemas/:film_thickness","title":"Mappings"},{"location":"film_thickness/#linkml-source","text":"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 domain_of: - Grid range: string","title":"LinkML Source"},{"location":"film_topology/","text":"Slot: Film_topology (film_topology) Topology of the support film URI: https://w3id.org/osc-em/oscem-schemas/:film_topology Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_topology native https://w3id.org/osc-em/oscem-schemas/:film_topology LinkML Source 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 domain_of: - Grid range: string","title":"Slot: Film_topology (film_topology)"},{"location":"film_topology/#slot-film_topology-film_topology","text":"Topology of the support film URI: https://w3id.org/osc-em/oscem-schemas/:film_topology","title":"Slot: Film_topology (film_topology)"},{"location":"film_topology/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"film_topology/#properties","text":"Range: String","title":"Properties"},{"location":"film_topology/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"film_topology/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"film_topology/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_topology native https://w3id.org/osc-em/oscem-schemas/:film_topology","title":"Mappings"},{"location":"film_topology/#linkml-source","text":"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 domain_of: - Grid range: string","title":"LinkML Source"},{"location":"first_name/","text":"Slot: first_name first name URI: https://w3id.org/osc-em/oscem-schemas/:first_name Applicable Classes Name Description Modifies Slot Author no Person no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:first_name native https://w3id.org/osc-em/oscem-schemas/:first_name LinkML Source name: first_name description: first name from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: first_name domain_of: - Person range: string","title":"Slot: first_name"},{"location":"first_name/#slot-first_name","text":"first name URI: https://w3id.org/osc-em/oscem-schemas/:first_name","title":"Slot: first_name"},{"location":"first_name/#applicable-classes","text":"Name Description Modifies Slot Author no Person no","title":"Applicable Classes"},{"location":"first_name/#properties","text":"Range: String","title":"Properties"},{"location":"first_name/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"first_name/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"first_name/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:first_name native https://w3id.org/osc-em/oscem-schemas/:first_name","title":"Mappings"},{"location":"first_name/#linkml-source","text":"name: first_name description: first name from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: first_name domain_of: - Person range: string","title":"LinkML Source"},{"location":"frames_per_movie/","text":"Slot: frames_per_movie Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors URI: https://w3id.org/osc-em/oscem-schemas/:frames_per_movie Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:frames_per_movie native https://w3id.org/osc-em/oscem-schemas/:frames_per_movie LinkML Source 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 domain_of: - Acquisition range: integer","title":"Slot: frames_per_movie"},{"location":"frames_per_movie/#slot-frames_per_movie","text":"Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors URI: https://w3id.org/osc-em/oscem-schemas/:frames_per_movie","title":"Slot: frames_per_movie"},{"location":"frames_per_movie/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"frames_per_movie/#properties","text":"Range: Integer","title":"Properties"},{"location":"frames_per_movie/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"frames_per_movie/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"frames_per_movie/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:frames_per_movie native https://w3id.org/osc-em/oscem-schemas/:frames_per_movie","title":"Mappings"},{"location":"frames_per_movie/#linkml-source","text":"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 domain_of: - Acquisition range: integer","title":"LinkML Source"},{"location":"funder/","text":"Slot: funder funder URI: https://w3id.org/osc-em/oscem-schemas/:funder Applicable Classes Name Description Modifies Slot Grant Grant no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:funder native https://w3id.org/osc-em/oscem-schemas/:funder LinkML Source name: funder description: funder from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: funder domain_of: - Grant range: string","title":"Slot: funder"},{"location":"funder/#slot-funder","text":"funder URI: https://w3id.org/osc-em/oscem-schemas/:funder","title":"Slot: funder"},{"location":"funder/#applicable-classes","text":"Name Description Modifies Slot Grant Grant no","title":"Applicable Classes"},{"location":"funder/#properties","text":"Range: String","title":"Properties"},{"location":"funder/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"funder/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"funder/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:funder native https://w3id.org/osc-em/oscem-schemas/:funder","title":"Mappings"},{"location":"funder/#linkml-source","text":"name: funder description: funder from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: funder domain_of: - Grant range: string","title":"LinkML Source"},{"location":"gainref_flip_rotate/","text":"Slot: gainref_flip_rotate Whether and how you have to flip or rotate the gainref in order to align with your acquired images URI: https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate native https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate LinkML Source 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 domain_of: - Acquisition range: string","title":"Slot: gainref_flip_rotate"},{"location":"gainref_flip_rotate/#slot-gainref_flip_rotate","text":"Whether and how you have to flip or rotate the gainref in order to align with your acquired images URI: https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate","title":"Slot: gainref_flip_rotate"},{"location":"gainref_flip_rotate/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"gainref_flip_rotate/#properties","text":"Range: String","title":"Properties"},{"location":"gainref_flip_rotate/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"gainref_flip_rotate/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"gainref_flip_rotate/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate native https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate","title":"Mappings"},{"location":"gainref_flip_rotate/#linkml-source","text":"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 domain_of: - Acquisition range: string","title":"LinkML Source"},{"location":"gene_name/","text":"Slot: Gene_name (gene_name) Name of the gene of interest URI: https://w3id.org/osc-em/oscem-schemas/:gene_name Applicable Classes Name Description Modifies Slot Molecule A class representing a molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:gene_name native https://w3id.org/osc-em/oscem-schemas/:gene_name LinkML Source 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 domain_of: - Molecule range: string","title":"Slot: Gene_name (gene_name)"},{"location":"gene_name/#slot-gene_name-gene_name","text":"Name of the gene of interest URI: https://w3id.org/osc-em/oscem-schemas/:gene_name","title":"Slot: Gene_name (gene_name)"},{"location":"gene_name/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"gene_name/#properties","text":"Range: String","title":"Properties"},{"location":"gene_name/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"gene_name/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"gene_name/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:gene_name native https://w3id.org/osc-em/oscem-schemas/:gene_name","title":"Mappings"},{"location":"gene_name/#linkml-source","text":"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 domain_of: - Molecule range: string","title":"LinkML Source"},{"location":"grants/","text":"Slot: Grants (grants) List of grants associated with the project URI: https://w3id.org/osc-em/oscem-schemas/:grants Applicable Classes Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes Properties Range: Grant Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:grants native https://w3id.org/osc-em/oscem-schemas/:grants LinkML Source 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 domain_of: - EMDataset range: Grant multivalued: true","title":"Slot: Grants (grants)"},{"location":"grants/#slot-grants-grants","text":"List of grants associated with the project URI: https://w3id.org/osc-em/oscem-schemas/:grants","title":"Slot: Grants (grants)"},{"location":"grants/#applicable-classes","text":"Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes","title":"Applicable Classes"},{"location":"grants/#properties","text":"Range: Grant Multivalued: True","title":"Properties"},{"location":"grants/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"grants/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"grants/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:grants native https://w3id.org/osc-em/oscem-schemas/:grants","title":"Mappings"},{"location":"grants/#linkml-source","text":"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 domain_of: - EMDataset range: Grant multivalued: true","title":"LinkML Source"},{"location":"grid/","text":"Slot: Grid (grid) Description of the grid used URI: https://w3id.org/osc-em/oscem-schemas/:grid Applicable Classes Name Description Modifies Slot Sample A class representing a sample yes Properties Range: Grid Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:grid native https://w3id.org/osc-em/oscem-schemas/:grid LinkML Source name: grid description: Description of the grid used title: Grid from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: grid domain_of: - Sample range: Grid","title":"Slot: Grid (grid)"},{"location":"grid/#slot-grid-grid","text":"Description of the grid used URI: https://w3id.org/osc-em/oscem-schemas/:grid","title":"Slot: Grid (grid)"},{"location":"grid/#applicable-classes","text":"Name Description Modifies Slot Sample A class representing a sample yes","title":"Applicable Classes"},{"location":"grid/#properties","text":"Range: Grid","title":"Properties"},{"location":"grid/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"grid/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"grid/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:grid native https://w3id.org/osc-em/oscem-schemas/:grid","title":"Mappings"},{"location":"grid/#linkml-source","text":"name: grid description: Description of the grid used title: Grid from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: grid domain_of: - Sample range: Grid","title":"LinkML Source"},{"location":"grids_imaged/","text":"Slot: grids_imaged Number of grids imaged for this project - here with qualifier during this data acquisition URI: https://w3id.org/osc-em/oscem-schemas/:grids_imaged Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:grids_imaged native https://w3id.org/osc-em/oscem-schemas/:grids_imaged LinkML Source 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 domain_of: - Acquisition range: integer","title":"Slot: grids_imaged"},{"location":"grids_imaged/#slot-grids_imaged","text":"Number of grids imaged for this project - here with qualifier during this data acquisition URI: https://w3id.org/osc-em/oscem-schemas/:grids_imaged","title":"Slot: grids_imaged"},{"location":"grids_imaged/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"grids_imaged/#properties","text":"Range: Integer","title":"Properties"},{"location":"grids_imaged/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"grids_imaged/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"grids_imaged/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:grids_imaged native https://w3id.org/osc-em/oscem-schemas/:grids_imaged","title":"Mappings"},{"location":"grids_imaged/#linkml-source","text":"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 domain_of: - Acquisition range: integer","title":"LinkML Source"},{"location":"has_unit/","text":"Slot: has_unit Unit URI: qudt:hasUnit Applicable Classes Name Description Modifies Slot QuantityValue Value together with unit no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self qudt:hasUnit native https://w3id.org/osc-em/oscem-schemas/:has_unit LinkML Source name: has_unit description: Unit from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: qudt:hasUnit alias: has_unit domain_of: - QuantityValue range: string","title":"Slot: has_unit"},{"location":"has_unit/#slot-has_unit","text":"Unit URI: qudt:hasUnit","title":"Slot: has_unit"},{"location":"has_unit/#applicable-classes","text":"Name Description Modifies Slot QuantityValue Value together with unit no","title":"Applicable Classes"},{"location":"has_unit/#properties","text":"Range: String","title":"Properties"},{"location":"has_unit/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"has_unit/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"has_unit/#mappings","text":"Mapping Type Mapped Value self qudt:hasUnit native https://w3id.org/osc-em/oscem-schemas/:has_unit","title":"Mappings"},{"location":"has_unit/#linkml-source","text":"name: has_unit description: Unit from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: qudt:hasUnit alias: has_unit domain_of: - QuantityValue range: string","title":"LinkML Source"},{"location":"has_value/","text":"Slot: has_value Value URI: qudt:hasQuantityKind Applicable Classes Name Description Modifies Slot QuantityValue Value together with unit no Properties Range: Double Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self qudt:hasQuantityKind native https://w3id.org/osc-em/oscem-schemas/:has_value LinkML Source name: has_value description: Value from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: qudt:hasQuantityKind alias: has_value domain_of: - QuantityValue range: double","title":"Slot: has_value"},{"location":"has_value/#slot-has_value","text":"Value URI: qudt:hasQuantityKind","title":"Slot: has_value"},{"location":"has_value/#applicable-classes","text":"Name Description Modifies Slot QuantityValue Value together with unit no","title":"Applicable Classes"},{"location":"has_value/#properties","text":"Range: Double","title":"Properties"},{"location":"has_value/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"has_value/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"has_value/#mappings","text":"Mapping Type Mapped Value self qudt:hasQuantityKind native https://w3id.org/osc-em/oscem-schemas/:has_value","title":"Mappings"},{"location":"has_value/#linkml-source","text":"name: has_value description: Value from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: qudt:hasQuantityKind alias: has_value domain_of: - QuantityValue range: double","title":"LinkML Source"},{"location":"height/","text":"Slot: height The height of a given item - unit depends on item URI: https://w3id.org/osc-em/oscem-schemas/:height Applicable Classes Name Description Modifies Slot ImageSize size of a 2D image (in integer units) no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:height native https://w3id.org/osc-em/oscem-schemas/:height LinkML Source 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 domain_of: - ImageSize range: integer","title":"Slot: height"},{"location":"height/#slot-height","text":"The height of a given item - unit depends on item URI: https://w3id.org/osc-em/oscem-schemas/:height","title":"Slot: height"},{"location":"height/#applicable-classes","text":"Name Description Modifies Slot ImageSize size of a 2D image (in integer units) no","title":"Applicable Classes"},{"location":"height/#properties","text":"Range: Integer","title":"Properties"},{"location":"height/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"height/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"height/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:height native https://w3id.org/osc-em/oscem-schemas/:height","title":"Mappings"},{"location":"height/#linkml-source","text":"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 domain_of: - ImageSize range: integer","title":"LinkML Source"},{"location":"holder/","text":"Slot: holder Speciman holder model URI: https://w3id.org/osc-em/oscem-schemas/:holder Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:holder native https://w3id.org/osc-em/oscem-schemas/:holder LinkML Source name: holder description: Speciman holder model from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: holder domain_of: - Acquisition range: string","title":"Slot: holder"},{"location":"holder/#slot-holder","text":"Speciman holder model URI: https://w3id.org/osc-em/oscem-schemas/:holder","title":"Slot: holder"},{"location":"holder/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"holder/#properties","text":"Range: String","title":"Properties"},{"location":"holder/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"holder/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"holder/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:holder native https://w3id.org/osc-em/oscem-schemas/:holder","title":"Mappings"},{"location":"holder/#linkml-source","text":"name: holder description: Speciman holder model from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: holder domain_of: - Acquisition range: string","title":"LinkML Source"},{"location":"holder_cryogen/","text":"Slot: holder_cryogen Type of cryogen used in the holder - if the holder is cooled seperately URI: https://w3id.org/osc-em/oscem-schemas/:holder_cryogen Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:holder_cryogen native https://w3id.org/osc-em/oscem-schemas/:holder_cryogen LinkML Source 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 domain_of: - Acquisition range: string","title":"Slot: holder_cryogen"},{"location":"holder_cryogen/#slot-holder_cryogen","text":"Type of cryogen used in the holder - if the holder is cooled seperately URI: https://w3id.org/osc-em/oscem-schemas/:holder_cryogen","title":"Slot: holder_cryogen"},{"location":"holder_cryogen/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"holder_cryogen/#properties","text":"Range: String","title":"Properties"},{"location":"holder_cryogen/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"holder_cryogen/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"holder_cryogen/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:holder_cryogen native https://w3id.org/osc-em/oscem-schemas/:holder_cryogen","title":"Mappings"},{"location":"holder_cryogen/#linkml-source","text":"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 domain_of: - Acquisition range: string","title":"LinkML Source"},{"location":"humidity/","text":"Slot: Humidity (humidity) Environmental humidity just before vitrification, in % URI: https://w3id.org/osc-em/oscem-schemas/:humidity Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:humidity native https://w3id.org/osc-em/oscem-schemas/:humidity LinkML Source name: humidity description: Environmental humidity just before vitrification, in % title: Humidity from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: humidity domain_of: - Specimen range: float","title":"Slot: Humidity (humidity)"},{"location":"humidity/#slot-humidity-humidity","text":"Environmental humidity just before vitrification, in % URI: https://w3id.org/osc-em/oscem-schemas/:humidity","title":"Slot: Humidity (humidity)"},{"location":"humidity/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"humidity/#properties","text":"Range: Float","title":"Properties"},{"location":"humidity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"humidity/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"humidity/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:humidity native https://w3id.org/osc-em/oscem-schemas/:humidity","title":"Mappings"},{"location":"humidity/#linkml-source","text":"name: humidity description: Environmental humidity just before vitrification, in % title: Humidity from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: humidity domain_of: - Specimen range: float","title":"LinkML Source"},{"location":"illumination/","text":"Slot: illumination Mode of illumination used during data collection URI: https://w3id.org/osc-em/oscem-schemas/:illumination Applicable Classes Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:illumination native https://w3id.org/osc-em/oscem-schemas/:illumination LinkML Source name: illumination description: Mode of illumination used during data collection from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: illumination domain_of: - Instrument range: string","title":"Slot: illumination"},{"location":"illumination/#slot-illumination","text":"Mode of illumination used during data collection URI: https://w3id.org/osc-em/oscem-schemas/:illumination","title":"Slot: illumination"},{"location":"illumination/#applicable-classes","text":"Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection yes","title":"Applicable Classes"},{"location":"illumination/#properties","text":"Range: String","title":"Properties"},{"location":"illumination/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"illumination/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"illumination/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:illumination native https://w3id.org/osc-em/oscem-schemas/:illumination","title":"Mappings"},{"location":"illumination/#linkml-source","text":"name: illumination description: Mode of illumination used during data collection from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: illumination domain_of: - Instrument range: string","title":"LinkML Source"},{"location":"image_size/","text":"Slot: image_size The size of the image in pixels, height and width given. URI: https://w3id.org/osc-em/oscem-schemas/:image_size Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: ImageSize Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:image_size native https://w3id.org/osc-em/oscem-schemas/:image_size LinkML Source 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 domain_of: - Acquisition range: ImageSize","title":"Slot: image_size"},{"location":"image_size/#slot-image_size","text":"The size of the image in pixels, height and width given. URI: https://w3id.org/osc-em/oscem-schemas/:image_size","title":"Slot: image_size"},{"location":"image_size/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"image_size/#properties","text":"Range: ImageSize","title":"Properties"},{"location":"image_size/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"image_size/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"image_size/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:image_size native https://w3id.org/osc-em/oscem-schemas/:image_size","title":"Mappings"},{"location":"image_size/#linkml-source","text":"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 domain_of: - Acquisition range: ImageSize","title":"LinkML Source"},{"location":"images_generated/","text":"Slot: images_generated 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 URI: https://w3id.org/osc-em/oscem-schemas/:images_generated Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:images_generated native https://w3id.org/osc-em/oscem-schemas/:images_generated LinkML Source 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 domain_of: - Acquisition range: integer","title":"Slot: images_generated"},{"location":"images_generated/#slot-images_generated","text":"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 URI: https://w3id.org/osc-em/oscem-schemas/:images_generated","title":"Slot: images_generated"},{"location":"images_generated/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"images_generated/#properties","text":"Range: Integer","title":"Properties"},{"location":"images_generated/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"images_generated/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"images_generated/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:images_generated native https://w3id.org/osc-em/oscem-schemas/:images_generated","title":"Mappings"},{"location":"images_generated/#linkml-source","text":"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 domain_of: - Acquisition range: integer","title":"LinkML Source"},{"location":"imageshift/","text":"Slot: imageshift Movement of the Beam below the image in order to shift the image on the detector. Given in \u00b5m. URI: https://w3id.org/osc-em/oscem-schemas/:imageshift Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: BoundingBox2D Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:imageshift native https://w3id.org/osc-em/oscem-schemas/:imageshift LinkML Source name: imageshift description: Movement of the Beam below the image in order to shift the image on the detector. Given in \u00b5m. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: imageshift domain_of: - Acquisition range: BoundingBox2D","title":"Slot: imageshift"},{"location":"imageshift/#slot-imageshift","text":"Movement of the Beam below the image in order to shift the image on the detector. Given in \u00b5m. URI: https://w3id.org/osc-em/oscem-schemas/:imageshift","title":"Slot: imageshift"},{"location":"imageshift/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"imageshift/#properties","text":"Range: BoundingBox2D","title":"Properties"},{"location":"imageshift/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"imageshift/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"imageshift/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:imageshift native https://w3id.org/osc-em/oscem-schemas/:imageshift","title":"Mappings"},{"location":"imageshift/#linkml-source","text":"name: imageshift description: Movement of the Beam below the image in order to shift the image on the detector. Given in \u00b5m. