Schema for the Open Standards Community for Electron Microscopy (OSC-EM)
In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "string".
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "integer".
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "boolean".
A real number that conforms to the xsd:float specification
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "float".
A real number that conforms to the xsd:double specification
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "double".
A real number with arbitrary precision that conforms to the xsd:decimal specification
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "decimal".
A time object represents a (local) time of day, independent of any particular day
URI is dateTime because OWL reasoners do not work with straight date or time
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "time".
a date (year, month and day) in an idealized calendar
URI is dateTime because OWL reasoners don't work with straight date or time
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date".
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "datetime".
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date_or_datetime".
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uriorcurie".
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "curie".
in RDF serializations this MUST be expanded to a URI
in non-RDF serializations MAY be serialized as the compact representation
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uri".
in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "ncname".
A URI or CURIE that represents an object in the model.
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "objectidentifier".
A URI, CURIE or BNODE that represents a node in a model.
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "nodeidentifier".
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.
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpointer".
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.
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpath".
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.
If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "sparqlpath".
Allowed molecule class values - compatible with the EMDB.
complex of different parts e.g. protein complex
Allowed molecular assembly values - compatible with the EMDB.
If your protein (complex) of interest is forming filaments
If your protein (complex) of interest is forming helical arrays (i.e. tubes)
If your protein (complex) of interest forms individual particles on the grid with no orderd interactions
Allowed values for authors organizations.
Specifies which Acquisition subschema/class is in use.
The total electron beam current hitting the viewing screen, in nA.
Target defocus set, min and max values in nm.
Machine estimated defocus, min and max values in µm. Has a tendency to be off.
Magnification level as indicated by the instrument, no unit
Type of cryogen used in the holder - if the holder is cooled seperately
Temperature during data collection, in K with min and max values.
Average dose per image/movie/tilt - given in electrons per square Angstrom
Whether an energy filter was used and its specifics.
whether a specific instrument was used during data acquisition
The size of the image in pixels, height and width given.
Time of data acquisition per movie/tilt - in s
Cryogen used in cooling the instrument and sample, usually nitrogen
Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
Number of grids imaged for this project - here with qualifier during this data acquisition
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
Level of binning on the images applied during data collection
Any type of special optics, such as a phaseplate
Phaseplate is a special optics device that can be used to enhance contrast
Details of a given specialist instrument
Specialist device to correct for spherical aberration of the microscope lenses
Specialist device to correct for chromatic aberration of the microscope lenses
Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
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.
Whether and how you have to flip or rotate the gainref in order to align with your acquired images
Mode of the detector, e.g. "counting", "ScanningDetector", "ImagingDetector", etc.
Dispersion of an analytical detector, in eV
Collection angle set, min and max values in mrad.
Mode of illumination used during data collection
Mode of imaging used during data collection
Type of electron source used in the microscope, such as FEG
Voltage used for the electron acceleration, in kV
C2 aperture size used in data acquisition, in µm
Spherical aberration of the instrument, in mm
Operating mode of the microscope, i.e. "TEM", "STEM"
Refers to how tightly or widely the electron beam is focused onto the sample, in mrad. Typically low convergence for TEM and high for STEM.
Description of the overall molecular type, i.e., a complex
Where the sample was taken from, i.e., natural host, recombinantly expressed, etc.
Name of an individual molecule (often protein) in the sample
Full sequence of the sample as in the data, i.e., cleaved tags should also be removed from sequence here
Scientific name of the natural host organism
Taxonomy ID of the natural source organism
Scientific name of the organism used to produce the molecule of interest
Taxonomy ID of the expression system organism
Provide a