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: imageshift domain_of: - Acquisition range: BoundingBox2D","title":"LinkML Source"},{"location":"imaging/","text":"Slot: imaging Mode of imaging used during data collection URI: https://w3id.org/osc-em/oscem-schemas/:imaging Applicable Classes Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:imaging native https://w3id.org/osc-em/oscem-schemas/:imaging LinkML Source name: imaging description: Mode of imaging used during data collection from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: imaging domain_of: - Instrument range: string","title":"Slot: imaging"},{"location":"imaging/#slot-imaging","text":"Mode of imaging used during data collection URI: https://w3id.org/osc-em/oscem-schemas/:imaging","title":"Slot: imaging"},{"location":"imaging/#applicable-classes","text":"Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection yes","title":"Applicable Classes"},{"location":"imaging/#properties","text":"Range: String","title":"Properties"},{"location":"imaging/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"imaging/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"imaging/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:imaging native https://w3id.org/osc-em/oscem-schemas/:imaging","title":"Mappings"},{"location":"imaging/#linkml-source","text":"name: imaging description: Mode of imaging used during data collection from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: imaging domain_of: - Instrument range: string","title":"LinkML Source"},{"location":"increment/","text":"Slot: increment Increment between elements of a series URI: https://w3id.org/osc-em/oscem-schemas/:increment Applicable Classes Name Description Modifies Slot TiltAngle The min, max and increment of the tilt angle in a tomography session no Series A series of numbers constructed from min, max, and increment no Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:increment native https://w3id.org/osc-em/oscem-schemas/:increment LinkML Source name: increment description: Increment between elements of a series from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: increment domain_of: - Series range: float","title":"Slot: increment"},{"location":"increment/#slot-increment","text":"Increment between elements of a series URI: https://w3id.org/osc-em/oscem-schemas/:increment","title":"Slot: increment"},{"location":"increment/#applicable-classes","text":"Name Description Modifies Slot TiltAngle The min, max and increment of the tilt angle in a tomography session no Series A series of numbers constructed from min, max, and increment no","title":"Applicable Classes"},{"location":"increment/#properties","text":"Range: Float","title":"Properties"},{"location":"increment/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"increment/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"increment/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:increment native https://w3id.org/osc-em/oscem-schemas/:increment","title":"Mappings"},{"location":"increment/#linkml-source","text":"name: increment description: Increment between elements of a series from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: increment domain_of: - Series range: float","title":"LinkML Source"},{"location":"instrument/","text":"Slot: Instrument (instrument) Describe the instrument used to acquire the data URI: https://w3id.org/osc-em/oscem-schemas/:instrument Applicable Classes Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes Properties Range: Instrument Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:instrument native https://w3id.org/osc-em/oscem-schemas/:instrument LinkML Source 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 domain_of: - EMDataset range: Instrument","title":"Slot: Instrument (instrument)"},{"location":"instrument/#slot-instrument-instrument","text":"Describe the instrument used to acquire the data URI: https://w3id.org/osc-em/oscem-schemas/:instrument","title":"Slot: Instrument (instrument)"},{"location":"instrument/#applicable-classes","text":"Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes","title":"Applicable Classes"},{"location":"instrument/#properties","text":"Range: Instrument","title":"Properties"},{"location":"instrument/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"instrument/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"instrument/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:instrument native https://w3id.org/osc-em/oscem-schemas/:instrument","title":"Mappings"},{"location":"instrument/#linkml-source","text":"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 domain_of: - EMDataset range: Instrument","title":"LinkML Source"},{"location":"ligands/","text":"Slot: Ligands (ligands) List of ligands associated with the sample URI: https://w3id.org/osc-em/oscem-schemas/:ligands Applicable Classes Name Description Modifies Slot Sample A class representing a sample yes Properties Range: Ligand Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:ligands native https://w3id.org/osc-em/oscem-schemas/:ligands LinkML Source 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 domain_of: - Sample range: Ligand multivalued: true","title":"Slot: Ligands (ligands)"},{"location":"ligands/#slot-ligands-ligands","text":"List of ligands associated with the sample URI: https://w3id.org/osc-em/oscem-schemas/:ligands","title":"Slot: Ligands (ligands)"},{"location":"ligands/#applicable-classes","text":"Name Description Modifies Slot Sample A class representing a sample yes","title":"Applicable Classes"},{"location":"ligands/#properties","text":"Range: Ligand Multivalued: True","title":"Properties"},{"location":"ligands/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ligands/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"ligands/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:ligands native https://w3id.org/osc-em/oscem-schemas/:ligands","title":"Mappings"},{"location":"ligands/#linkml-source","text":"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 domain_of: - Sample range: Ligand multivalued: true","title":"LinkML Source"},{"location":"manufacturer/","text":"Slot: Manufacturer (manufacturer) Grid manufacturer URI: https://w3id.org/osc-em/oscem-schemas/:manufacturer Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:manufacturer native https://w3id.org/osc-em/oscem-schemas/:manufacturer LinkML Source name: manufacturer description: Grid manufacturer title: Manufacturer from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: manufacturer domain_of: - Grid range: string","title":"Slot: Manufacturer (manufacturer)"},{"location":"manufacturer/#slot-manufacturer-manufacturer","text":"Grid manufacturer URI: https://w3id.org/osc-em/oscem-schemas/:manufacturer","title":"Slot: Manufacturer (manufacturer)"},{"location":"manufacturer/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"manufacturer/#properties","text":"Range: String","title":"Properties"},{"location":"manufacturer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"manufacturer/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"manufacturer/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:manufacturer native https://w3id.org/osc-em/oscem-schemas/:manufacturer","title":"Mappings"},{"location":"manufacturer/#linkml-source","text":"name: manufacturer description: Grid manufacturer title: Manufacturer from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: manufacturer domain_of: - 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Grid range: string","title":"LinkML Source"},{"location":"maximal/","text":"Slot: maximal Maximal value of a given dataset property URI: https://w3id.org/osc-em/oscem-schemas/:maximal Applicable Classes Name Description Modifies Slot Range A range constructed from min and max no TiltAngle The min, max and increment of the tilt angle in a tomography session no Series A series of numbers constructed from min, max, and increment no Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:maximal native https://w3id.org/osc-em/oscem-schemas/:maximal LinkML Source name: maximal description: Maximal value of a given dataset property from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: maximal domain_of: - Range range: float","title":"Slot: maximal"},{"location":"maximal/#slot-maximal","text":"Maximal value of a given dataset property URI: https://w3id.org/osc-em/oscem-schemas/:maximal","title":"Slot: maximal"},{"location":"maximal/#applicable-classes","text":"Name Description Modifies Slot Range A range constructed from min and max no TiltAngle The min, max and increment of the tilt angle in a tomography session no Series A series of numbers constructed from min, max, and increment no","title":"Applicable Classes"},{"location":"maximal/#properties","text":"Range: Float","title":"Properties"},{"location":"maximal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"maximal/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"maximal/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:maximal native https://w3id.org/osc-em/oscem-schemas/:maximal","title":"Mappings"},{"location":"maximal/#linkml-source","text":"name: maximal description: Maximal value of a given dataset property from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: maximal domain_of: - 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OverallMolecule range: float","title":"LinkML Source"},{"location":"molecule/","text":"Slot: Molecule (molecule) List of molecule associated with the sample URI: https://w3id.org/osc-em/oscem-schemas/:molecule Applicable Classes Name Description Modifies Slot Sample A class representing a sample yes Properties Range: Molecule Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:molecule native https://w3id.org/osc-em/oscem-schemas/:molecule LinkML Source 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 domain_of: - Sample range: Molecule multivalued: true","title":"Slot: Molecule (molecule)"},{"location":"molecule/#slot-molecule-molecule","text":"List of molecule associated with the sample URI: https://w3id.org/osc-em/oscem-schemas/:molecule","title":"Slot: Molecule (molecule)"},{"location":"molecule/#applicable-classes","text":"Name Description Modifies Slot Sample A class representing a sample yes","title":"Applicable Classes"},{"location":"molecule/#properties","text":"Range: Molecule Multivalued: True","title":"Properties"},{"location":"molecule/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"molecule/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"molecule/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:molecule native https://w3id.org/osc-em/oscem-schemas/:molecule","title":"Mappings"},{"location":"molecule/#linkml-source","text":"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 domain_of: - 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Author range: string","title":"LinkML Source"},{"location":"name_sample/","text":"Slot: Name (name_sample) Name of the full sample URI: https://w3id.org/osc-em/oscem-schemas/:name_sample Applicable Classes Name Description Modifies Slot OverallMolecule A class representing the overall molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:name_sample native https://w3id.org/osc-em/oscem-schemas/:name_sample LinkML Source 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 domain_of: - OverallMolecule range: string","title":"Slot: Name (name_sample)"},{"location":"name_sample/#slot-name-name_sample","text":"Name of the full sample URI: https://w3id.org/osc-em/oscem-schemas/:name_sample","title":"Slot: Name (name_sample)"},{"location":"name_sample/#applicable-classes","text":"Name Description Modifies Slot OverallMolecule A class representing the overall molecule yes","title":"Applicable Classes"},{"location":"name_sample/#properties","text":"Range: String","title":"Properties"},{"location":"name_sample/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"name_sample/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"name_sample/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:name_sample native https://w3id.org/osc-em/oscem-schemas/:name_sample","title":"Mappings"},{"location":"name_sample/#linkml-source","text":"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 domain_of: - 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Molecule range: string","title":"LinkML Source"},{"location":"nominal_defocus/","text":"Slot: nominal_defocus Target defocus set, min and max values in \u00b5m. URI: https://w3id.org/osc-em/oscem-schemas/:nominal_defocus Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Range Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:nominal_defocus native https://w3id.org/osc-em/oscem-schemas/:nominal_defocus LinkML Source name: nominal_defocus description: Target defocus set, min and max values in \u00b5m. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: nominal_defocus domain_of: - Acquisition range: Range","title":"Slot: nominal_defocus"},{"location":"nominal_defocus/#slot-nominal_defocus","text":"Target defocus set, min and max values in \u00b5m. URI: https://w3id.org/osc-em/oscem-schemas/:nominal_defocus","title":"Slot: nominal_defocus"},{"location":"nominal_defocus/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"nominal_defocus/#properties","text":"Range: Range","title":"Properties"},{"location":"nominal_defocus/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"nominal_defocus/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"nominal_defocus/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:nominal_defocus native https://w3id.org/osc-em/oscem-schemas/:nominal_defocus","title":"Mappings"},{"location":"nominal_defocus/#linkml-source","text":"name: nominal_defocus description: Target defocus set, min and max values in \u00b5m. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: nominal_defocus domain_of: - Acquisition range: Range","title":"LinkML Source"},{"location":"nominal_magnification/","text":"Slot: nominal_magnification Magnification level as indicated by the instrument, no unit URI: https://w3id.org/osc-em/oscem-schemas/:nominal_magnification Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:nominal_magnification native https://w3id.org/osc-em/oscem-schemas/:nominal_magnification LinkML Source 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 domain_of: - Acquisition range: integer","title":"Slot: nominal_magnification"},{"location":"nominal_magnification/#slot-nominal_magnification","text":"Magnification level as indicated by the instrument, no unit URI: https://w3id.org/osc-em/oscem-schemas/:nominal_magnification","title":"Slot: nominal_magnification"},{"location":"nominal_magnification/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"nominal_magnification/#properties","text":"Range: Integer","title":"Properties"},{"location":"nominal_magnification/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"nominal_magnification/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"nominal_magnification/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:nominal_magnification native https://w3id.org/osc-em/oscem-schemas/:nominal_magnification","title":"Mappings"},{"location":"nominal_magnification/#linkml-source","text":"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 domain_of: - Acquisition range: integer","title":"LinkML Source"},{"location":"orcid/","text":"Slot: ORCID (orcid) ORCID of the author, a type of unique identifier URI: https://w3id.org/osc-em/oscem-schemas/:orcid Applicable Classes Name Description Modifies Slot Author yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:orcid native https://w3id.org/osc-em/oscem-schemas/:orcid LinkML Source 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 domain_of: - Author range: string","title":"Slot: ORCID (orcid)"},{"location":"orcid/#slot-orcid-orcid","text":"ORCID of the author, a type of unique identifier URI: https://w3id.org/osc-em/oscem-schemas/:orcid","title":"Slot: ORCID (orcid)"},{"location":"orcid/#applicable-classes","text":"Name Description Modifies Slot Author yes","title":"Applicable Classes"},{"location":"orcid/#properties","text":"Range: String","title":"Properties"},{"location":"orcid/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"orcid/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"orcid/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:orcid native https://w3id.org/osc-em/oscem-schemas/:orcid","title":"Mappings"},{"location":"orcid/#linkml-source","text":"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 domain_of: - Author range: string","title":"LinkML Source"},{"location":"oscem-schemas/","text":"oscem-schemas Schema for the Open Standards Community for Electron Microscopy (OSC-EM) URI: https://w3id.org/osc-em/oscem-schemas","title":"oscem-schemas"},{"location":"oscem-schemas/#oscem-schemas","text":"Schema for the Open Standards Community for Electron Microscopy (OSC-EM) URI: https://w3id.org/osc-em/oscem-schemas","title":"oscem-schemas"},{"location":"overall_molecule/","text":"Slot: Overall_Molecule (overall_molecule) Description of the overall molecule URI: https://w3id.org/osc-em/oscem-schemas/:overall_molecule Applicable Classes Name Description Modifies Slot Sample A class representing a sample yes Properties Range: OverallMolecule Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:overall_molecule native https://w3id.org/osc-em/oscem-schemas/:overall_molecule LinkML Source 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 domain_of: - 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Sample range: OverallMolecule","title":"LinkML Source"},{"location":"person/","text":"Slot: person person URI: schema:Person Properties Range: Person Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self schema:Person native https://w3id.org/osc-em/oscem-schemas/:person LinkML Source name: person description: person from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:Person alias: person range: Person","title":"Slot: person"},{"location":"person/#slot-person","text":"person URI: schema:Person","title":"Slot: person"},{"location":"person/#properties","text":"Range: Person","title":"Properties"},{"location":"person/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"person/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"person/#mappings","text":"Mapping Type Mapped Value self schema:Person native https://w3id.org/osc-em/oscem-schemas/:person","title":"Mappings"},{"location":"person/#linkml-source","text":"name: person description: person from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:Person alias: person range: Person","title":"LinkML Source"},{"location":"ph/","text":"Slot: pH (ph) pH of the sample buffer URI: https://w3id.org/osc-em/oscem-schemas/:ph Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:ph native https://w3id.org/osc-em/oscem-schemas/:ph LinkML Source name: ph description: pH of the sample buffer title: pH from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: ph domain_of: - Specimen range: float","title":"Slot: pH (ph)"},{"location":"ph/#slot-ph-ph","text":"pH of the sample buffer URI: https://w3id.org/osc-em/oscem-schemas/:ph","title":"Slot: pH (ph)"},{"location":"ph/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"ph/#properties","text":"Range: Float","title":"Properties"},{"location":"ph/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ph/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"ph/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:ph native https://w3id.org/osc-em/oscem-schemas/:ph","title":"Mappings"},{"location":"ph/#linkml-source","text":"name: ph description: pH of the sample buffer title: pH from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: ph domain_of: - Specimen range: float","title":"LinkML Source"},{"location":"phaseplate/","text":"Slot: phaseplate Phaseplate is a special optics device that can be used to enhance contrast URI: https://w3id.org/osc-em/oscem-schemas/:phaseplate Applicable Classes Name Description Modifies Slot SpecialistOptics no Properties Range: Phaseplate Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:phaseplate native https://w3id.org/osc-em/oscem-schemas/:phaseplate LinkML Source 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 domain_of: - SpecialistOptics range: Phaseplate","title":"Slot: phaseplate"},{"location":"phaseplate/#slot-phaseplate","text":"Phaseplate is a special optics device that can be used to enhance contrast URI: https://w3id.org/osc-em/oscem-schemas/:phaseplate","title":"Slot: phaseplate"},{"location":"phaseplate/#applicable-classes","text":"Name Description Modifies Slot SpecialistOptics no","title":"Applicable Classes"},{"location":"phaseplate/#properties","text":"Range: Phaseplate","title":"Properties"},{"location":"phaseplate/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"phaseplate/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"phaseplate/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:phaseplate native https://w3id.org/osc-em/oscem-schemas/:phaseplate","title":"Mappings"},{"location":"phaseplate/#linkml-source","text":"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 domain_of: - SpecialistOptics range: Phaseplate","title":"LinkML Source"},{"location":"pixel_size/","text":"Slot: pixel_size Pixel size, in Angstrom URI: https://w3id.org/osc-em/oscem-schemas/:pixel_size Applicable Classes Name Description Modifies Slot Acquisition yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pixel_size native https://w3id.org/osc-em/oscem-schemas/:pixel_size LinkML Source name: pixel_size description: Pixel size, in Angstrom from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: pixel_size domain_of: - Acquisition range: float","title":"Slot: pixel_size"},{"location":"pixel_size/#slot-pixel_size","text":"Pixel size, in Angstrom URI: https://w3id.org/osc-em/oscem-schemas/:pixel_size","title":"Slot: pixel_size"},{"location":"pixel_size/#applicable-classes","text":"Name Description Modifies Slot Acquisition yes","title":"Applicable Classes"},{"location":"pixel_size/#properties","text":"Range: Float","title":"Properties"},{"location":"pixel_size/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"pixel_size/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"pixel_size/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pixel_size native https://w3id.org/osc-em/oscem-schemas/:pixel_size","title":"Mappings"},{"location":"pixel_size/#linkml-source","text":"name: pixel_size description: Pixel size, in Angstrom from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: pixel_size domain_of: - Acquisition range: float","title":"LinkML Source"},{"location":"present/","text":"Slot: Present (present) Whether the model contains any ligands URI: https://w3id.org/osc-em/oscem-schemas/:present Applicable Classes Name Description Modifies Slot Ligand A class representing a ligand yes Properties Range: Boolean Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:present native https://w3id.org/osc-em/oscem-schemas/:present LinkML Source name: present description: Whether the model contains any ligands title: Present from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: present domain_of: - Ligand range: boolean","title":"Slot: Present (present)"},{"location":"present/#slot-present-present","text":"Whether the model contains any ligands URI: https://w3id.org/osc-em/oscem-schemas/:present","title":"Slot: Present (present)"},{"location":"present/#applicable-classes","text":"Name Description Modifies Slot Ligand A class representing a ligand yes","title":"Applicable Classes"},{"location":"present/#properties","text":"Range: Boolean","title":"Properties"},{"location":"present/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"present/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"present/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:present native https://w3id.org/osc-em/oscem-schemas/:present","title":"Mappings"},{"location":"present/#linkml-source","text":"name: present description: Whether the model contains any ligands title: Present from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: present domain_of: - Ligand range: boolean","title":"LinkML Source"},{"location":"pretreatment_atmosphere/","text":"Slot: Pretreatment_atmosphere (pretreatment_atmosphere) Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc. URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere native https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere LinkML Source 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 domain_of: - Grid range: string","title":"Slot: Pretreatment_atmosphere (pretreatment_atmosphere)"},{"location":"pretreatment_atmosphere/#slot-pretreatment_atmosphere-pretreatment_atmosphere","text":"Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc. URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere","title":"Slot: Pretreatment_atmosphere (pretreatment_atmosphere)"},{"location":"pretreatment_atmosphere/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"pretreatment_atmosphere/#properties","text":"Range: String","title":"Properties"},{"location":"pretreatment_atmosphere/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"pretreatment_atmosphere/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"pretreatment_atmosphere/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere native https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere","title":"Mappings"},{"location":"pretreatment_atmosphere/#linkml-source","text":"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 domain_of: - Grid range: string","title":"LinkML Source"},{"location":"pretreatment_pressure/","text":"Slot: Pretreatment_pressure (pretreatment_pressure) Pressure of the chamber during pretreatment, in Pa URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure native https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure LinkML Source 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 domain_of: - Grid range: float","title":"Slot: Pretreatment_pressure (pretreatment_pressure)"},{"location":"pretreatment_pressure/#slot-pretreatment_pressure-pretreatment_pressure","text":"Pressure of the chamber during pretreatment, in Pa URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure","title":"Slot: Pretreatment_pressure (pretreatment_pressure)"},{"location":"pretreatment_pressure/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"pretreatment_pressure/#properties","text":"Range: Float","title":"Properties"},{"location":"pretreatment_pressure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"pretreatment_pressure/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"pretreatment_pressure/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure native https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure","title":"Mappings"},{"location":"pretreatment_pressure/#linkml-source","text":"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 domain_of: - Grid range: float","title":"LinkML Source"},{"location":"pretreatment_time/","text":"Slot: Pretreatment_time (pretreatment_time) Length of time of the pretreatment in s URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_time Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_time native https://w3id.org/osc-em/oscem-schemas/:pretreatment_time LinkML Source 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 domain_of: - Grid range: float","title":"Slot: Pretreatment_time (pretreatment_time)"},{"location":"pretreatment_time/#slot-pretreatment_time-pretreatment_time","text":"Length of time of the pretreatment in s URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_time","title":"Slot: Pretreatment_time (pretreatment_time)"},{"location":"pretreatment_time/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"pretreatment_time/#properties","text":"Range: Float","title":"Properties"},{"location":"pretreatment_time/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"pretreatment_time/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"pretreatment_time/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_time native https://w3id.org/osc-em/oscem-schemas/:pretreatment_time","title":"Mappings"},{"location":"pretreatment_time/#linkml-source","text":"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 domain_of: - Grid range: float","title":"LinkML Source"},{"location":"pretreatment_type/","text":"Slot: Pretreatment_type (pretreatment_type) Type of pretreatment of the grid, i.e., glow discharge URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_type Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_type native https://w3id.org/osc-em/oscem-schemas/:pretreatment_type LinkML Source 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 domain_of: - Grid range: string","title":"Slot: Pretreatment_type (pretreatment_type)"},{"location":"pretreatment_type/#slot-pretreatment_type-pretreatment_type","text":"Type of pretreatment of the grid, i.e., glow discharge URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_type","title":"Slot: Pretreatment_type (pretreatment_type)"},{"location":"pretreatment_type/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"pretreatment_type/#properties","text":"Range: String","title":"Properties"},{"location":"pretreatment_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"pretreatment_type/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"pretreatment_type/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_type native https://w3id.org/osc-em/oscem-schemas/:pretreatment_type","title":"Mappings"},{"location":"pretreatment_type/#linkml-source","text":"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 domain_of: - Grid range: string","title":"LinkML Source"},{"location":"project_id/","text":"Slot: project_id project id URI: schema:identifier Applicable Classes Name Description Modifies Slot Grant Grant no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self schema:identifier native https://w3id.org/osc-em/oscem-schemas/:project_id LinkML Source name: project_id description: project id from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:identifier alias: project_id domain_of: - Grant range: string","title":"Slot: project_id"},{"location":"project_id/#slot-project_id","text":"project id URI: schema:identifier","title":"Slot: project_id"},{"location":"project_id/#applicable-classes","text":"Name Description Modifies Slot Grant Grant no","title":"Applicable Classes"},{"location":"project_id/#properties","text":"Range: String","title":"Properties"},{"location":"project_id/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"project_id/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"project_id/#mappings","text":"Mapping Type Mapped Value self schema:identifier native https://w3id.org/osc-em/oscem-schemas/:project_id","title":"Mappings"},{"location":"project_id/#linkml-source","text":"name: project_id description: project id from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:identifier alias: project_id domain_of: - Grant range: string","title":"LinkML Source"},{"location":"reference/","text":"Slot: Reference (reference) Link to a reference of your ligand, i.e., CCD, PubChem, etc. URI: https://w3id.org/osc-em/oscem-schemas/:reference Applicable Classes Name Description Modifies Slot Ligand A class representing a ligand no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:reference native https://w3id.org/osc-em/oscem-schemas/:reference LinkML Source 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 domain_of: - Ligand range: string","title":"Slot: Reference (reference)"},{"location":"reference/#slot-reference-reference","text":"Link to a reference of your ligand, i.e., CCD, PubChem, etc. URI: https://w3id.org/osc-em/oscem-schemas/:reference","title":"Slot: Reference (reference)"},{"location":"reference/#applicable-classes","text":"Name Description Modifies Slot Ligand A class representing a ligand no","title":"Applicable Classes"},{"location":"reference/#properties","text":"Range: String","title":"Properties"},{"location":"reference/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"reference/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"reference/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:reference native https://w3id.org/osc-em/oscem-schemas/:reference","title":"Mappings"},{"location":"reference/#linkml-source","text":"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 domain_of: - Ligand range: string","title":"LinkML Source"},{"location":"role/","text":"Slot: Role (role) Role of the author, i.e., principal investigator URI: https://w3id.org/osc-em/oscem-schemas/:role Applicable Classes Name Description Modifies Slot Author no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:role native https://w3id.org/osc-em/oscem-schemas/:role LinkML Source 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 domain_of: - Author range: string","title":"Slot: Role (role)"},{"location":"role/#slot-role-role","text":"Role of the author, i.e., principal investigator URI: https://w3id.org/osc-em/oscem-schemas/:role","title":"Slot: Role (role)"},{"location":"role/#applicable-classes","text":"Name Description Modifies Slot Author no","title":"Applicable Classes"},{"location":"role/#properties","text":"Range: String","title":"Properties"},{"location":"role/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"role/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"role/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:role native https://w3id.org/osc-em/oscem-schemas/:role","title":"Mappings"},{"location":"role/#linkml-source","text":"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 domain_of: - Author range: string","title":"LinkML Source"},{"location":"sample/","text":"Slot: Sample (sample) Sample information URI: https://w3id.org/osc-em/oscem-schemas/:sample Applicable Classes Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes Properties Range: Sample Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:sample native https://w3id.org/osc-em/oscem-schemas/:sample LinkML Source name: sample description: Sample information title: Sample from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: sample domain_of: - EMDataset range: Sample","title":"Slot: Sample (sample)"},{"location":"sample/#slot-sample-sample","text":"Sample information URI: https://w3id.org/osc-em/oscem-schemas/:sample","title":"Slot: Sample (sample)"},{"location":"sample/#applicable-classes","text":"Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes","title":"Applicable Classes"},{"location":"sample/#properties","text":"Range: Sample","title":"Properties"},{"location":"sample/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"sample/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"sample/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:sample native https://w3id.org/osc-em/oscem-schemas/:sample","title":"Mappings"},{"location":"sample/#linkml-source","text":"name: sample description: Sample information title: Sample from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: sample domain_of: - EMDataset range: Sample","title":"LinkML Source"},{"location":"sequence/","text":"Slot: Sequence (sequence) Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here URI: https://w3id.org/osc-em/oscem-schemas/:sequence Applicable Classes Name Description Modifies Slot Molecule A class representing a molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:sequence native https://w3id.org/osc-em/oscem-schemas/:sequence LinkML Source 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 domain_of: - Molecule range: string","title":"Slot: Sequence (sequence)"},{"location":"sequence/#slot-sequence-sequence","text":"Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here URI: https://w3id.org/osc-em/oscem-schemas/:sequence","title":"Slot: Sequence (sequence)"},{"location":"sequence/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"sequence/#properties","text":"Range: String","title":"Properties"},{"location":"sequence/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"sequence/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"sequence/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:sequence native https://w3id.org/osc-em/oscem-schemas/:sequence","title":"Mappings"},{"location":"sequence/#linkml-source","text":"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 domain_of: - Molecule range: string","title":"LinkML Source"},{"location":"shadowing/","text":"Slot: Shadowing (shadowing) Whether the sample was shadowed URI: https://w3id.org/osc-em/oscem-schemas/:shadowing Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: Boolean Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:shadowing native https://w3id.org/osc-em/oscem-schemas/:shadowing LinkML Source name: shadowing description: Whether the sample was shadowed title: Shadowing from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: shadowing domain_of: - Specimen range: boolean","title":"Slot: Shadowing (shadowing)"},{"location":"shadowing/#slot-shadowing-shadowing","text":"Whether the sample was shadowed URI: https://w3id.org/osc-em/oscem-schemas/:shadowing","title":"Slot: Shadowing (shadowing)"},{"location":"shadowing/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"shadowing/#properties","text":"Range: Boolean","title":"Properties"},{"location":"shadowing/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"shadowing/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"shadowing/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:shadowing native https://w3id.org/osc-em/oscem-schemas/:shadowing","title":"Mappings"},{"location":"shadowing/#linkml-source","text":"name: shadowing description: Whether the sample was shadowed title: Shadowing from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: shadowing domain_of: - Specimen range: boolean","title":"LinkML Source"},{"location":"smile/","text":"Slot: SMILE (smile) Provide a valid SMILE string of your ligand URI: https://w3id.org/osc-em/oscem-schemas/:smile Applicable Classes Name Description Modifies Slot Ligand A class representing a ligand no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:smile native https://w3id.org/osc-em/oscem-schemas/:smile LinkML Source name: smile description: Provide a valid SMILE string of your ligand title: SMILE from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: smile domain_of: - Ligand range: string","title":"Slot: SMILE (smile)"},{"location":"smile/#slot-smile-smile","text":"Provide a valid SMILE string of your ligand URI: https://w3id.org/osc-em/oscem-schemas/:smile","title":"Slot: SMILE (smile)"},{"location":"smile/#applicable-classes","text":"Name Description Modifies Slot Ligand A class representing a ligand no","title":"Applicable Classes"},{"location":"smile/#properties","text":"Range: String","title":"Properties"},{"location":"smile/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"smile/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"smile/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:smile native https://w3id.org/osc-em/oscem-schemas/:smile","title":"Mappings"},{"location":"smile/#linkml-source","text":"name: smile description: Provide a valid SMILE string of your ligand title: SMILE from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: smile domain_of: - Ligand range: string","title":"LinkML Source"},{"location":"source/","text":"Slot: Source (source) Where the sample was taken from, i.e., natural host, recombinantly expressed, etc. URI: https://w3id.org/osc-em/oscem-schemas/:source Applicable Classes Name Description Modifies Slot OverallMolecule A class representing the overall molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:source native https://w3id.org/osc-em/oscem-schemas/:source LinkML 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 domain_of: - OverallMolecule range: string","title":"Slot: Source (source)"},{"location":"source/#slot-source-source","text":"Where the sample was taken from, i.e., natural host, recombinantly expressed, etc. URI: https://w3id.org/osc-em/oscem-schemas/:source","title":"Slot: Source (source)"},{"location":"source/#applicable-classes","text":"Name Description Modifies Slot OverallMolecule A class representing the overall molecule yes","title":"Applicable Classes"},{"location":"source/#properties","text":"Range: String","title":"Properties"},{"location":"source/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"source/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"source/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:source native https://w3id.org/osc-em/oscem-schemas/:source","title":"Mappings"},{"location":"source/#linkml-source","text":"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 domain_of: - OverallMolecule range: string","title":"LinkML Source"},{"location":"specialist_optics/","text":"Slot: specialist_optics Any type of special optics, such as a phaseplate URI: https://w3id.org/osc-em/oscem-schemas/:specialist_optics Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: SpecialistOptics Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:specialist_optics native https://w3id.org/osc-em/oscem-schemas/:specialist_optics LinkML Source 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 domain_of: - Acquisition range: SpecialistOptics","title":"Slot: specialist_optics"},{"location":"specialist_optics/#slot-specialist_optics","text":"Any type of special optics, such as a phaseplate URI: https://w3id.org/osc-em/oscem-schemas/:specialist_optics","title":"Slot: specialist_optics"},{"location":"specialist_optics/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"specialist_optics/#properties","text":"Range: SpecialistOptics","title":"Properties"},{"location":"specialist_optics/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"specialist_optics/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"specialist_optics/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:specialist_optics native https://w3id.org/osc-em/oscem-schemas/:specialist_optics","title":"Mappings"},{"location":"specialist_optics/#linkml-source","text":"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 domain_of: - Acquisition range: SpecialistOptics","title":"LinkML Source"},{"location":"specimen/","text":"Slot: Specimen (specimen) Description of the specimen URI: https://w3id.org/osc-em/oscem-schemas/:specimen Applicable Classes Name Description Modifies Slot Sample A class representing a sample yes Properties Range: Specimen Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:specimen native https://w3id.org/osc-em/oscem-schemas/:specimen LinkML Source name: specimen description: Description of the specimen title: Specimen from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: specimen domain_of: - Sample range: Specimen","title":"Slot: Specimen (specimen)"},{"location":"specimen/#slot-specimen-specimen","text":"Description of the specimen URI: https://w3id.org/osc-em/oscem-schemas/:specimen","title":"Slot: Specimen (specimen)"},{"location":"specimen/#applicable-classes","text":"Name Description Modifies Slot Sample A class representing a sample yes","title":"Applicable Classes"},{"location":"specimen/#properties","text":"Range: Specimen","title":"Properties"},{"location":"specimen/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"specimen/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"specimen/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:specimen native https://w3id.org/osc-em/oscem-schemas/:specimen","title":"Mappings"},{"location":"specimen/#linkml-source","text":"name: specimen description: Description of the specimen title: Specimen from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: specimen domain_of: - 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Specimen range: boolean","title":"LinkML Source"},{"location":"start_date/","text":"Slot: start_date start date URI: https://w3id.org/osc-em/oscem-schemas/:start_date Applicable Classes Name Description Modifies Slot Grant Grant no Properties Range: Date Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:start_date native https://w3id.org/osc-em/oscem-schemas/:start_date LinkML Source name: start_date description: start date from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: start_date domain_of: - Grant range: date","title":"Slot: start_date"},{"location":"start_date/#slot-start_date","text":"start date URI: https://w3id.org/osc-em/oscem-schemas/:start_date","title":"Slot: start_date"},{"location":"start_date/#applicable-classes","text":"Name Description Modifies Slot Grant Grant no","title":"Applicable Classes"},{"location":"start_date/#properties","text":"Range: Date","title":"Properties"},{"location":"start_date/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"start_date/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"start_date/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:start_date native https://w3id.org/osc-em/oscem-schemas/:start_date","title":"Mappings"},{"location":"start_date/#linkml-source","text":"name: start_date description: start date from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: start_date domain_of: - 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Molecule range: string","title":"LinkML Source"},{"location":"taxonomy_id_source/","text":"Slot: Taxonomy_ID_source (taxonomy_id_source) Taxonomy ID of the natural source organism URI: https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source Applicable Classes Name Description Modifies Slot Molecule A class representing a molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source native https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source LinkML 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 domain_of: - Molecule range: string","title":"Slot: Taxonomy_ID_source (taxonomy_id_source)"},{"location":"taxonomy_id_source/#slot-taxonomy_id_source-taxonomy_id_source","text":"Taxonomy ID of the natural source organism URI: https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source","title":"Slot: Taxonomy_ID_source (taxonomy_id_source)"},{"location":"taxonomy_id_source/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"taxonomy_id_source/#properties","text":"Range: String","title":"Properties"},{"location":"taxonomy_id_source/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"taxonomy_id_source/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"taxonomy_id_source/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source native https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source","title":"Mappings"},{"location":"taxonomy_id_source/#linkml-source","text":"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 domain_of: - 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URI: https://w3id.org/osc-em/oscem-schemas/:temperature_range Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Range Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:temperature_range native https://w3id.org/osc-em/oscem-schemas/:temperature_range LinkML Source 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 domain_of: - Acquisition range: Range","title":"Slot: temperature_range"},{"location":"temperature_range/#slot-temperature_range","text":"Temperature during data collection, in K with min and max values. URI: https://w3id.org/osc-em/oscem-schemas/:temperature_range","title":"Slot: temperature_range"},{"location":"temperature_range/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"temperature_range/#properties","text":"Range: Range","title":"Properties"},{"location":"temperature_range/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"temperature_range/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"temperature_range/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:temperature_range native https://w3id.org/osc-em/oscem-schemas/:temperature_range","title":"Mappings"},{"location":"temperature_range/#linkml-source","text":"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 domain_of: - Acquisition range: Range","title":"LinkML Source"},{"location":"tilt_angle/","text":"Slot: tilt_angle The min, max and increment of the tilt angle in a tomography session. 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here with qualifier during this dat... has_unit Unit has_value Value height The height of a given item - unit depends on item holder Speciman holder model holder_cryogen Type of cryogen used in the holder - if the holder is cooled seperately humidity Environmental humidity just before vitrification, in % illumination Mode of illumination used during data collection image_size The size of the image in pixels, height and width given images_generated Number of images generated total for this data collection - might need a qual... imageshift Movement of the Beam below the image in order to shift the image on the detec... imaging Mode of imaging used during data collection increment Increment between elements of a series instrument Describe the instrument used to acquire the data ligands List of ligands associated with the sample manufacturer Grid manufacturer material Material out of which the grid is made maximal Maximal value of a given dataset property mesh Grid mesh in lines per inch microscope Name/Type of the Microscope microscope_software Software used for instrument control, minimal Minimal value of a given dataset property model Make and model of a specialized device molecular_class Class of the molecule molecular_type Description of the overall supramolecular type, i molecular_weight Molecular weight in Da molecule List of molecule associated with the sample name name name_mol Name of an individual molecule (often protein) in the sample name_org Name of the organization name_sample Name of the full sample natural_source Scientific name of the natural host organism nominal_defocus Target defocus set, min and max values in \u00b5m nominal_magnification Magnification level as indicated by the instrument, no unit orcid ORCID of the author, a type of unique identifier overall_molecule Description of the overall molecule person person ph pH of the sample buffer phaseplate Phaseplate is a special optics device that can be used to enhance contrast pixel_size Pixel size, in Angstrom present Whether the model contains any ligands pretreatment_atmosphere Atmospheric conditions in the chamber during pretreatment, i pretreatment_pressure Pressure of the chamber during pretreatment, in Pa pretreatment_time Length of time of the pretreatment in s pretreatment_type Type of pretreatment of the grid, i project_id project id reference Link to a reference of your ligand, i role Role of the author, i sample Sample information sequence Full sequence of the sample as in the data, i shadowing Whether the sample was shadowed smile Provide a valid SMILE string of your ligand source Where the sample was taken from, i specialist_optics Any type of special optics, such as a phaseplate specimen Description of the specimen spherical_aberration_corrector Specialist device to correct for spherical aberration of the microscope lense... staining Whether the sample was stained start_date start date taxonomy_id_expression Taxonomy ID of the expression system organism taxonomy_id_source Taxonomy ID of the natural source organism temperature Environmental temperature just before vitrification, in K temperature_range Temperature during data collection, in K with min and max values tilt_angle The min, max and increment of the tilt angle in a tomography session tilt_axis_angle The tilt axis angle of a tomography series type_org Type of organization, academic, commercial, governmental, etc used whether a specific instrument was used during data acquisition vitrification Whether the sample was vitrified vitrification_cryogen Which cryogen was used for vitrification width The width of a given item - unit depends on item work_phone work phone work_status work status x_max maximum x x_min minimum x y_max maximum y y_min minimum y","title":"Slots"},{"location":"#enumerations","text":"Enumeration Description MoleculeClassEnum OrganizationTypeEnum","title":"Enumerations"},{"location":"#types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE","title":"Types"},{"location":"#subsets","text":"Subset Description","title":"Subsets"},{"location":"Acquisition/","text":"Class: Acquisition URI: https://w3id.org/osc-em/oscem-schemas/:Acquisition classDiagram class Acquisition click Acquisition href \"../Acquisition\" Acquisition : beamshift Acquisition --> \"0..1\" BoundingBox2D : beamshift click BoundingBox2D href \"../BoundingBox2D\" Acquisition : beamtilt Acquisition --> \"0..1\" BoundingBox2D : beamtilt click BoundingBox2D href \"../BoundingBox2D\" Acquisition : beamtiltgroups Acquisition : binning_camera Acquisition : calibrated_defocus Acquisition --> \"0..1\" Range : calibrated_defocus click Range href \"../Range\" Acquisition : calibrated_magnification Acquisition : cryogen Acquisition : date_time Acquisition --> \"1\" Any : date_time click Any href \"../Any\" Acquisition : detector Acquisition : detector_mode Acquisition : dose_per_movie Acquisition : energy_filter Acquisition --> \"0..1\" EnergyFilter : energy_filter click EnergyFilter href \"../EnergyFilter\" Acquisition : exposure_time Acquisition : frames_per_movie Acquisition : gainref_flip_rotate Acquisition : grids_imaged Acquisition : holder Acquisition : holder_cryogen Acquisition : image_size Acquisition --> \"0..1\" ImageSize : image_size click ImageSize href \"../ImageSize\" Acquisition : images_generated Acquisition : imageshift Acquisition --> \"0..1\" BoundingBox2D : imageshift click BoundingBox2D href \"../BoundingBox2D\" Acquisition : microscope_software Acquisition : nominal_defocus Acquisition --> \"0..1\" Range : nominal_defocus click Range href \"../Range\" Acquisition : nominal_magnification Acquisition : pixel_size Acquisition : specialist_optics Acquisition --> \"0..1\" SpecialistOptics : specialist_optics click SpecialistOptics href \"../SpecialistOptics\" Acquisition : temperature_range Acquisition --> \"0..1\" Range : temperature_range click Range href \"../Range\" Slots Name Cardinality and Range Description Inheritance nominal_defocus 0..1 Range Target defocus set, min and max values in \u00b5m direct calibrated_defocus 0..1 Range Machine estimated defocus, min and max values in \u00b5m 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 Float 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 Float 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 Float 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 Usages used by used in type used EMDataset acquisition range Acquisition Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Acquisition native https://w3id.org/osc-em/oscem-schemas/:Acquisition LinkML Source Direct 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 Induced 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 \u00b5m. 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 \u00b5m. 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: float 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: float 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: float 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 \u00b5m. 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","title":"Class: Acquisition"},{"location":"Acquisition/#class-acquisition","text":"URI: https://w3id.org/osc-em/oscem-schemas/:Acquisition classDiagram class Acquisition click Acquisition href \"../Acquisition\" Acquisition : beamshift Acquisition --> \"0..1\" BoundingBox2D : beamshift click BoundingBox2D href \"../BoundingBox2D\" Acquisition : beamtilt Acquisition --> \"0..1\" BoundingBox2D : beamtilt click BoundingBox2D href \"../BoundingBox2D\" Acquisition : beamtiltgroups Acquisition : binning_camera Acquisition : calibrated_defocus Acquisition --> \"0..1\" Range : calibrated_defocus click Range href \"../Range\" Acquisition : calibrated_magnification Acquisition : cryogen Acquisition : date_time Acquisition --> \"1\" Any : date_time click Any href \"../Any\" Acquisition : detector Acquisition : detector_mode Acquisition : dose_per_movie Acquisition : energy_filter Acquisition --> \"0..1\" EnergyFilter : energy_filter click EnergyFilter href \"../EnergyFilter\" Acquisition : exposure_time Acquisition : frames_per_movie Acquisition : gainref_flip_rotate Acquisition : grids_imaged Acquisition : holder Acquisition : holder_cryogen Acquisition : image_size Acquisition --> \"0..1\" ImageSize : image_size click ImageSize href \"../ImageSize\" Acquisition : images_generated Acquisition : imageshift Acquisition --> \"0..1\" BoundingBox2D : imageshift click BoundingBox2D href \"../BoundingBox2D\" Acquisition : microscope_software Acquisition : nominal_defocus Acquisition --> \"0..1\" Range : nominal_defocus click Range href \"../Range\" Acquisition : nominal_magnification Acquisition : pixel_size Acquisition : specialist_optics Acquisition --> \"0..1\" SpecialistOptics : specialist_optics click SpecialistOptics href \"../SpecialistOptics\" Acquisition : temperature_range Acquisition --> \"0..1\" Range : temperature_range click Range href \"../Range\"","title":"Class: Acquisition"},{"location":"Acquisition/#slots","text":"Name Cardinality and Range Description Inheritance nominal_defocus 0..1 Range Target defocus set, min and max values in \u00b5m direct calibrated_defocus 0..1 Range Machine estimated defocus, min and max values in \u00b5m 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 Float 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 Float 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 Float 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","title":"Slots"},{"location":"Acquisition/#usages","text":"used by used in type used EMDataset acquisition range Acquisition","title":"Usages"},{"location":"Acquisition/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Acquisition/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Acquisition/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Acquisition native https://w3id.org/osc-em/oscem-schemas/:Acquisition","title":"Mappings"},{"location":"Acquisition/#linkml-source","text":"","title":"LinkML Source"},{"location":"Acquisition/#direct","text":"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","title":"Direct"},{"location":"Acquisition/#induced","text":"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 \u00b5m. 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 \u00b5m. 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: float 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: float 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: float 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 \u00b5m. 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","title":"Induced"},{"location":"Any/","text":"Class: Any Any type, used as the base for type-narrowing. __ See https://linkml.io/linkml/schemas/advanced.html URI: linkml:Any classDiagram class Any click Any href \"../Any\" Slots Name Cardinality and Range Description Inheritance Usages used by used in type used Acquisition date_time range Any Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self linkml:Any native https://w3id.org/osc-em/oscem-schemas/:Any LinkML Source Direct name: Any description: 'Any type, used as the base for type-narrowing. 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Mapped Value self xsd:date native https://w3id.org/osc-em/oscem-schemas/:date exact schema:Date","title":"Mappings"},{"location":"DateOrDatetime/","text":"Type: DateOrDatetime Either a date or a datetime URI: linkml:DateOrDatetime base : str uri : linkml:DateOrDatetime repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self linkml:DateOrDatetime native https://w3id.org/osc-em/oscem-schemas/:date_or_datetime","title":"Type: DateOrDatetime"},{"location":"DateOrDatetime/#type-dateordatetime","text":"Either a date or a datetime URI: linkml:DateOrDatetime base : str uri : linkml:DateOrDatetime repr : str","title":"Type: DateOrDatetime"},{"location":"DateOrDatetime/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DateOrDatetime/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"DateOrDatetime/#mappings","text":"Mapping Type Mapped Value self linkml:DateOrDatetime native https://w3id.org/osc-em/oscem-schemas/:date_or_datetime","title":"Mappings"},{"location":"Datetime/","text":"Type: Datetime The combination of a date and time URI: xsd:dateTime base : XSDDateTime uri : xsd:dateTime repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:dateTime native https://w3id.org/osc-em/oscem-schemas/:datetime exact schema:DateTime","title":"Type: Datetime"},{"location":"Datetime/#type-datetime","text":"The combination of a date and time URI: xsd:dateTime base : XSDDateTime uri : xsd:dateTime repr : str","title":"Type: Datetime"},{"location":"Datetime/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Datetime/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Datetime/#mappings","text":"Mapping Type Mapped Value self xsd:dateTime native https://w3id.org/osc-em/oscem-schemas/:datetime exact schema:DateTime","title":"Mappings"},{"location":"Decimal/","text":"Type: Decimal A real number with arbitrary precision that conforms to the xsd:decimal specification URI: xsd:decimal base : Decimal uri : xsd:decimal Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:decimal native https://w3id.org/osc-em/oscem-schemas/:decimal broad schema:Number","title":"Type: Decimal"},{"location":"Decimal/#type-decimal","text":"A real number with arbitrary precision that conforms to the xsd:decimal specification URI: xsd:decimal base : Decimal uri : xsd:decimal","title":"Type: Decimal"},{"location":"Decimal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Decimal/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Decimal/#mappings","text":"Mapping Type Mapped Value self xsd:decimal native https://w3id.org/osc-em/oscem-schemas/:decimal broad schema:Number","title":"Mappings"},{"location":"Double/","text":"Type: Double A real number that conforms to the xsd:double specification URI: xsd:double base : float uri : xsd:double Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:double native https://w3id.org/osc-em/oscem-schemas/:double close schema:Float","title":"Type: Double"},{"location":"Double/#type-double","text":"A real number that conforms to the xsd:double specification URI: xsd:double base : float uri : xsd:double","title":"Type: Double"},{"location":"Double/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping 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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 Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:EMDataset native https://w3id.org/osc-em/oscem-schemas/:EMDataset LinkML Source Direct 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 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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","title":"Class: EMDataset"},{"location":"EMDataset/#class-emdataset","text":"OSC-EM Metadata for a dataset URI: https://w3id.org/osc-em/oscem-schemas/:EMDataset classDiagram class EMDataset click EMDataset href \"../EMDataset\" EMDataset : acquisition EMDataset --> \"1\" Acquisition : acquisition click Acquisition href \"../Acquisition\" EMDataset : authors EMDataset --> \"1..*\" Author : authors click Author href \"../Author\" EMDataset : grants EMDataset --> \"1..*\" Grant : grants click Grant href \"../Grant\" EMDataset : instrument EMDataset --> \"1\" Instrument : instrument click Instrument href \"../Instrument\" EMDataset : sample EMDataset --> \"1\" Sample : sample click Sample href \"../Sample\"","title":"Class: EMDataset"},{"location":"EMDataset/#slots","text":"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","title":"Slots"},{"location":"EMDataset/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping 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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","title":"Induced"},{"location":"EnergyFilter/","text":"Class: EnergyFilter URI: https://w3id.org/osc-em/oscem-schemas/:EnergyFilter classDiagram class EnergyFilter click EnergyFilter href \"../EnergyFilter\" EnergyFilter : model EnergyFilter : used EnergyFilter : width Slots 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 specialized device direct width 1 Integer The width of a given item - unit depends on item direct Usages used by used in type used Acquisition energy_filter range EnergyFilter Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:EnergyFilter native https://w3id.org/osc-em/oscem-schemas/:EnergyFilter LinkML Source Direct 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 Induced 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 specialized device from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: model owner: EnergyFilter domain_of: - EnergyFilter - Phaseplate - SphericalAberrationCorrector - ChromaticAberrationCorrector 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","title":"Class: EnergyFilter"},{"location":"EnergyFilter/#class-energyfilter","text":"URI: https://w3id.org/osc-em/oscem-schemas/:EnergyFilter classDiagram class EnergyFilter click EnergyFilter href \"../EnergyFilter\" EnergyFilter : model EnergyFilter : used EnergyFilter : width","title":"Class: EnergyFilter"},{"location":"EnergyFilter/#slots","text":"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 specialized device direct width 1 Integer The width of a given item - unit depends on item direct","title":"Slots"},{"location":"EnergyFilter/#usages","text":"used by used in type used Acquisition energy_filter range EnergyFilter","title":"Usages"},{"location":"EnergyFilter/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"EnergyFilter/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"EnergyFilter/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:EnergyFilter native https://w3id.org/osc-em/oscem-schemas/:EnergyFilter","title":"Mappings"},{"location":"EnergyFilter/#linkml-source","text":"","title":"LinkML Source"},{"location":"EnergyFilter/#direct","text":"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","title":"Direct"},{"location":"EnergyFilter/#induced","text":"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 specialized device from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: model owner: EnergyFilter domain_of: - EnergyFilter - Phaseplate - SphericalAberrationCorrector - ChromaticAberrationCorrector 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","title":"Induced"},{"location":"Float/","text":"Type: Float A real number that conforms to the xsd:float specification URI: xsd:float base : float uri : xsd:float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:float native https://w3id.org/osc-em/oscem-schemas/:float exact schema:Float","title":"Type: Float"},{"location":"Float/#type-float","text":"A real number that conforms to the xsd:float specification URI: xsd:float base : float uri : xsd:float","title":"Type: Float"},{"location":"Float/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Float/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Float/#mappings","text":"Mapping Type Mapped Value self xsd:float native https://w3id.org/osc-em/oscem-schemas/:float exact schema:Float","title":"Mappings"},{"location":"Grant/","text":"Class: Grant Grant URI: schema:Grant classDiagram class Grant click Grant href \"../Grant\" Grant : budget Grant --> \"0..1\" QuantityValue : budget click QuantityValue href \"../QuantityValue\" Grant : end_date Grant : funder Grant : name Grant : project_id Grant : start_date Slots 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 Usages used by used in type used EMDataset grants range Grant Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self schema:Grant native https://w3id.org/osc-em/oscem-schemas/:Grant LinkML Source Direct name: Grant description: Grant from_schema: https://w3id.org/osc-em/oscem-schemas slots: - name - funder - start_date - end_date - budget - project_id class_uri: schema:Grant Induced 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 class_uri: schema:Grant","title":"Class: Grant"},{"location":"Grant/#class-grant","text":"Grant URI: schema:Grant classDiagram class Grant click Grant href \"../Grant\" Grant : budget Grant --> \"0..1\" QuantityValue : budget click QuantityValue href \"../QuantityValue\" Grant : end_date Grant : funder Grant : name Grant : project_id Grant : start_date","title":"Class: Grant"},{"location":"Grant/#slots","text":"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","title":"Slots"},{"location":"Grant/#usages","text":"used by used in type used EMDataset grants range Grant","title":"Usages"},{"location":"Grant/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Grant/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Grant/#mappings","text":"Mapping Type Mapped Value self schema:Grant native https://w3id.org/osc-em/oscem-schemas/:Grant","title":"Mappings"},{"location":"Grant/#linkml-source","text":"","title":"LinkML Source"},{"location":"Grant/#direct","text":"name: Grant description: Grant from_schema: https://w3id.org/osc-em/oscem-schemas slots: - name - funder - start_date - end_date - budget - project_id class_uri: schema:Grant","title":"Direct"},{"location":"Grant/#induced","text":"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 class_uri: schema:Grant","title":"Induced"},{"location":"Grid/","text":"Class: Grid (Grid) A class representing a grid URI: https://w3id.org/osc-em/oscem-schemas/:Grid classDiagram class Grid click Grid href \"../Grid\" Grid : film_material Grid : film_support Grid : film_thickness Grid : film_topology Grid : manufacturer Grid : material Grid : mesh Grid : pretreatment_atmosphere Grid : pretreatment_pressure Grid : pretreatment_time Grid : pretreatment_type Slots 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 Float Length of time of the pretreatment in s direct pretreatment_pressure 0..1 Float Pressure of the chamber during pretreatment, in Pa direct pretreatment_atmosphere 0..1 String Atmospheric conditions in the chamber during pretreatment, i direct Usages used by used in type used Sample grid range Grid Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Grid native https://w3id.org/osc-em/oscem-schemas/:Grid LinkML Source Direct 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 Induced 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: float 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: float 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","title":"Class: Grid (Grid)"},{"location":"Grid/#class-grid-grid","text":"A class representing a grid URI: https://w3id.org/osc-em/oscem-schemas/:Grid classDiagram class Grid click Grid href \"../Grid\" Grid : film_material Grid : film_support Grid : film_thickness Grid : film_topology Grid : manufacturer Grid : material Grid : mesh Grid : pretreatment_atmosphere Grid : pretreatment_pressure Grid : pretreatment_time Grid : pretreatment_type","title":"Class: Grid (Grid)"},{"location":"Grid/#slots","text":"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 Float Length of time of the pretreatment in s direct pretreatment_pressure 0..1 Float Pressure of 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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","title":"Direct"},{"location":"Grid/#induced","text":"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: float 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: float 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","title":"Induced"},{"location":"ImageSize/","text":"Class: ImageSize size of a 2D image (in integer units) URI: https://w3id.org/osc-em/oscem-schemas/:ImageSize classDiagram class ImageSize 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range ImageSize","title":"Usages"},{"location":"ImageSize/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ImageSize/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"ImageSize/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:ImageSize native https://w3id.org/osc-em/oscem-schemas/:ImageSize","title":"Mappings"},{"location":"ImageSize/#linkml-source","text":"","title":"LinkML Source"},{"location":"ImageSize/#direct","text":"name: ImageSize description: size of a 2D image (in integer units) from_schema: https://w3id.org/osc-em/oscem-schemas slots: - height - width","title":"Direct"},{"location":"ImageSize/#induced","text":"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","title":"Induced"},{"location":"Instrument/","text":"Class: Instrument Instrument values, mostly constant across a data collection. URI: https://w3id.org/osc-em/oscem-schemas/:Instrument classDiagram class Instrument click Instrument href \"../Instrument\" Instrument : acceleration_voltage Instrument : c2_aperture Instrument : cs Instrument : electron_source Instrument : illumination Instrument : imaging Instrument : microscope Slots 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 Integer Voltage used for the electron acceleration, in kV direct c2_aperture 0..1 Integer C2 aperture size used in data acquisition, in \u00b5m direct cs 1 Float Spherical aberration of the instrument, in mm direct Usages used by used in type used EMDataset instrument range Instrument Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Instrument native https://w3id.org/osc-em/oscem-schemas/:Instrument LinkML Source Direct 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 Induced 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: integer required: true c2_aperture: name: c2_aperture description: C2 aperture size used in data acquisition, in \u00b5m from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: c2_aperture owner: Instrument domain_of: - Instrument range: integer 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: float required: true","title":"Class: Instrument"},{"location":"Instrument/#class-instrument","text":"Instrument values, mostly constant across a data collection. URI: https://w3id.org/osc-em/oscem-schemas/:Instrument classDiagram class Instrument click Instrument href \"../Instrument\" Instrument : acceleration_voltage Instrument : c2_aperture Instrument : cs Instrument : electron_source Instrument : illumination Instrument : imaging Instrument : microscope","title":"Class: Instrument"},{"location":"Instrument/#slots","text":"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 Integer Voltage used for the electron acceleration, in kV direct c2_aperture 0..1 Integer C2 aperture size used in data acquisition, in \u00b5m direct cs 1 Float Spherical aberration of the instrument, in mm direct","title":"Slots"},{"location":"Instrument/#usages","text":"used by used in type used EMDataset instrument range Instrument","title":"Usages"},{"location":"Instrument/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Instrument/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Instrument/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Instrument native https://w3id.org/osc-em/oscem-schemas/:Instrument","title":"Mappings"},{"location":"Instrument/#linkml-source","text":"","title":"LinkML Source"},{"location":"Instrument/#direct","text":"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","title":"Direct"},{"location":"Instrument/#induced","text":"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: integer required: true c2_aperture: name: c2_aperture description: C2 aperture size used in data acquisition, in \u00b5m from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: c2_aperture owner: Instrument domain_of: - Instrument range: integer 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: float required: true","title":"Induced"},{"location":"Integer/","text":"Type: Integer An integer URI: xsd:integer base : int uri : xsd:integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:integer native https://w3id.org/osc-em/oscem-schemas/:integer exact schema:Integer","title":"Type: Integer"},{"location":"Integer/#type-integer","text":"An integer URI: xsd:integer base : int uri : xsd:integer","title":"Type: Integer"},{"location":"Integer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Integer/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Integer/#mappings","text":"Mapping Type Mapped Value self xsd:integer native https://w3id.org/osc-em/oscem-schemas/:integer exact schema:Integer","title":"Mappings"},{"location":"Jsonpath/","text":"Type: Jsonpath 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 base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:jsonpath","title":"Type: Jsonpath"},{"location":"Jsonpath/#type-jsonpath","text":"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 base : str uri : xsd:string repr : str","title":"Type: Jsonpath"},{"location":"Jsonpath/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Jsonpath/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Jsonpath/#mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:jsonpath","title":"Mappings"},{"location":"Jsonpointer/","text":"Type: Jsonpointer 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 base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:jsonpointer","title":"Type: Jsonpointer"},{"location":"Jsonpointer/#type-jsonpointer","text":"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 base : str uri : xsd:string repr : str","title":"Type: Jsonpointer"},{"location":"Jsonpointer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Jsonpointer/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Jsonpointer/#mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:jsonpointer","title":"Mappings"},{"location":"Ligand/","text":"Class: Ligand (Ligand) A class representing a ligand URI: https://w3id.org/osc-em/oscem-schemas/:Ligand classDiagram class Ligand click Ligand href \"../Ligand\" Ligand : present Ligand : reference Ligand : smile Slots Name Cardinality and Range Description Inheritance present 1 Boolean Whether the model contains any ligands direct smile 0..1 String Provide a valid SMILE string of your ligand direct reference 0..1 String Link to a reference of your ligand, i direct Usages used by used in type used Sample ligands range Ligand Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Ligand native https://w3id.org/osc-em/oscem-schemas/:Ligand LinkML Source Direct name: Ligand description: A class representing a ligand title: Ligand from_schema: https://w3id.org/osc-em/oscem-schemas slots: - present - smile - reference slot_usage: present: name: present required: true Induced 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 smile: name: smile description: Provide a valid SMILE string of your ligand title: SMILE from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: smile 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","title":"Class: Ligand (Ligand)"},{"location":"Ligand/#class-ligand-ligand","text":"A class representing a ligand URI: https://w3id.org/osc-em/oscem-schemas/:Ligand classDiagram class Ligand click Ligand href \"../Ligand\" Ligand : present Ligand : reference Ligand : smile","title":"Class: Ligand (Ligand)"},{"location":"Ligand/#slots","text":"Name Cardinality and Range Description Inheritance present 1 Boolean Whether the model contains any ligands direct smile 0..1 String Provide a valid SMILE string of your ligand direct reference 0..1 String Link to a reference of your ligand, i direct","title":"Slots"},{"location":"Ligand/#usages","text":"used by used in type used Sample ligands range Ligand","title":"Usages"},{"location":"Ligand/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Ligand/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Ligand/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Ligand native https://w3id.org/osc-em/oscem-schemas/:Ligand","title":"Mappings"},{"location":"Ligand/#linkml-source","text":"","title":"LinkML Source"},{"location":"Ligand/#direct","text":"name: Ligand description: A class representing a ligand title: Ligand from_schema: https://w3id.org/osc-em/oscem-schemas slots: - present - smile - reference slot_usage: present: name: present required: true","title":"Direct"},{"location":"Ligand/#induced","text":"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 smile: name: smile description: Provide a valid SMILE string of your ligand title: SMILE from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: smile 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","title":"Induced"},{"location":"Molecule/","text":"Class: Molecule (Molecule) A class representing a molecule URI: https://w3id.org/osc-em/oscem-schemas/:Molecule classDiagram class Molecule click Molecule href \"../Molecule\" Molecule : expression_system Molecule : gene_name Molecule : molecular_class Molecule --> \"1\" MoleculeClassEnum : molecular_class click MoleculeClassEnum href \"../MoleculeClassEnum\" Molecule : molecular_type Molecule : name_mol Molecule : natural_source Molecule : sequence Molecule : taxonomy_id_expression Molecule : taxonomy_id_source Slots 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 supramolecular 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 Usages used by used in type used Sample molecule range Molecule Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Molecule native https://w3id.org/osc-em/oscem-schemas/:Molecule LinkML Source Direct 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 Induced 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: - 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Molecule range: string required: true molecular_type: name: molecular_type description: Description of the overall supramolecular 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: - 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Molecule range: string","title":"Induced"},{"location":"MoleculeClassEnum/","text":"Enum: MoleculeClassEnum URI: MoleculeClassEnum Permissible Values Value Meaning Description Antibiotic None Antibiotic Carbohydrate None Carbohydrate Chimera None Chimera None of these None None of these Slots Name Description molecular_class Class of the molecule Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas LinkML Source 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","title":"Enum: MoleculeClassEnum"},{"location":"MoleculeClassEnum/#enum-moleculeclassenum","text":"URI: MoleculeClassEnum","title":"Enum: MoleculeClassEnum"},{"location":"MoleculeClassEnum/#permissible-values","text":"Value Meaning Description Antibiotic None Antibiotic Carbohydrate None Carbohydrate Chimera None Chimera None of these None None of these","title":"Permissible Values"},{"location":"MoleculeClassEnum/#slots","text":"Name Description molecular_class Class of the molecule","title":"Slots"},{"location":"MoleculeClassEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"MoleculeClassEnum/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"MoleculeClassEnum/#linkml-source","text":"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","title":"LinkML Source"},{"location":"Ncname/","text":"Type: Ncname Prefix part of CURIE URI: xsd:string base : NCName uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:ncname","title":"Type: Ncname"},{"location":"Ncname/#type-ncname","text":"Prefix part of CURIE URI: xsd:string base : NCName uri : xsd:string repr : str","title":"Type: Ncname"},{"location":"Ncname/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Ncname/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Ncname/#mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:ncname","title":"Mappings"},{"location":"Nodeidentifier/","text":"Type: Nodeidentifier A URI, CURIE or BNODE that represents a node in a model. URI: shex:nonLiteral base : NodeIdentifier uri : shex:nonLiteral repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self shex:nonLiteral native https://w3id.org/osc-em/oscem-schemas/:nodeidentifier","title":"Type: Nodeidentifier"},{"location":"Nodeidentifier/#type-nodeidentifier","text":"A URI, CURIE or BNODE that represents a node in a model. URI: shex:nonLiteral base : NodeIdentifier uri : shex:nonLiteral repr : str","title":"Type: Nodeidentifier"},{"location":"Nodeidentifier/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Nodeidentifier/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Nodeidentifier/#mappings","text":"Mapping Type Mapped Value self shex:nonLiteral native https://w3id.org/osc-em/oscem-schemas/:nodeidentifier","title":"Mappings"},{"location":"Objectidentifier/","text":"Type: Objectidentifier A URI or CURIE that represents an object in the model. URI: shex:iri base : ElementIdentifier uri : shex:iri repr : str Comments Used for inheritance and type checking Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self shex:iri native https://w3id.org/osc-em/oscem-schemas/:objectidentifier","title":"Type: Objectidentifier"},{"location":"Objectidentifier/#type-objectidentifier","text":"A URI or CURIE that represents an object in the model. URI: shex:iri base : ElementIdentifier uri : shex:iri repr : str","title":"Type: Objectidentifier"},{"location":"Objectidentifier/#comments","text":"Used for inheritance and type checking","title":"Comments"},{"location":"Objectidentifier/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Objectidentifier/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Objectidentifier/#mappings","text":"Mapping Type Mapped Value self shex:iri native https://w3id.org/osc-em/oscem-schemas/:objectidentifier","title":"Mappings"},{"location":"OrganizationTypeEnum/","text":"Enum: OrganizationTypeEnum URI: OrganizationTypeEnum Permissible Values Value Meaning Description Academic None Academic institution Commercial None Commercial entity Government None Government organization Other None Other types of organizations Slots Name Description type_org Type of organization, academic, commercial, governmental, etc Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas LinkML Source 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","title":"Enum: OrganizationTypeEnum"},{"location":"OrganizationTypeEnum/#enum-organizationtypeenum","text":"URI: OrganizationTypeEnum","title":"Enum: OrganizationTypeEnum"},{"location":"OrganizationTypeEnum/#permissible-values","text":"Value Meaning Description Academic None Academic institution Commercial None Commercial entity Government None Government organization Other None Other types of organizations","title":"Permissible Values"},{"location":"OrganizationTypeEnum/#slots","text":"Name Description type_org Type of organization, academic, commercial, governmental, etc","title":"Slots"},{"location":"OrganizationTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"OrganizationTypeEnum/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"OrganizationTypeEnum/#linkml-source","text":"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","title":"LinkML Source"},{"location":"OverallMolecule/","text":"Class: OverallMolecule (OverallMolecule) A class representing the overall molecule URI: https://w3id.org/osc-em/oscem-schemas/:OverallMolecule classDiagram class OverallMolecule click OverallMolecule href \"../OverallMolecule\" OverallMolecule : molecular_type OverallMolecule : molecular_weight OverallMolecule : name_sample OverallMolecule : source Slots Name Cardinality and Range Description Inheritance molecular_type 1 String Description of the overall supramolecular 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 Float Molecular weight in Da direct Usages used by used in type used Sample overall_molecule range OverallMolecule Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:OverallMolecule native https://w3id.org/osc-em/oscem-schemas/:OverallMolecule LinkML Source Direct name: OverallMolecule description: A class representing the overall molecule title: OverallMolecule from_schema: https://w3id.org/osc-em/oscem-schemas slots: - 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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: float","title":"Class: OverallMolecule (OverallMolecule)"},{"location":"OverallMolecule/#class-overallmolecule-overallmolecule","text":"A class representing the overall molecule URI: https://w3id.org/osc-em/oscem-schemas/:OverallMolecule classDiagram class OverallMolecule click OverallMolecule href \"../OverallMolecule\" OverallMolecule : molecular_type OverallMolecule : molecular_weight OverallMolecule : name_sample OverallMolecule : source","title":"Class: OverallMolecule (OverallMolecule)"},{"location":"OverallMolecule/#slots","text":"Name Cardinality and Range Description Inheritance molecular_type 1 String Description of the overall supramolecular 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 Float Molecular weight in Da direct","title":"Slots"},{"location":"OverallMolecule/#usages","text":"used by used in type used Sample overall_molecule range OverallMolecule","title":"Usages"},{"location":"OverallMolecule/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"OverallMolecule/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"OverallMolecule/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:OverallMolecule native https://w3id.org/osc-em/oscem-schemas/:OverallMolecule","title":"Mappings"},{"location":"OverallMolecule/#linkml-source","text":"","title":"LinkML Source"},{"location":"OverallMolecule/#direct","text":"name: OverallMolecule description: A class representing the overall molecule title: OverallMolecule from_schema: https://w3id.org/osc-em/oscem-schemas slots: - 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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: float","title":"Induced"},{"location":"Person/","text":"Class: Person URI: schema:Person classDiagram class Person click Person href \"../Person\" Person <|-- Author click Author href \"../Author\" Person : email Person : first_name Person : name Person : work_phone Person : work_status Inheritance Person Author Slots 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 email 0..1 String email direct work_phone 0..1 String work phone direct Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self schema:Person native https://w3id.org/osc-em/oscem-schemas/:Person LinkML Source Direct name: Person from_schema: https://w3id.org/osc-em/oscem-schemas slots: - name - first_name - work_status - email - work_phone class_uri: schema:Person Induced 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: - 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minimal - maximal","title":"Direct"},{"location":"Range/#induced","text":"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: float 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: float","title":"Induced"},{"location":"Sample/","text":"Class: Sample (Sample) A class representing a sample URI: https://w3id.org/osc-em/oscem-schemas/:Sample classDiagram class Sample click Sample href \"../Sample\" Sample : grid Sample --> \"0..1\" Grid : grid click Grid href \"../Grid\" Sample : ligands Sample --> \"*\" Ligand : ligands click Ligand href \"../Ligand\" Sample : molecule Sample --> \"1..*\" Molecule : molecule click Molecule href \"../Molecule\" Sample : overall_molecule Sample --> \"1\" OverallMolecule : overall_molecule click OverallMolecule href \"../OverallMolecule\" Sample : specimen Sample --> \"1\" Specimen : specimen click Specimen href \"../Specimen\" Slots 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 Usages used by used in type used EMDataset sample range Sample Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Sample native https://w3id.org/osc-em/oscem-schemas/:Sample LinkML Source Direct name: Sample description: A class representing a sample title: Sample from_schema: https://w3id.org/osc-em/oscem-schemas slots: - 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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","title":"Induced"},{"location":"Series/","text":"Class: Series A series of numbers constructed from min, max, and increment URI: https://w3id.org/osc-em/oscem-schemas/:Series classDiagram class Series click Series href \"../Series\" Range <|-- Series click Range href \"../Range\" Series <|-- TiltAngle click TiltAngle href \"../TiltAngle\" Series : increment Series : maximal Series : minimal Inheritance Range Series TiltAngle Slots Name Cardinality and Range Description Inheritance increment 0..1 Float Increment between elements of a series direct minimal 0..1 Float Minimal value of a given dataset property Range maximal 0..1 Float Maximal value of a given dataset property Range Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Series native https://w3id.org/osc-em/oscem-schemas/:Series LinkML Source Direct 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: - 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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 base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:sparqlpath","title":"Type: Sparqlpath"},{"location":"Sparqlpath/#type-sparqlpath","text":"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 base : str uri : xsd:string repr : str","title":"Type: Sparqlpath"},{"location":"Sparqlpath/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Sparqlpath/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Sparqlpath/#mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/osc-em/oscem-schemas/:sparqlpath","title":"Mappings"},{"location":"SpecialistOptics/","text":"Class: SpecialistOptics URI: https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics classDiagram class SpecialistOptics click SpecialistOptics href \"../SpecialistOptics\" SpecialistOptics : chromatic_aberration_corrector SpecialistOptics --> \"0..1\" ChromaticAberrationCorrector : chromatic_aberration_corrector click ChromaticAberrationCorrector href \"../ChromaticAberrationCorrector\" SpecialistOptics : phaseplate SpecialistOptics --> \"0..1\" Phaseplate : phaseplate click Phaseplate href \"../Phaseplate\" SpecialistOptics : spherical_aberration_corrector SpecialistOptics --> \"0..1\" SphericalAberrationCorrector : spherical_aberration_corrector click SphericalAberrationCorrector href \"../SphericalAberrationCorrector\" Slots 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 Usages used by used in type used Acquisition specialist_optics range SpecialistOptics Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics native https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics LinkML Source Direct name: SpecialistOptics from_schema: https://w3id.org/osc-em/oscem-schemas slots: - phaseplate - spherical_aberration_corrector - chromatic_aberration_corrector Induced 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","title":"Class: SpecialistOptics"},{"location":"SpecialistOptics/#class-specialistoptics","text":"URI: https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics classDiagram class SpecialistOptics click SpecialistOptics href \"../SpecialistOptics\" SpecialistOptics : chromatic_aberration_corrector SpecialistOptics --> \"0..1\" ChromaticAberrationCorrector : chromatic_aberration_corrector click ChromaticAberrationCorrector href \"../ChromaticAberrationCorrector\" SpecialistOptics : phaseplate SpecialistOptics --> \"0..1\" Phaseplate : phaseplate click Phaseplate href \"../Phaseplate\" SpecialistOptics : spherical_aberration_corrector SpecialistOptics --> \"0..1\" SphericalAberrationCorrector : spherical_aberration_corrector click SphericalAberrationCorrector href \"../SphericalAberrationCorrector\"","title":"Class: SpecialistOptics"},{"location":"SpecialistOptics/#slots","text":"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","title":"Slots"},{"location":"SpecialistOptics/#usages","text":"used by used in type used Acquisition specialist_optics range SpecialistOptics","title":"Usages"},{"location":"SpecialistOptics/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecialistOptics/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"SpecialistOptics/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics native https://w3id.org/osc-em/oscem-schemas/:SpecialistOptics","title":"Mappings"},{"location":"SpecialistOptics/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecialistOptics/#direct","text":"name: SpecialistOptics from_schema: https://w3id.org/osc-em/oscem-schemas slots: - 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SpecialistOptics range: ChromaticAberrationCorrector","title":"Induced"},{"location":"Specimen/","text":"Class: Specimen (Specimen) A class representing a specimen URI: https://w3id.org/osc-em/oscem-schemas/:Specimen classDiagram class Specimen click Specimen href \"../Specimen\" Specimen : buffer Specimen : concentration Specimen : embedding Specimen : humidity Specimen : ph Specimen : shadowing Specimen : staining Specimen : temperature Specimen : vitrification Specimen : vitrification_cryogen Slots Name Cardinality and Range Description Inheritance buffer 0..1 String Name/composition of the (chemical) sample buffer during grid preparation direct concentration 0..1 Float Concentration of the (supra)molecule in the sample, in M 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 Float Environmental humidity just before vitrification, in % direct temperature 0..1 Float 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 Usages used by used in type used Sample specimen range Specimen Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:Specimen native https://w3id.org/osc-em/oscem-schemas/:Specimen LinkML Source Direct name: Specimen description: A class representing a specimen title: Specimen from_schema: https://w3id.org/osc-em/oscem-schemas slots: - 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Mapped Value self xsd:anyURI native https://w3id.org/osc-em/oscem-schemas/:uri close schema:URL","title":"Mappings"},{"location":"Uriorcurie/","text":"Type: Uriorcurie a URI or a CURIE URI: xsd:anyURI base : URIorCURIE uri : xsd:anyURI repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self xsd:anyURI native https://w3id.org/osc-em/oscem-schemas/:uriorcurie","title":"Type: Uriorcurie"},{"location":"Uriorcurie/#type-uriorcurie","text":"a URI or a CURIE URI: xsd:anyURI base : URIorCURIE uri : xsd:anyURI repr : str","title":"Type: Uriorcurie"},{"location":"Uriorcurie/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Uriorcurie/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"Uriorcurie/#mappings","text":"Mapping Type Mapped Value self xsd:anyURI native https://w3id.org/osc-em/oscem-schemas/:uriorcurie","title":"Mappings"},{"location":"about/","text":"oscem-schemas Schema for the Open Standards Community for Electron Microscopy (OSC-EM)","title":"About"},{"location":"about/#oscem-schemas","text":"Schema for the Open Standards Community for Electron Microscopy (OSC-EM)","title":"oscem-schemas"},{"location":"acceleration_voltage/","text":"Slot: acceleration_voltage Voltage used for the electron acceleration, in kV URI: https://w3id.org/osc-em/oscem-schemas/:acceleration_voltage Applicable Classes Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection yes Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:acceleration_voltage native https://w3id.org/osc-em/oscem-schemas/:acceleration_voltage LinkML Source name: acceleration_voltage 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https://w3id.org/osc-em/oscem-schemas/:acquisition native https://w3id.org/osc-em/oscem-schemas/:acquisition LinkML Source 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","title":"Slot: Acquisition (acquisition)"},{"location":"acquisition/#slot-acquisition-acquisition","text":"Describe the data acquisition parameters URI: https://w3id.org/osc-em/oscem-schemas/:acquisition","title":"Slot: Acquisition (acquisition)"},{"location":"acquisition/#applicable-classes","text":"Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes","title":"Applicable Classes"},{"location":"acquisition/#properties","text":"Range: Acquisition","title":"Properties"},{"location":"acquisition/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"acquisition/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"acquisition/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:acquisition native https://w3id.org/osc-em/oscem-schemas/:acquisition","title":"Mappings"},{"location":"acquisition/#linkml-source","text":"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","title":"LinkML Source"},{"location":"authors/","text":"Slot: Authors (authors) List of authors associated with the project URI: https://w3id.org/osc-em/oscem-schemas/:authors Applicable Classes Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes Properties Range: Author Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:authors native https://w3id.org/osc-em/oscem-schemas/:authors LinkML Source 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 domain_of: - EMDataset range: Author multivalued: true","title":"Slot: Authors (authors)"},{"location":"authors/#slot-authors-authors","text":"List of authors associated with the project URI: https://w3id.org/osc-em/oscem-schemas/:authors","title":"Slot: Authors (authors)"},{"location":"authors/#applicable-classes","text":"Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes","title":"Applicable Classes"},{"location":"authors/#properties","text":"Range: Author Multivalued: True","title":"Properties"},{"location":"authors/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"authors/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"authors/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:authors native https://w3id.org/osc-em/oscem-schemas/:authors","title":"Mappings"},{"location":"authors/#linkml-source","text":"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 domain_of: - EMDataset range: Author multivalued: true","title":"LinkML Source"},{"location":"beamshift/","text":"Slot: beamshift Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad. URI: https://w3id.org/osc-em/oscem-schemas/:beamshift Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: BoundingBox2D Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:beamshift native https://w3id.org/osc-em/oscem-schemas/:beamshift LinkML Source 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 domain_of: - Acquisition range: BoundingBox2D","title":"Slot: beamshift"},{"location":"beamshift/#slot-beamshift","text":"Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad. URI: https://w3id.org/osc-em/oscem-schemas/:beamshift","title":"Slot: beamshift"},{"location":"beamshift/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"beamshift/#properties","text":"Range: BoundingBox2D","title":"Properties"},{"location":"beamshift/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"beamshift/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"beamshift/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:beamshift native https://w3id.org/osc-em/oscem-schemas/:beamshift","title":"Mappings"},{"location":"beamshift/#linkml-source","text":"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 domain_of: - Acquisition range: BoundingBox2D","title":"LinkML Source"},{"location":"beamtilt/","text":"Slot: beamtilt Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad. URI: https://w3id.org/osc-em/oscem-schemas/:beamtilt Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: BoundingBox2D Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:beamtilt native https://w3id.org/osc-em/oscem-schemas/:beamtilt LinkML Source 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 domain_of: - Acquisition range: BoundingBox2D","title":"Slot: beamtilt"},{"location":"beamtilt/#slot-beamtilt","text":"Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad. URI: https://w3id.org/osc-em/oscem-schemas/:beamtilt","title":"Slot: beamtilt"},{"location":"beamtilt/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"beamtilt/#properties","text":"Range: BoundingBox2D","title":"Properties"},{"location":"beamtilt/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"beamtilt/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"beamtilt/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:beamtilt native https://w3id.org/osc-em/oscem-schemas/:beamtilt","title":"Mappings"},{"location":"beamtilt/#linkml-source","text":"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 domain_of: - Acquisition range: BoundingBox2D","title":"LinkML Source"},{"location":"beamtiltgroups/","text":"Slot: beamtiltgroups 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. URI: https://w3id.org/osc-em/oscem-schemas/:beamtiltgroups Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:beamtiltgroups native https://w3id.org/osc-em/oscem-schemas/:beamtiltgroups LinkML Source 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 domain_of: - Acquisition range: integer","title":"Slot: beamtiltgroups"},{"location":"beamtiltgroups/#slot-beamtiltgroups","text":"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. URI: https://w3id.org/osc-em/oscem-schemas/:beamtiltgroups","title":"Slot: beamtiltgroups"},{"location":"beamtiltgroups/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"beamtiltgroups/#properties","text":"Range: Integer","title":"Properties"},{"location":"beamtiltgroups/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"beamtiltgroups/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"beamtiltgroups/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:beamtiltgroups native https://w3id.org/osc-em/oscem-schemas/:beamtiltgroups","title":"Mappings"},{"location":"beamtiltgroups/#linkml-source","text":"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 domain_of: - Acquisition range: integer","title":"LinkML Source"},{"location":"binning_camera/","text":"Slot: binning_camera Level of binning on the images applied during data collection URI: https://w3id.org/osc-em/oscem-schemas/:binning_camera Applicable Classes Name Description Modifies Slot Acquisition yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:binning_camera native https://w3id.org/osc-em/oscem-schemas/:binning_camera LinkML Source 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 domain_of: - Acquisition range: float","title":"Slot: binning_camera"},{"location":"binning_camera/#slot-binning_camera","text":"Level of binning on the images applied during data collection URI: https://w3id.org/osc-em/oscem-schemas/:binning_camera","title":"Slot: binning_camera"},{"location":"binning_camera/#applicable-classes","text":"Name Description Modifies Slot Acquisition yes","title":"Applicable Classes"},{"location":"binning_camera/#properties","text":"Range: Float","title":"Properties"},{"location":"binning_camera/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"binning_camera/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"binning_camera/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:binning_camera native https://w3id.org/osc-em/oscem-schemas/:binning_camera","title":"Mappings"},{"location":"binning_camera/#linkml-source","text":"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 domain_of: - Acquisition range: float","title":"LinkML Source"},{"location":"budget/","text":"Slot: budget budget URI: https://w3id.org/osc-em/oscem-schemas/:budget Applicable Classes Name Description Modifies Slot Grant Grant no Properties Range: QuantityValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:budget native https://w3id.org/osc-em/oscem-schemas/:budget LinkML Source name: budget description: budget from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: budget domain_of: - Grant range: QuantityValue","title":"Slot: budget"},{"location":"budget/#slot-budget","text":"budget URI: https://w3id.org/osc-em/oscem-schemas/:budget","title":"Slot: budget"},{"location":"budget/#applicable-classes","text":"Name Description Modifies Slot Grant Grant no","title":"Applicable Classes"},{"location":"budget/#properties","text":"Range: QuantityValue","title":"Properties"},{"location":"budget/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"budget/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"budget/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:budget native https://w3id.org/osc-em/oscem-schemas/:budget","title":"Mappings"},{"location":"budget/#linkml-source","text":"name: budget description: budget from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: budget domain_of: - Grant range: QuantityValue","title":"LinkML Source"},{"location":"buffer/","text":"Slot: Buffer (buffer) Name/composition of the (chemical) sample buffer during grid preparation URI: https://w3id.org/osc-em/oscem-schemas/:buffer Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:buffer native https://w3id.org/osc-em/oscem-schemas/:buffer LinkML Source 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 domain_of: - Specimen range: string","title":"Slot: Buffer (buffer)"},{"location":"buffer/#slot-buffer-buffer","text":"Name/composition of the (chemical) sample buffer during grid preparation URI: https://w3id.org/osc-em/oscem-schemas/:buffer","title":"Slot: Buffer (buffer)"},{"location":"buffer/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"buffer/#properties","text":"Range: String","title":"Properties"},{"location":"buffer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"buffer/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"buffer/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:buffer native https://w3id.org/osc-em/oscem-schemas/:buffer","title":"Mappings"},{"location":"buffer/#linkml-source","text":"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 domain_of: - Specimen range: string","title":"LinkML Source"},{"location":"c2_aperture/","text":"Slot: c2_aperture C2 aperture size used in data acquisition, in \u00b5m URI: https://w3id.org/osc-em/oscem-schemas/:c2_aperture Applicable Classes Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:c2_aperture native https://w3id.org/osc-em/oscem-schemas/:c2_aperture LinkML Source name: c2_aperture description: C2 aperture size used in data acquisition, in \u00b5m from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: c2_aperture domain_of: - Instrument range: integer","title":"Slot: c2_aperture"},{"location":"c2_aperture/#slot-c2_aperture","text":"C2 aperture size used in data acquisition, in \u00b5m URI: https://w3id.org/osc-em/oscem-schemas/:c2_aperture","title":"Slot: c2_aperture"},{"location":"c2_aperture/#applicable-classes","text":"Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection no","title":"Applicable Classes"},{"location":"c2_aperture/#properties","text":"Range: Integer","title":"Properties"},{"location":"c2_aperture/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"c2_aperture/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"c2_aperture/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:c2_aperture native https://w3id.org/osc-em/oscem-schemas/:c2_aperture","title":"Mappings"},{"location":"c2_aperture/#linkml-source","text":"name: c2_aperture description: C2 aperture size used in data acquisition, in \u00b5m from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: c2_aperture domain_of: - Instrument range: integer","title":"LinkML Source"},{"location":"calibrated_defocus/","text":"Slot: calibrated_defocus Machine estimated defocus, min and max values in \u00b5m. Has a tendency to be off. URI: https://w3id.org/osc-em/oscem-schemas/:calibrated_defocus Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Range Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:calibrated_defocus native https://w3id.org/osc-em/oscem-schemas/:calibrated_defocus LinkML Source name: calibrated_defocus description: Machine estimated defocus, min and max values in \u00b5m. Has a tendency to be off. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: calibrated_defocus domain_of: - Acquisition range: Range","title":"Slot: calibrated_defocus"},{"location":"calibrated_defocus/#slot-calibrated_defocus","text":"Machine estimated defocus, min and max values in \u00b5m. Has a tendency to be off. 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URI: https://w3id.org/osc-em/oscem-schemas/:energy_filter Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: EnergyFilter Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:energy_filter native https://w3id.org/osc-em/oscem-schemas/:energy_filter LinkML Source 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 domain_of: - Acquisition range: EnergyFilter","title":"Slot: energy_filter"},{"location":"energy_filter/#slot-energy_filter","text":"Wether an energy filter was used and its specifics. URI: https://w3id.org/osc-em/oscem-schemas/:energy_filter","title":"Slot: energy_filter"},{"location":"energy_filter/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"energy_filter/#properties","text":"Range: EnergyFilter","title":"Properties"},{"location":"energy_filter/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"energy_filter/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"energy_filter/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:energy_filter native https://w3id.org/osc-em/oscem-schemas/:energy_filter","title":"Mappings"},{"location":"energy_filter/#linkml-source","text":"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 domain_of: - Acquisition range: EnergyFilter","title":"LinkML Source"},{"location":"exposure_time/","text":"Slot: exposure_time Time of data acquisition per movie/tilt - in s URI: https://w3id.org/osc-em/oscem-schemas/:exposure_time Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:exposure_time native https://w3id.org/osc-em/oscem-schemas/:exposure_time LinkML Source 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 domain_of: - Acquisition range: float","title":"Slot: exposure_time"},{"location":"exposure_time/#slot-exposure_time","text":"Time of data acquisition per movie/tilt - in s URI: https://w3id.org/osc-em/oscem-schemas/:exposure_time","title":"Slot: exposure_time"},{"location":"exposure_time/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"exposure_time/#properties","text":"Range: Float","title":"Properties"},{"location":"exposure_time/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"exposure_time/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"exposure_time/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:exposure_time native https://w3id.org/osc-em/oscem-schemas/:exposure_time","title":"Mappings"},{"location":"exposure_time/#linkml-source","text":"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 domain_of: - Acquisition range: float","title":"LinkML Source"},{"location":"expression_system/","text":"Slot: Expression_system (expression_system) Scientific name of the organism used to produce the molecule of interest URI: https://w3id.org/osc-em/oscem-schemas/:expression_system Applicable Classes Name Description Modifies Slot Molecule A class representing a molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:expression_system native https://w3id.org/osc-em/oscem-schemas/:expression_system LinkML Source 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 domain_of: - Molecule range: string","title":"Slot: Expression_system (expression_system)"},{"location":"expression_system/#slot-expression_system-expression_system","text":"Scientific name of the organism used to produce the molecule of interest URI: https://w3id.org/osc-em/oscem-schemas/:expression_system","title":"Slot: Expression_system (expression_system)"},{"location":"expression_system/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"expression_system/#properties","text":"Range: String","title":"Properties"},{"location":"expression_system/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"expression_system/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"expression_system/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:expression_system native https://w3id.org/osc-em/oscem-schemas/:expression_system","title":"Mappings"},{"location":"expression_system/#linkml-source","text":"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 domain_of: - Molecule range: string","title":"LinkML Source"},{"location":"film_material/","text":"Slot: Film_material (film_material) Type of material the support film is made of URI: https://w3id.org/osc-em/oscem-schemas/:film_material Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_material native https://w3id.org/osc-em/oscem-schemas/:film_material LinkML Source 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 domain_of: - Grid range: string","title":"Slot: Film_material (film_material)"},{"location":"film_material/#slot-film_material-film_material","text":"Type of material the support film is made of URI: https://w3id.org/osc-em/oscem-schemas/:film_material","title":"Slot: Film_material (film_material)"},{"location":"film_material/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"film_material/#properties","text":"Range: String","title":"Properties"},{"location":"film_material/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"film_material/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"film_material/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_material native https://w3id.org/osc-em/oscem-schemas/:film_material","title":"Mappings"},{"location":"film_material/#linkml-source","text":"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 domain_of: - Grid range: string","title":"LinkML Source"},{"location":"film_support/","text":"Slot: Film_support (film_support) Whether a support film was used URI: https://w3id.org/osc-em/oscem-schemas/:film_support Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: Boolean Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_support native https://w3id.org/osc-em/oscem-schemas/:film_support LinkML Source 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 domain_of: - Grid range: boolean","title":"Slot: Film_support (film_support)"},{"location":"film_support/#slot-film_support-film_support","text":"Whether a support film was used URI: https://w3id.org/osc-em/oscem-schemas/:film_support","title":"Slot: Film_support (film_support)"},{"location":"film_support/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"film_support/#properties","text":"Range: Boolean","title":"Properties"},{"location":"film_support/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"film_support/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"film_support/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_support native https://w3id.org/osc-em/oscem-schemas/:film_support","title":"Mappings"},{"location":"film_support/#linkml-source","text":"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 domain_of: - Grid range: boolean","title":"LinkML Source"},{"location":"film_thickness/","text":"Slot: Film_thickness (film_thickness) Thickness of the support film URI: https://w3id.org/osc-em/oscem-schemas/:film_thickness Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_thickness native https://w3id.org/osc-em/oscem-schemas/:film_thickness LinkML Source 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 domain_of: - Grid range: string","title":"Slot: Film_thickness (film_thickness)"},{"location":"film_thickness/#slot-film_thickness-film_thickness","text":"Thickness of the support film URI: https://w3id.org/osc-em/oscem-schemas/:film_thickness","title":"Slot: Film_thickness (film_thickness)"},{"location":"film_thickness/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"film_thickness/#properties","text":"Range: String","title":"Properties"},{"location":"film_thickness/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"film_thickness/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"film_thickness/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_thickness native https://w3id.org/osc-em/oscem-schemas/:film_thickness","title":"Mappings"},{"location":"film_thickness/#linkml-source","text":"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 domain_of: - Grid range: string","title":"LinkML Source"},{"location":"film_topology/","text":"Slot: Film_topology (film_topology) Topology of the support film URI: https://w3id.org/osc-em/oscem-schemas/:film_topology Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_topology native https://w3id.org/osc-em/oscem-schemas/:film_topology LinkML Source 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 domain_of: - Grid range: string","title":"Slot: Film_topology (film_topology)"},{"location":"film_topology/#slot-film_topology-film_topology","text":"Topology of the support film URI: https://w3id.org/osc-em/oscem-schemas/:film_topology","title":"Slot: Film_topology (film_topology)"},{"location":"film_topology/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"film_topology/#properties","text":"Range: String","title":"Properties"},{"location":"film_topology/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"film_topology/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"film_topology/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:film_topology native https://w3id.org/osc-em/oscem-schemas/:film_topology","title":"Mappings"},{"location":"film_topology/#linkml-source","text":"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 domain_of: - Grid range: string","title":"LinkML Source"},{"location":"first_name/","text":"Slot: first_name first name URI: https://w3id.org/osc-em/oscem-schemas/:first_name Applicable Classes Name Description Modifies Slot Author no Person no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:first_name native https://w3id.org/osc-em/oscem-schemas/:first_name LinkML Source name: first_name description: first name from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: first_name domain_of: - Person range: string","title":"Slot: first_name"},{"location":"first_name/#slot-first_name","text":"first name URI: https://w3id.org/osc-em/oscem-schemas/:first_name","title":"Slot: first_name"},{"location":"first_name/#applicable-classes","text":"Name Description Modifies Slot Author no Person no","title":"Applicable Classes"},{"location":"first_name/#properties","text":"Range: String","title":"Properties"},{"location":"first_name/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"first_name/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"first_name/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:first_name native https://w3id.org/osc-em/oscem-schemas/:first_name","title":"Mappings"},{"location":"first_name/#linkml-source","text":"name: first_name description: first name from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: first_name domain_of: - Person range: string","title":"LinkML Source"},{"location":"frames_per_movie/","text":"Slot: frames_per_movie Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors URI: https://w3id.org/osc-em/oscem-schemas/:frames_per_movie Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:frames_per_movie native https://w3id.org/osc-em/oscem-schemas/:frames_per_movie LinkML Source 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 domain_of: - Acquisition range: integer","title":"Slot: frames_per_movie"},{"location":"frames_per_movie/#slot-frames_per_movie","text":"Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors URI: https://w3id.org/osc-em/oscem-schemas/:frames_per_movie","title":"Slot: frames_per_movie"},{"location":"frames_per_movie/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"frames_per_movie/#properties","text":"Range: Integer","title":"Properties"},{"location":"frames_per_movie/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"frames_per_movie/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"frames_per_movie/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:frames_per_movie native https://w3id.org/osc-em/oscem-schemas/:frames_per_movie","title":"Mappings"},{"location":"frames_per_movie/#linkml-source","text":"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 domain_of: - Acquisition range: integer","title":"LinkML Source"},{"location":"funder/","text":"Slot: funder funder URI: https://w3id.org/osc-em/oscem-schemas/:funder Applicable Classes Name Description Modifies Slot Grant Grant no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:funder native https://w3id.org/osc-em/oscem-schemas/:funder LinkML Source name: funder description: funder from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: funder domain_of: - Grant range: string","title":"Slot: funder"},{"location":"funder/#slot-funder","text":"funder URI: https://w3id.org/osc-em/oscem-schemas/:funder","title":"Slot: funder"},{"location":"funder/#applicable-classes","text":"Name Description Modifies Slot Grant Grant no","title":"Applicable Classes"},{"location":"funder/#properties","text":"Range: String","title":"Properties"},{"location":"funder/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"funder/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"funder/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:funder native https://w3id.org/osc-em/oscem-schemas/:funder","title":"Mappings"},{"location":"funder/#linkml-source","text":"name: funder description: funder from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: funder domain_of: - Grant range: string","title":"LinkML Source"},{"location":"gainref_flip_rotate/","text":"Slot: gainref_flip_rotate Whether and how you have to flip or rotate the gainref in order to align with your acquired images URI: https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate native https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate LinkML Source 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 domain_of: - Acquisition range: string","title":"Slot: gainref_flip_rotate"},{"location":"gainref_flip_rotate/#slot-gainref_flip_rotate","text":"Whether and how you have to flip or rotate the gainref in order to align with your acquired images URI: https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate","title":"Slot: gainref_flip_rotate"},{"location":"gainref_flip_rotate/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"gainref_flip_rotate/#properties","text":"Range: String","title":"Properties"},{"location":"gainref_flip_rotate/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"gainref_flip_rotate/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"gainref_flip_rotate/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate native https://w3id.org/osc-em/oscem-schemas/:gainref_flip_rotate","title":"Mappings"},{"location":"gainref_flip_rotate/#linkml-source","text":"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 domain_of: - Acquisition range: string","title":"LinkML Source"},{"location":"gene_name/","text":"Slot: Gene_name (gene_name) Name of the gene of interest URI: https://w3id.org/osc-em/oscem-schemas/:gene_name Applicable Classes Name Description Modifies Slot Molecule A class representing a molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:gene_name native https://w3id.org/osc-em/oscem-schemas/:gene_name LinkML Source 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 domain_of: - Molecule range: string","title":"Slot: Gene_name (gene_name)"},{"location":"gene_name/#slot-gene_name-gene_name","text":"Name of the gene of interest URI: https://w3id.org/osc-em/oscem-schemas/:gene_name","title":"Slot: Gene_name (gene_name)"},{"location":"gene_name/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"gene_name/#properties","text":"Range: String","title":"Properties"},{"location":"gene_name/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"gene_name/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"gene_name/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:gene_name native https://w3id.org/osc-em/oscem-schemas/:gene_name","title":"Mappings"},{"location":"gene_name/#linkml-source","text":"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 domain_of: - Molecule range: string","title":"LinkML Source"},{"location":"grants/","text":"Slot: Grants (grants) List of grants associated with the project URI: https://w3id.org/osc-em/oscem-schemas/:grants Applicable Classes Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes Properties Range: Grant Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:grants native https://w3id.org/osc-em/oscem-schemas/:grants LinkML Source 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 domain_of: - EMDataset range: Grant multivalued: true","title":"Slot: Grants (grants)"},{"location":"grants/#slot-grants-grants","text":"List of grants associated with the project URI: https://w3id.org/osc-em/oscem-schemas/:grants","title":"Slot: Grants (grants)"},{"location":"grants/#applicable-classes","text":"Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes","title":"Applicable Classes"},{"location":"grants/#properties","text":"Range: Grant Multivalued: True","title":"Properties"},{"location":"grants/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"grants/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"grants/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:grants native https://w3id.org/osc-em/oscem-schemas/:grants","title":"Mappings"},{"location":"grants/#linkml-source","text":"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 domain_of: - 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Sample range: Grid","title":"LinkML Source"},{"location":"grids_imaged/","text":"Slot: grids_imaged Number of grids imaged for this project - here with qualifier during this data acquisition URI: https://w3id.org/osc-em/oscem-schemas/:grids_imaged Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:grids_imaged native https://w3id.org/osc-em/oscem-schemas/:grids_imaged LinkML Source 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 domain_of: - Acquisition range: integer","title":"Slot: grids_imaged"},{"location":"grids_imaged/#slot-grids_imaged","text":"Number of grids imaged for this project - here with qualifier during this data acquisition URI: https://w3id.org/osc-em/oscem-schemas/:grids_imaged","title":"Slot: grids_imaged"},{"location":"grids_imaged/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"grids_imaged/#properties","text":"Range: Integer","title":"Properties"},{"location":"grids_imaged/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"grids_imaged/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"grids_imaged/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:grids_imaged native https://w3id.org/osc-em/oscem-schemas/:grids_imaged","title":"Mappings"},{"location":"grids_imaged/#linkml-source","text":"name: grids_imaged description: Number of grids imaged for this project - 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QuantityValue range: string","title":"LinkML Source"},{"location":"has_value/","text":"Slot: has_value Value URI: qudt:hasQuantityKind Applicable Classes Name Description Modifies Slot QuantityValue Value together with unit no Properties Range: Double Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self qudt:hasQuantityKind native https://w3id.org/osc-em/oscem-schemas/:has_value LinkML Source name: has_value description: Value from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: qudt:hasQuantityKind alias: has_value domain_of: - QuantityValue range: double","title":"Slot: has_value"},{"location":"has_value/#slot-has_value","text":"Value URI: qudt:hasQuantityKind","title":"Slot: has_value"},{"location":"has_value/#applicable-classes","text":"Name Description Modifies Slot QuantityValue Value together with unit no","title":"Applicable Classes"},{"location":"has_value/#properties","text":"Range: Double","title":"Properties"},{"location":"has_value/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"has_value/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"has_value/#mappings","text":"Mapping Type Mapped Value self qudt:hasQuantityKind native https://w3id.org/osc-em/oscem-schemas/:has_value","title":"Mappings"},{"location":"has_value/#linkml-source","text":"name: has_value description: Value from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: qudt:hasQuantityKind alias: has_value domain_of: - QuantityValue range: double","title":"LinkML Source"},{"location":"height/","text":"Slot: height The height of a given item - unit depends on item URI: https://w3id.org/osc-em/oscem-schemas/:height Applicable Classes Name Description Modifies Slot ImageSize size of a 2D image (in integer units) no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:height native https://w3id.org/osc-em/oscem-schemas/:height LinkML Source 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 domain_of: - ImageSize range: integer","title":"Slot: height"},{"location":"height/#slot-height","text":"The height of a given item - unit depends on item URI: https://w3id.org/osc-em/oscem-schemas/:height","title":"Slot: height"},{"location":"height/#applicable-classes","text":"Name Description Modifies Slot ImageSize size of a 2D image (in integer units) no","title":"Applicable Classes"},{"location":"height/#properties","text":"Range: Integer","title":"Properties"},{"location":"height/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"height/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"height/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:height native https://w3id.org/osc-em/oscem-schemas/:height","title":"Mappings"},{"location":"height/#linkml-source","text":"name: height description: The height of a given item - 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Acquisition range: string","title":"LinkML Source"},{"location":"holder_cryogen/","text":"Slot: holder_cryogen Type of cryogen used in the holder - if the holder is cooled seperately URI: https://w3id.org/osc-em/oscem-schemas/:holder_cryogen Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:holder_cryogen native https://w3id.org/osc-em/oscem-schemas/:holder_cryogen LinkML Source 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 domain_of: - Acquisition range: string","title":"Slot: holder_cryogen"},{"location":"holder_cryogen/#slot-holder_cryogen","text":"Type of cryogen used in the holder - if the holder is cooled seperately URI: https://w3id.org/osc-em/oscem-schemas/:holder_cryogen","title":"Slot: holder_cryogen"},{"location":"holder_cryogen/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"holder_cryogen/#properties","text":"Range: String","title":"Properties"},{"location":"holder_cryogen/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"holder_cryogen/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"holder_cryogen/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:holder_cryogen native https://w3id.org/osc-em/oscem-schemas/:holder_cryogen","title":"Mappings"},{"location":"holder_cryogen/#linkml-source","text":"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 domain_of: - Acquisition range: string","title":"LinkML Source"},{"location":"humidity/","text":"Slot: Humidity (humidity) Environmental humidity just before vitrification, in % URI: https://w3id.org/osc-em/oscem-schemas/:humidity Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:humidity native https://w3id.org/osc-em/oscem-schemas/:humidity LinkML Source name: humidity description: Environmental humidity just before vitrification, in % title: Humidity from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: humidity domain_of: - Specimen range: float","title":"Slot: Humidity (humidity)"},{"location":"humidity/#slot-humidity-humidity","text":"Environmental humidity just before vitrification, in % URI: https://w3id.org/osc-em/oscem-schemas/:humidity","title":"Slot: Humidity (humidity)"},{"location":"humidity/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"humidity/#properties","text":"Range: Float","title":"Properties"},{"location":"humidity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"humidity/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"humidity/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:humidity native https://w3id.org/osc-em/oscem-schemas/:humidity","title":"Mappings"},{"location":"humidity/#linkml-source","text":"name: humidity description: Environmental humidity just before vitrification, in % title: Humidity from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: humidity domain_of: - Specimen range: float","title":"LinkML Source"},{"location":"illumination/","text":"Slot: illumination Mode of illumination used during data collection URI: https://w3id.org/osc-em/oscem-schemas/:illumination Applicable Classes Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:illumination native https://w3id.org/osc-em/oscem-schemas/:illumination LinkML Source name: illumination description: Mode of illumination used during data collection from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: illumination domain_of: - Instrument range: string","title":"Slot: illumination"},{"location":"illumination/#slot-illumination","text":"Mode of illumination used during data collection URI: https://w3id.org/osc-em/oscem-schemas/:illumination","title":"Slot: illumination"},{"location":"illumination/#applicable-classes","text":"Name Description Modifies Slot Instrument Instrument values, mostly constant across a data collection yes","title":"Applicable Classes"},{"location":"illumination/#properties","text":"Range: String","title":"Properties"},{"location":"illumination/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"illumination/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"illumination/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:illumination native https://w3id.org/osc-em/oscem-schemas/:illumination","title":"Mappings"},{"location":"illumination/#linkml-source","text":"name: illumination description: Mode of illumination used during data collection from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: illumination domain_of: - Instrument range: string","title":"LinkML Source"},{"location":"image_size/","text":"Slot: image_size The size of the image in pixels, height and width given. URI: https://w3id.org/osc-em/oscem-schemas/:image_size Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: ImageSize Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:image_size native https://w3id.org/osc-em/oscem-schemas/:image_size LinkML Source 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 domain_of: - Acquisition range: ImageSize","title":"Slot: image_size"},{"location":"image_size/#slot-image_size","text":"The size of the image in pixels, height and width given. URI: https://w3id.org/osc-em/oscem-schemas/:image_size","title":"Slot: image_size"},{"location":"image_size/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"image_size/#properties","text":"Range: ImageSize","title":"Properties"},{"location":"image_size/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"image_size/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"image_size/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:image_size native https://w3id.org/osc-em/oscem-schemas/:image_size","title":"Mappings"},{"location":"image_size/#linkml-source","text":"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 domain_of: - Acquisition range: ImageSize","title":"LinkML Source"},{"location":"images_generated/","text":"Slot: images_generated 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 URI: https://w3id.org/osc-em/oscem-schemas/:images_generated Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:images_generated native https://w3id.org/osc-em/oscem-schemas/:images_generated LinkML Source 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 domain_of: - Acquisition range: integer","title":"Slot: images_generated"},{"location":"images_generated/#slot-images_generated","text":"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 URI: https://w3id.org/osc-em/oscem-schemas/:images_generated","title":"Slot: images_generated"},{"location":"images_generated/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"images_generated/#properties","text":"Range: Integer","title":"Properties"},{"location":"images_generated/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"images_generated/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"images_generated/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:images_generated native https://w3id.org/osc-em/oscem-schemas/:images_generated","title":"Mappings"},{"location":"images_generated/#linkml-source","text":"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 domain_of: - Acquisition range: integer","title":"LinkML Source"},{"location":"imageshift/","text":"Slot: imageshift Movement of the Beam below the image in order to shift the image on the detector. Given in \u00b5m. URI: https://w3id.org/osc-em/oscem-schemas/:imageshift Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: BoundingBox2D Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:imageshift native https://w3id.org/osc-em/oscem-schemas/:imageshift LinkML Source name: imageshift description: Movement of the Beam below the image in order to shift the image on the detector. Given in \u00b5m. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: imageshift domain_of: - Acquisition range: BoundingBox2D","title":"Slot: imageshift"},{"location":"imageshift/#slot-imageshift","text":"Movement of the Beam below the image in order to shift the image on the detector. Given in \u00b5m. 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OverallMolecule - Molecule range: string","title":"LinkML Source"},{"location":"molecular_weight/","text":"Slot: Molecular_weight (molecular_weight) Molecular weight in Da URI: https://w3id.org/osc-em/oscem-schemas/:molecular_weight Applicable Classes Name Description Modifies Slot OverallMolecule A class representing the overall molecule yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:molecular_weight native https://w3id.org/osc-em/oscem-schemas/:molecular_weight LinkML Source 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 domain_of: - OverallMolecule range: float","title":"Slot: Molecular_weight (molecular_weight)"},{"location":"molecular_weight/#slot-molecular_weight-molecular_weight","text":"Molecular weight in Da URI: https://w3id.org/osc-em/oscem-schemas/:molecular_weight","title":"Slot: Molecular_weight (molecular_weight)"},{"location":"molecular_weight/#applicable-classes","text":"Name Description Modifies Slot OverallMolecule A class representing the overall molecule yes","title":"Applicable Classes"},{"location":"molecular_weight/#properties","text":"Range: Float","title":"Properties"},{"location":"molecular_weight/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"molecular_weight/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"molecular_weight/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:molecular_weight native https://w3id.org/osc-em/oscem-schemas/:molecular_weight","title":"Mappings"},{"location":"molecular_weight/#linkml-source","text":"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 domain_of: - OverallMolecule range: float","title":"LinkML Source"},{"location":"molecule/","text":"Slot: Molecule (molecule) List of molecule associated with the sample URI: https://w3id.org/osc-em/oscem-schemas/:molecule Applicable Classes Name Description Modifies Slot Sample A class representing a sample yes Properties Range: Molecule Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:molecule native https://w3id.org/osc-em/oscem-schemas/:molecule LinkML Source 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 domain_of: - Sample range: Molecule multivalued: true","title":"Slot: Molecule (molecule)"},{"location":"molecule/#slot-molecule-molecule","text":"List of molecule associated with the sample URI: https://w3id.org/osc-em/oscem-schemas/:molecule","title":"Slot: Molecule (molecule)"},{"location":"molecule/#applicable-classes","text":"Name Description Modifies Slot Sample A class representing a sample yes","title":"Applicable Classes"},{"location":"molecule/#properties","text":"Range: Molecule Multivalued: True","title":"Properties"},{"location":"molecule/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"molecule/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"molecule/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:molecule native https://w3id.org/osc-em/oscem-schemas/:molecule","title":"Mappings"},{"location":"molecule/#linkml-source","text":"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 domain_of: - Sample range: Molecule multivalued: true","title":"LinkML Source"},{"location":"name/","text":"Slot: name name URI: schema:name Applicable Classes Name Description Modifies Slot Author yes Grant Grant no Person no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self schema:name native https://w3id.org/osc-em/oscem-schemas/:name LinkML Source name: name description: name from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:name alias: name domain_of: - Person - Grant range: string","title":"Slot: name"},{"location":"name/#slot-name","text":"name URI: schema:name","title":"Slot: name"},{"location":"name/#applicable-classes","text":"Name Description Modifies Slot Author yes Grant Grant no Person no","title":"Applicable Classes"},{"location":"name/#properties","text":"Range: String","title":"Properties"},{"location":"name/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"name/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"name/#mappings","text":"Mapping Type Mapped Value self schema:name native https://w3id.org/osc-em/oscem-schemas/:name","title":"Mappings"},{"location":"name/#linkml-source","text":"name: name description: name from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:name alias: name domain_of: - Person - Grant range: string","title":"LinkML Source"},{"location":"name_mol/","text":"Slot: Name (name_mol) Name of an individual molecule (often protein) in the sample URI: https://w3id.org/osc-em/oscem-schemas/:name_mol Applicable Classes Name Description Modifies Slot Molecule A class representing a molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:name_mol native https://w3id.org/osc-em/oscem-schemas/:name_mol LinkML Source 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 domain_of: - Molecule range: string","title":"Slot: Name (name_mol)"},{"location":"name_mol/#slot-name-name_mol","text":"Name of an individual molecule (often protein) in the sample URI: https://w3id.org/osc-em/oscem-schemas/:name_mol","title":"Slot: Name (name_mol)"},{"location":"name_mol/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"name_mol/#properties","text":"Range: String","title":"Properties"},{"location":"name_mol/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"name_mol/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"name_mol/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:name_mol native https://w3id.org/osc-em/oscem-schemas/:name_mol","title":"Mappings"},{"location":"name_mol/#linkml-source","text":"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 domain_of: - Molecule range: string","title":"LinkML Source"},{"location":"name_org/","text":"Slot: Name_org (name_org) Name of the organization URI: https://w3id.org/osc-em/oscem-schemas/:name_org Applicable Classes Name Description Modifies Slot Author yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:name_org native https://w3id.org/osc-em/oscem-schemas/:name_org LinkML Source 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 domain_of: - Author range: string","title":"Slot: Name_org (name_org)"},{"location":"name_org/#slot-name_org-name_org","text":"Name of the organization URI: https://w3id.org/osc-em/oscem-schemas/:name_org","title":"Slot: Name_org (name_org)"},{"location":"name_org/#applicable-classes","text":"Name Description Modifies Slot Author yes","title":"Applicable Classes"},{"location":"name_org/#properties","text":"Range: String","title":"Properties"},{"location":"name_org/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"name_org/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"name_org/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:name_org native https://w3id.org/osc-em/oscem-schemas/:name_org","title":"Mappings"},{"location":"name_org/#linkml-source","text":"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 domain_of: - Author range: string","title":"LinkML Source"},{"location":"name_sample/","text":"Slot: Name (name_sample) Name of the full sample URI: https://w3id.org/osc-em/oscem-schemas/:name_sample Applicable Classes Name Description Modifies Slot OverallMolecule A class representing the overall molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:name_sample native https://w3id.org/osc-em/oscem-schemas/:name_sample LinkML Source 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 domain_of: - OverallMolecule range: string","title":"Slot: Name (name_sample)"},{"location":"name_sample/#slot-name-name_sample","text":"Name of the full sample URI: https://w3id.org/osc-em/oscem-schemas/:name_sample","title":"Slot: Name (name_sample)"},{"location":"name_sample/#applicable-classes","text":"Name Description Modifies Slot OverallMolecule A class representing the overall molecule yes","title":"Applicable Classes"},{"location":"name_sample/#properties","text":"Range: String","title":"Properties"},{"location":"name_sample/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"name_sample/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"name_sample/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:name_sample native https://w3id.org/osc-em/oscem-schemas/:name_sample","title":"Mappings"},{"location":"name_sample/#linkml-source","text":"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 domain_of: - OverallMolecule range: string","title":"LinkML Source"},{"location":"natural_source/","text":"Slot: Natural_source (natural_source) Scientific name of the natural host organism URI: https://w3id.org/osc-em/oscem-schemas/:natural_source Applicable Classes Name Description Modifies Slot Molecule A class representing a molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:natural_source native https://w3id.org/osc-em/oscem-schemas/:natural_source LinkML 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 domain_of: - Molecule range: string","title":"Slot: Natural_source (natural_source)"},{"location":"natural_source/#slot-natural_source-natural_source","text":"Scientific name of the natural host organism URI: https://w3id.org/osc-em/oscem-schemas/:natural_source","title":"Slot: Natural_source (natural_source)"},{"location":"natural_source/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"natural_source/#properties","text":"Range: String","title":"Properties"},{"location":"natural_source/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"natural_source/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"natural_source/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:natural_source native https://w3id.org/osc-em/oscem-schemas/:natural_source","title":"Mappings"},{"location":"natural_source/#linkml-source","text":"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 domain_of: - Molecule range: string","title":"LinkML Source"},{"location":"nominal_defocus/","text":"Slot: nominal_defocus Target defocus set, min and max values in \u00b5m. URI: https://w3id.org/osc-em/oscem-schemas/:nominal_defocus Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Range Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:nominal_defocus native https://w3id.org/osc-em/oscem-schemas/:nominal_defocus LinkML Source name: nominal_defocus description: Target defocus set, min and max values in \u00b5m. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: nominal_defocus domain_of: - Acquisition range: Range","title":"Slot: nominal_defocus"},{"location":"nominal_defocus/#slot-nominal_defocus","text":"Target defocus set, min and max values in \u00b5m. URI: https://w3id.org/osc-em/oscem-schemas/:nominal_defocus","title":"Slot: nominal_defocus"},{"location":"nominal_defocus/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"nominal_defocus/#properties","text":"Range: Range","title":"Properties"},{"location":"nominal_defocus/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"nominal_defocus/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"nominal_defocus/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:nominal_defocus native https://w3id.org/osc-em/oscem-schemas/:nominal_defocus","title":"Mappings"},{"location":"nominal_defocus/#linkml-source","text":"name: nominal_defocus description: Target defocus set, min and max values in \u00b5m. from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: nominal_defocus domain_of: - Acquisition range: Range","title":"LinkML Source"},{"location":"nominal_magnification/","text":"Slot: nominal_magnification Magnification level as indicated by the instrument, no unit URI: https://w3id.org/osc-em/oscem-schemas/:nominal_magnification Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:nominal_magnification native https://w3id.org/osc-em/oscem-schemas/:nominal_magnification LinkML Source 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 domain_of: - Acquisition range: integer","title":"Slot: nominal_magnification"},{"location":"nominal_magnification/#slot-nominal_magnification","text":"Magnification level as indicated by the instrument, no unit URI: https://w3id.org/osc-em/oscem-schemas/:nominal_magnification","title":"Slot: nominal_magnification"},{"location":"nominal_magnification/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"nominal_magnification/#properties","text":"Range: Integer","title":"Properties"},{"location":"nominal_magnification/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"nominal_magnification/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"nominal_magnification/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:nominal_magnification native https://w3id.org/osc-em/oscem-schemas/:nominal_magnification","title":"Mappings"},{"location":"nominal_magnification/#linkml-source","text":"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 domain_of: - Acquisition range: integer","title":"LinkML Source"},{"location":"orcid/","text":"Slot: ORCID (orcid) ORCID of the author, a type of unique identifier URI: https://w3id.org/osc-em/oscem-schemas/:orcid Applicable Classes Name Description Modifies Slot Author yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:orcid native https://w3id.org/osc-em/oscem-schemas/:orcid LinkML Source 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 domain_of: - Author range: string","title":"Slot: ORCID (orcid)"},{"location":"orcid/#slot-orcid-orcid","text":"ORCID of the author, a type of unique identifier URI: https://w3id.org/osc-em/oscem-schemas/:orcid","title":"Slot: ORCID (orcid)"},{"location":"orcid/#applicable-classes","text":"Name Description Modifies Slot Author yes","title":"Applicable Classes"},{"location":"orcid/#properties","text":"Range: String","title":"Properties"},{"location":"orcid/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"orcid/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"orcid/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:orcid native https://w3id.org/osc-em/oscem-schemas/:orcid","title":"Mappings"},{"location":"orcid/#linkml-source","text":"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 domain_of: - Author range: string","title":"LinkML Source"},{"location":"oscem-schemas/","text":"oscem-schemas Schema for the Open Standards Community for Electron Microscopy (OSC-EM) URI: https://w3id.org/osc-em/oscem-schemas","title":"oscem-schemas"},{"location":"oscem-schemas/#oscem-schemas","text":"Schema for the Open Standards Community for Electron Microscopy (OSC-EM) URI: https://w3id.org/osc-em/oscem-schemas","title":"oscem-schemas"},{"location":"overall_molecule/","text":"Slot: Overall_Molecule (overall_molecule) Description of the overall molecule URI: https://w3id.org/osc-em/oscem-schemas/:overall_molecule Applicable Classes Name Description Modifies Slot Sample A class representing a sample yes Properties Range: OverallMolecule Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:overall_molecule native https://w3id.org/osc-em/oscem-schemas/:overall_molecule LinkML Source 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 domain_of: - Sample range: OverallMolecule","title":"Slot: Overall_Molecule (overall_molecule)"},{"location":"overall_molecule/#slot-overall_molecule-overall_molecule","text":"Description of the overall molecule URI: https://w3id.org/osc-em/oscem-schemas/:overall_molecule","title":"Slot: Overall_Molecule (overall_molecule)"},{"location":"overall_molecule/#applicable-classes","text":"Name Description Modifies Slot Sample A class representing a sample yes","title":"Applicable Classes"},{"location":"overall_molecule/#properties","text":"Range: OverallMolecule","title":"Properties"},{"location":"overall_molecule/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"overall_molecule/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"overall_molecule/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:overall_molecule native https://w3id.org/osc-em/oscem-schemas/:overall_molecule","title":"Mappings"},{"location":"overall_molecule/#linkml-source","text":"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 domain_of: - Sample range: OverallMolecule","title":"LinkML Source"},{"location":"person/","text":"Slot: person person URI: schema:Person Properties Range: Person Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self schema:Person native https://w3id.org/osc-em/oscem-schemas/:person LinkML Source name: person description: person from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:Person alias: person range: Person","title":"Slot: person"},{"location":"person/#slot-person","text":"person URI: schema:Person","title":"Slot: person"},{"location":"person/#properties","text":"Range: Person","title":"Properties"},{"location":"person/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"person/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"person/#mappings","text":"Mapping Type Mapped Value self schema:Person native https://w3id.org/osc-em/oscem-schemas/:person","title":"Mappings"},{"location":"person/#linkml-source","text":"name: person description: person from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:Person alias: person range: Person","title":"LinkML Source"},{"location":"ph/","text":"Slot: pH (ph) pH of the sample buffer URI: https://w3id.org/osc-em/oscem-schemas/:ph Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:ph native https://w3id.org/osc-em/oscem-schemas/:ph LinkML Source name: ph description: pH of the sample buffer title: pH from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: ph domain_of: - Specimen range: float","title":"Slot: pH (ph)"},{"location":"ph/#slot-ph-ph","text":"pH of the sample buffer URI: https://w3id.org/osc-em/oscem-schemas/:ph","title":"Slot: pH (ph)"},{"location":"ph/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"ph/#properties","text":"Range: Float","title":"Properties"},{"location":"ph/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ph/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"ph/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:ph native https://w3id.org/osc-em/oscem-schemas/:ph","title":"Mappings"},{"location":"ph/#linkml-source","text":"name: ph description: pH of the sample buffer title: pH from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: ph domain_of: - Specimen range: float","title":"LinkML Source"},{"location":"phaseplate/","text":"Slot: phaseplate Phaseplate is a special optics device that can be used to enhance contrast URI: https://w3id.org/osc-em/oscem-schemas/:phaseplate Applicable Classes Name Description Modifies Slot SpecialistOptics no Properties Range: Phaseplate Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:phaseplate native https://w3id.org/osc-em/oscem-schemas/:phaseplate LinkML Source 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 domain_of: - SpecialistOptics range: Phaseplate","title":"Slot: phaseplate"},{"location":"phaseplate/#slot-phaseplate","text":"Phaseplate is a special optics device that can be used to enhance contrast URI: https://w3id.org/osc-em/oscem-schemas/:phaseplate","title":"Slot: phaseplate"},{"location":"phaseplate/#applicable-classes","text":"Name Description Modifies Slot SpecialistOptics no","title":"Applicable Classes"},{"location":"phaseplate/#properties","text":"Range: Phaseplate","title":"Properties"},{"location":"phaseplate/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"phaseplate/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"phaseplate/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:phaseplate native https://w3id.org/osc-em/oscem-schemas/:phaseplate","title":"Mappings"},{"location":"phaseplate/#linkml-source","text":"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 domain_of: - SpecialistOptics range: Phaseplate","title":"LinkML Source"},{"location":"pixel_size/","text":"Slot: pixel_size Pixel size, in Angstrom URI: https://w3id.org/osc-em/oscem-schemas/:pixel_size Applicable Classes Name Description Modifies Slot Acquisition yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pixel_size native https://w3id.org/osc-em/oscem-schemas/:pixel_size LinkML Source name: pixel_size description: Pixel size, in Angstrom from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: pixel_size domain_of: - Acquisition range: float","title":"Slot: pixel_size"},{"location":"pixel_size/#slot-pixel_size","text":"Pixel size, in Angstrom URI: https://w3id.org/osc-em/oscem-schemas/:pixel_size","title":"Slot: pixel_size"},{"location":"pixel_size/#applicable-classes","text":"Name Description Modifies Slot Acquisition yes","title":"Applicable Classes"},{"location":"pixel_size/#properties","text":"Range: Float","title":"Properties"},{"location":"pixel_size/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"pixel_size/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"pixel_size/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pixel_size native https://w3id.org/osc-em/oscem-schemas/:pixel_size","title":"Mappings"},{"location":"pixel_size/#linkml-source","text":"name: pixel_size description: Pixel size, in Angstrom from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: pixel_size domain_of: - Acquisition range: float","title":"LinkML Source"},{"location":"present/","text":"Slot: Present (present) Whether the model contains any ligands URI: https://w3id.org/osc-em/oscem-schemas/:present Applicable Classes Name Description Modifies Slot Ligand A class representing a ligand yes Properties Range: Boolean Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:present native https://w3id.org/osc-em/oscem-schemas/:present LinkML Source name: present description: Whether the model contains any ligands title: Present from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: present domain_of: - Ligand range: boolean","title":"Slot: Present (present)"},{"location":"present/#slot-present-present","text":"Whether the model contains any ligands URI: https://w3id.org/osc-em/oscem-schemas/:present","title":"Slot: Present (present)"},{"location":"present/#applicable-classes","text":"Name Description Modifies Slot Ligand A class representing a ligand yes","title":"Applicable Classes"},{"location":"present/#properties","text":"Range: Boolean","title":"Properties"},{"location":"present/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"present/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"present/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:present native https://w3id.org/osc-em/oscem-schemas/:present","title":"Mappings"},{"location":"present/#linkml-source","text":"name: present description: Whether the model contains any ligands title: Present from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: present domain_of: - Ligand range: boolean","title":"LinkML Source"},{"location":"pretreatment_atmosphere/","text":"Slot: Pretreatment_atmosphere (pretreatment_atmosphere) Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc. URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere native https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere LinkML Source 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 domain_of: - Grid range: string","title":"Slot: Pretreatment_atmosphere (pretreatment_atmosphere)"},{"location":"pretreatment_atmosphere/#slot-pretreatment_atmosphere-pretreatment_atmosphere","text":"Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc. URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere","title":"Slot: Pretreatment_atmosphere (pretreatment_atmosphere)"},{"location":"pretreatment_atmosphere/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"pretreatment_atmosphere/#properties","text":"Range: String","title":"Properties"},{"location":"pretreatment_atmosphere/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"pretreatment_atmosphere/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"pretreatment_atmosphere/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere native https://w3id.org/osc-em/oscem-schemas/:pretreatment_atmosphere","title":"Mappings"},{"location":"pretreatment_atmosphere/#linkml-source","text":"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 domain_of: - Grid range: string","title":"LinkML Source"},{"location":"pretreatment_pressure/","text":"Slot: Pretreatment_pressure (pretreatment_pressure) Pressure of the chamber during pretreatment, in Pa URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure native https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure LinkML Source 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 domain_of: - Grid range: float","title":"Slot: Pretreatment_pressure (pretreatment_pressure)"},{"location":"pretreatment_pressure/#slot-pretreatment_pressure-pretreatment_pressure","text":"Pressure of the chamber during pretreatment, in Pa URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure","title":"Slot: Pretreatment_pressure (pretreatment_pressure)"},{"location":"pretreatment_pressure/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"pretreatment_pressure/#properties","text":"Range: Float","title":"Properties"},{"location":"pretreatment_pressure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"pretreatment_pressure/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"pretreatment_pressure/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure native https://w3id.org/osc-em/oscem-schemas/:pretreatment_pressure","title":"Mappings"},{"location":"pretreatment_pressure/#linkml-source","text":"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 domain_of: - Grid range: float","title":"LinkML Source"},{"location":"pretreatment_time/","text":"Slot: Pretreatment_time (pretreatment_time) Length of time of the pretreatment in s URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_time Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: Float Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_time native https://w3id.org/osc-em/oscem-schemas/:pretreatment_time LinkML Source 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 domain_of: - Grid range: float","title":"Slot: Pretreatment_time (pretreatment_time)"},{"location":"pretreatment_time/#slot-pretreatment_time-pretreatment_time","text":"Length of time of the pretreatment in s URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_time","title":"Slot: Pretreatment_time (pretreatment_time)"},{"location":"pretreatment_time/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"pretreatment_time/#properties","text":"Range: Float","title":"Properties"},{"location":"pretreatment_time/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"pretreatment_time/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"pretreatment_time/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_time native https://w3id.org/osc-em/oscem-schemas/:pretreatment_time","title":"Mappings"},{"location":"pretreatment_time/#linkml-source","text":"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 domain_of: - Grid range: float","title":"LinkML Source"},{"location":"pretreatment_type/","text":"Slot: Pretreatment_type (pretreatment_type) Type of pretreatment of the grid, i.e., glow discharge URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_type Applicable Classes Name Description Modifies Slot Grid A class representing a grid yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_type native https://w3id.org/osc-em/oscem-schemas/:pretreatment_type LinkML Source 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 domain_of: - Grid range: string","title":"Slot: Pretreatment_type (pretreatment_type)"},{"location":"pretreatment_type/#slot-pretreatment_type-pretreatment_type","text":"Type of pretreatment of the grid, i.e., glow discharge URI: https://w3id.org/osc-em/oscem-schemas/:pretreatment_type","title":"Slot: Pretreatment_type (pretreatment_type)"},{"location":"pretreatment_type/#applicable-classes","text":"Name Description Modifies Slot Grid A class representing a grid yes","title":"Applicable Classes"},{"location":"pretreatment_type/#properties","text":"Range: String","title":"Properties"},{"location":"pretreatment_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"pretreatment_type/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"pretreatment_type/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:pretreatment_type native https://w3id.org/osc-em/oscem-schemas/:pretreatment_type","title":"Mappings"},{"location":"pretreatment_type/#linkml-source","text":"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 domain_of: - Grid range: string","title":"LinkML Source"},{"location":"project_id/","text":"Slot: project_id project id URI: schema:identifier Applicable Classes Name Description Modifies Slot Grant Grant no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self schema:identifier native https://w3id.org/osc-em/oscem-schemas/:project_id LinkML Source name: project_id description: project id from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:identifier alias: project_id domain_of: - Grant range: string","title":"Slot: project_id"},{"location":"project_id/#slot-project_id","text":"project id URI: schema:identifier","title":"Slot: project_id"},{"location":"project_id/#applicable-classes","text":"Name Description Modifies Slot Grant Grant no","title":"Applicable Classes"},{"location":"project_id/#properties","text":"Range: String","title":"Properties"},{"location":"project_id/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"project_id/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"project_id/#mappings","text":"Mapping Type Mapped Value self schema:identifier native https://w3id.org/osc-em/oscem-schemas/:project_id","title":"Mappings"},{"location":"project_id/#linkml-source","text":"name: project_id description: project id from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 slot_uri: schema:identifier alias: project_id domain_of: - Grant range: string","title":"LinkML Source"},{"location":"reference/","text":"Slot: Reference (reference) Link to a reference of your ligand, i.e., CCD, PubChem, etc. URI: https://w3id.org/osc-em/oscem-schemas/:reference Applicable Classes Name Description Modifies Slot Ligand A class representing a ligand no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:reference native https://w3id.org/osc-em/oscem-schemas/:reference LinkML Source 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 domain_of: - Ligand range: string","title":"Slot: Reference (reference)"},{"location":"reference/#slot-reference-reference","text":"Link to a reference of your ligand, i.e., CCD, PubChem, etc. URI: https://w3id.org/osc-em/oscem-schemas/:reference","title":"Slot: Reference (reference)"},{"location":"reference/#applicable-classes","text":"Name Description Modifies Slot Ligand A class representing a ligand no","title":"Applicable Classes"},{"location":"reference/#properties","text":"Range: String","title":"Properties"},{"location":"reference/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"reference/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"reference/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:reference native https://w3id.org/osc-em/oscem-schemas/:reference","title":"Mappings"},{"location":"reference/#linkml-source","text":"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 domain_of: - Ligand range: string","title":"LinkML Source"},{"location":"role/","text":"Slot: Role (role) Role of the author, i.e., principal investigator URI: https://w3id.org/osc-em/oscem-schemas/:role Applicable Classes Name Description Modifies Slot Author no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:role native https://w3id.org/osc-em/oscem-schemas/:role LinkML Source 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 domain_of: - Author range: string","title":"Slot: Role (role)"},{"location":"role/#slot-role-role","text":"Role of the author, i.e., principal investigator URI: https://w3id.org/osc-em/oscem-schemas/:role","title":"Slot: Role (role)"},{"location":"role/#applicable-classes","text":"Name Description Modifies Slot Author no","title":"Applicable Classes"},{"location":"role/#properties","text":"Range: String","title":"Properties"},{"location":"role/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"role/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"role/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:role native https://w3id.org/osc-em/oscem-schemas/:role","title":"Mappings"},{"location":"role/#linkml-source","text":"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 domain_of: - Author range: string","title":"LinkML Source"},{"location":"sample/","text":"Slot: Sample (sample) Sample information URI: https://w3id.org/osc-em/oscem-schemas/:sample Applicable Classes Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes Properties Range: Sample Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:sample native https://w3id.org/osc-em/oscem-schemas/:sample LinkML Source name: sample description: Sample information title: Sample from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: sample domain_of: - EMDataset range: Sample","title":"Slot: Sample (sample)"},{"location":"sample/#slot-sample-sample","text":"Sample information URI: https://w3id.org/osc-em/oscem-schemas/:sample","title":"Slot: Sample (sample)"},{"location":"sample/#applicable-classes","text":"Name Description Modifies Slot EMDataset OSC-EM Metadata for a dataset yes","title":"Applicable Classes"},{"location":"sample/#properties","text":"Range: Sample","title":"Properties"},{"location":"sample/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"sample/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"sample/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:sample native https://w3id.org/osc-em/oscem-schemas/:sample","title":"Mappings"},{"location":"sample/#linkml-source","text":"name: sample description: Sample information title: Sample from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: sample domain_of: - EMDataset range: Sample","title":"LinkML Source"},{"location":"sequence/","text":"Slot: Sequence (sequence) Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here URI: https://w3id.org/osc-em/oscem-schemas/:sequence Applicable Classes Name Description Modifies Slot Molecule A class representing a molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:sequence native https://w3id.org/osc-em/oscem-schemas/:sequence LinkML Source 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 domain_of: - Molecule range: string","title":"Slot: Sequence (sequence)"},{"location":"sequence/#slot-sequence-sequence","text":"Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here URI: https://w3id.org/osc-em/oscem-schemas/:sequence","title":"Slot: Sequence (sequence)"},{"location":"sequence/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"sequence/#properties","text":"Range: String","title":"Properties"},{"location":"sequence/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"sequence/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"sequence/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:sequence native https://w3id.org/osc-em/oscem-schemas/:sequence","title":"Mappings"},{"location":"sequence/#linkml-source","text":"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 domain_of: - Molecule range: string","title":"LinkML Source"},{"location":"shadowing/","text":"Slot: Shadowing (shadowing) Whether the sample was shadowed URI: https://w3id.org/osc-em/oscem-schemas/:shadowing Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: Boolean Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:shadowing native https://w3id.org/osc-em/oscem-schemas/:shadowing LinkML Source name: shadowing description: Whether the sample was shadowed title: Shadowing from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: shadowing domain_of: - Specimen range: boolean","title":"Slot: Shadowing (shadowing)"},{"location":"shadowing/#slot-shadowing-shadowing","text":"Whether the sample was shadowed URI: https://w3id.org/osc-em/oscem-schemas/:shadowing","title":"Slot: Shadowing (shadowing)"},{"location":"shadowing/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"shadowing/#properties","text":"Range: Boolean","title":"Properties"},{"location":"shadowing/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"shadowing/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"shadowing/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:shadowing native https://w3id.org/osc-em/oscem-schemas/:shadowing","title":"Mappings"},{"location":"shadowing/#linkml-source","text":"name: shadowing description: Whether the sample was shadowed title: Shadowing from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: shadowing domain_of: - Specimen range: boolean","title":"LinkML Source"},{"location":"smile/","text":"Slot: SMILE (smile) Provide a valid SMILE string of your ligand URI: https://w3id.org/osc-em/oscem-schemas/:smile Applicable Classes Name Description Modifies Slot Ligand A class representing a ligand no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:smile native https://w3id.org/osc-em/oscem-schemas/:smile LinkML Source name: smile description: Provide a valid SMILE string of your ligand title: SMILE from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: smile domain_of: - Ligand range: string","title":"Slot: SMILE (smile)"},{"location":"smile/#slot-smile-smile","text":"Provide a valid SMILE string of your ligand URI: https://w3id.org/osc-em/oscem-schemas/:smile","title":"Slot: SMILE (smile)"},{"location":"smile/#applicable-classes","text":"Name Description Modifies Slot Ligand A class representing a ligand no","title":"Applicable Classes"},{"location":"smile/#properties","text":"Range: String","title":"Properties"},{"location":"smile/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"smile/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"smile/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:smile native https://w3id.org/osc-em/oscem-schemas/:smile","title":"Mappings"},{"location":"smile/#linkml-source","text":"name: smile description: Provide a valid SMILE string of your ligand title: SMILE from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: smile domain_of: - Ligand range: string","title":"LinkML Source"},{"location":"source/","text":"Slot: Source (source) Where the sample was taken from, i.e., natural host, recombinantly expressed, etc. URI: https://w3id.org/osc-em/oscem-schemas/:source Applicable Classes Name Description Modifies Slot OverallMolecule A class representing the overall molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:source native https://w3id.org/osc-em/oscem-schemas/:source LinkML 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 domain_of: - OverallMolecule range: string","title":"Slot: Source (source)"},{"location":"source/#slot-source-source","text":"Where the sample was taken from, i.e., natural host, recombinantly expressed, etc. URI: https://w3id.org/osc-em/oscem-schemas/:source","title":"Slot: Source (source)"},{"location":"source/#applicable-classes","text":"Name Description Modifies Slot OverallMolecule A class representing the overall molecule yes","title":"Applicable Classes"},{"location":"source/#properties","text":"Range: String","title":"Properties"},{"location":"source/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"source/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"source/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:source native https://w3id.org/osc-em/oscem-schemas/:source","title":"Mappings"},{"location":"source/#linkml-source","text":"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 domain_of: - OverallMolecule range: string","title":"LinkML Source"},{"location":"specialist_optics/","text":"Slot: specialist_optics Any type of special optics, such as a phaseplate URI: https://w3id.org/osc-em/oscem-schemas/:specialist_optics Applicable Classes Name Description Modifies Slot Acquisition no Properties Range: SpecialistOptics Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:specialist_optics native https://w3id.org/osc-em/oscem-schemas/:specialist_optics LinkML Source 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 domain_of: - Acquisition range: SpecialistOptics","title":"Slot: specialist_optics"},{"location":"specialist_optics/#slot-specialist_optics","text":"Any type of special optics, such as a phaseplate URI: https://w3id.org/osc-em/oscem-schemas/:specialist_optics","title":"Slot: specialist_optics"},{"location":"specialist_optics/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"specialist_optics/#properties","text":"Range: SpecialistOptics","title":"Properties"},{"location":"specialist_optics/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"specialist_optics/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"specialist_optics/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:specialist_optics native https://w3id.org/osc-em/oscem-schemas/:specialist_optics","title":"Mappings"},{"location":"specialist_optics/#linkml-source","text":"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 domain_of: - Acquisition range: SpecialistOptics","title":"LinkML Source"},{"location":"specimen/","text":"Slot: Specimen (specimen) Description of the specimen URI: https://w3id.org/osc-em/oscem-schemas/:specimen Applicable Classes Name Description Modifies Slot Sample A class representing a sample yes Properties Range: Specimen Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:specimen native https://w3id.org/osc-em/oscem-schemas/:specimen LinkML Source name: specimen description: Description of the specimen title: Specimen from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: specimen domain_of: - Sample range: Specimen","title":"Slot: Specimen (specimen)"},{"location":"specimen/#slot-specimen-specimen","text":"Description of the specimen URI: https://w3id.org/osc-em/oscem-schemas/:specimen","title":"Slot: Specimen (specimen)"},{"location":"specimen/#applicable-classes","text":"Name Description Modifies Slot Sample A class representing a sample yes","title":"Applicable Classes"},{"location":"specimen/#properties","text":"Range: Specimen","title":"Properties"},{"location":"specimen/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"specimen/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"specimen/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:specimen native https://w3id.org/osc-em/oscem-schemas/:specimen","title":"Mappings"},{"location":"specimen/#linkml-source","text":"name: specimen description: Description of the specimen title: Specimen from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: specimen domain_of: - Sample range: Specimen","title":"LinkML Source"},{"location":"spherical_aberration_corrector/","text":"Slot: spherical_aberration_corrector Specialist device to correct for spherical aberration of the microscope lenses URI: https://w3id.org/osc-em/oscem-schemas/:spherical_aberration_corrector Applicable Classes Name Description Modifies Slot SpecialistOptics no Properties Range: SphericalAberrationCorrector Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:spherical_aberration_corrector native https://w3id.org/osc-em/oscem-schemas/:spherical_aberration_corrector LinkML Source 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 domain_of: - SpecialistOptics range: SphericalAberrationCorrector","title":"Slot: spherical_aberration_corrector"},{"location":"spherical_aberration_corrector/#slot-spherical_aberration_corrector","text":"Specialist device to correct for spherical aberration of the microscope lenses URI: https://w3id.org/osc-em/oscem-schemas/:spherical_aberration_corrector","title":"Slot: spherical_aberration_corrector"},{"location":"spherical_aberration_corrector/#applicable-classes","text":"Name Description Modifies Slot SpecialistOptics no","title":"Applicable Classes"},{"location":"spherical_aberration_corrector/#properties","text":"Range: SphericalAberrationCorrector","title":"Properties"},{"location":"spherical_aberration_corrector/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"spherical_aberration_corrector/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"spherical_aberration_corrector/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:spherical_aberration_corrector native https://w3id.org/osc-em/oscem-schemas/:spherical_aberration_corrector","title":"Mappings"},{"location":"spherical_aberration_corrector/#linkml-source","text":"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 domain_of: - SpecialistOptics range: SphericalAberrationCorrector","title":"LinkML Source"},{"location":"staining/","text":"Slot: Staining (staining) Whether the sample was stained URI: https://w3id.org/osc-em/oscem-schemas/:staining Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: Boolean Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:staining native https://w3id.org/osc-em/oscem-schemas/:staining LinkML Source name: staining description: Whether the sample was stained title: Staining from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: staining domain_of: - Specimen range: boolean","title":"Slot: Staining (staining)"},{"location":"staining/#slot-staining-staining","text":"Whether the sample was stained URI: https://w3id.org/osc-em/oscem-schemas/:staining","title":"Slot: Staining (staining)"},{"location":"staining/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"staining/#properties","text":"Range: Boolean","title":"Properties"},{"location":"staining/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"staining/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"staining/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:staining native https://w3id.org/osc-em/oscem-schemas/:staining","title":"Mappings"},{"location":"staining/#linkml-source","text":"name: staining description: Whether the sample was stained title: Staining from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: staining domain_of: - Specimen range: boolean","title":"LinkML Source"},{"location":"start_date/","text":"Slot: start_date start date URI: https://w3id.org/osc-em/oscem-schemas/:start_date Applicable Classes Name Description Modifies Slot Grant Grant no Properties Range: Date Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:start_date native https://w3id.org/osc-em/oscem-schemas/:start_date LinkML Source name: start_date description: start date from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: start_date domain_of: - Grant range: date","title":"Slot: start_date"},{"location":"start_date/#slot-start_date","text":"start date URI: https://w3id.org/osc-em/oscem-schemas/:start_date","title":"Slot: start_date"},{"location":"start_date/#applicable-classes","text":"Name Description Modifies Slot Grant Grant no","title":"Applicable Classes"},{"location":"start_date/#properties","text":"Range: Date","title":"Properties"},{"location":"start_date/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"start_date/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"start_date/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:start_date native https://w3id.org/osc-em/oscem-schemas/:start_date","title":"Mappings"},{"location":"start_date/#linkml-source","text":"name: start_date description: start date from_schema: https://w3id.org/osc-em/oscem-schemas rank: 1000 alias: start_date domain_of: - Grant range: date","title":"LinkML Source"},{"location":"taxonomy_id_expression/","text":"Slot: Taxonomy_ID_expression (taxonomy_id_expression) Taxonomy ID of the expression system organism URI: https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_expression Applicable Classes Name Description Modifies Slot Molecule A class representing a molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_expression native https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_expression LinkML Source 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 domain_of: - Molecule range: string","title":"Slot: Taxonomy_ID_expression (taxonomy_id_expression)"},{"location":"taxonomy_id_expression/#slot-taxonomy_id_expression-taxonomy_id_expression","text":"Taxonomy ID of the expression system organism URI: https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_expression","title":"Slot: Taxonomy_ID_expression (taxonomy_id_expression)"},{"location":"taxonomy_id_expression/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"taxonomy_id_expression/#properties","text":"Range: String","title":"Properties"},{"location":"taxonomy_id_expression/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"taxonomy_id_expression/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"taxonomy_id_expression/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_expression native https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_expression","title":"Mappings"},{"location":"taxonomy_id_expression/#linkml-source","text":"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 domain_of: - Molecule range: string","title":"LinkML Source"},{"location":"taxonomy_id_source/","text":"Slot: Taxonomy_ID_source (taxonomy_id_source) Taxonomy ID of the natural source organism URI: https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source Applicable Classes Name Description Modifies Slot Molecule A class representing a molecule yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source native https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source LinkML 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 domain_of: - Molecule range: string","title":"Slot: Taxonomy_ID_source (taxonomy_id_source)"},{"location":"taxonomy_id_source/#slot-taxonomy_id_source-taxonomy_id_source","text":"Taxonomy ID of the natural source organism URI: https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source","title":"Slot: Taxonomy_ID_source (taxonomy_id_source)"},{"location":"taxonomy_id_source/#applicable-classes","text":"Name Description Modifies Slot Molecule A class representing a molecule yes","title":"Applicable Classes"},{"location":"taxonomy_id_source/#properties","text":"Range: String","title":"Properties"},{"location":"taxonomy_id_source/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"taxonomy_id_source/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"taxonomy_id_source/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source native https://w3id.org/osc-em/oscem-schemas/:taxonomy_id_source","title":"Mappings"},{"location":"taxonomy_id_source/#linkml-source","text":"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 domain_of: - Molecule range: string","title":"LinkML Source"},{"location":"temperature/","text":"Slot: Temperature (temperature) Environmental temperature just before vitrification, in K URI: https://w3id.org/osc-em/oscem-schemas/:temperature Applicable Classes Name Description Modifies Slot Specimen A class representing a specimen yes Properties Range: Float Minimum Value: 0 Identifier and Mapping Information Schema Source from schema: https://w3id.org/osc-em/oscem-schemas Mappings Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:temperature native https://w3id.org/osc-em/oscem-schemas/:temperature LinkML Source 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 domain_of: - Specimen range: float minimum_value: 0.0","title":"Slot: Temperature (temperature)"},{"location":"temperature/#slot-temperature-temperature","text":"Environmental temperature just before vitrification, in K URI: https://w3id.org/osc-em/oscem-schemas/:temperature","title":"Slot: Temperature (temperature)"},{"location":"temperature/#applicable-classes","text":"Name Description Modifies Slot Specimen A class representing a specimen yes","title":"Applicable Classes"},{"location":"temperature/#properties","text":"Range: Float Minimum Value: 0","title":"Properties"},{"location":"temperature/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"temperature/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"temperature/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:temperature native https://w3id.org/osc-em/oscem-schemas/:temperature","title":"Mappings"},{"location":"temperature/#linkml-source","text":"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 domain_of: - Specimen range: float minimum_value: 0.0","title":"LinkML Source"},{"location":"temperature_range/","text":"Slot: temperature_range Temperature during data collection, in K with min and max values. 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URI: https://w3id.org/osc-em/oscem-schemas/:temperature_range","title":"Slot: temperature_range"},{"location":"temperature_range/#applicable-classes","text":"Name Description Modifies Slot Acquisition no","title":"Applicable Classes"},{"location":"temperature_range/#properties","text":"Range: Range","title":"Properties"},{"location":"temperature_range/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"temperature_range/#schema-source","text":"from schema: https://w3id.org/osc-em/oscem-schemas","title":"Schema Source"},{"location":"temperature_range/#mappings","text":"Mapping Type Mapped Value self https://w3id.org/osc-em/oscem-schemas/:temperature_range native https://w3id.org/osc-em/oscem-schemas/:temperature_range","title":"Mappings"},{"location":"temperature_range/#linkml-source","text":"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 domain_of: - Acquisition range: Range","title":"LinkML Source"},{"location":"tilt_angle/","text":"Slot: tilt_angle The min, max and increment of the tilt angle in a tomography session. 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BoundingBox2D range: float","title":"LinkML Source"}]} \ No newline at end of file diff --git a/used/index.html b/used/index.html index 1d0ab9b..83ce8f7 100644 --- a/used/index.html +++ b/used/index.html @@ -344,7 +344,7 @@

Applicable Classes

yes -SphericalAberrationCorrector +ChromaticAberrationCorrector yes @@ -354,7 +354,7 @@

Applicable Classes

yes -ChromaticAberrationCorrector +SphericalAberrationCorrector yes diff --git a/width/index.html b/width/index.html index 677b9b7..fd0ed46 100644 --- a/width/index.html +++ b/width/index.html @@ -339,15 +339,15 @@

Applicable Classes

-EnergyFilter - -yes - - ImageSize size of a 2D image (in integer units) no + +EnergyFilter + +yes +

Properties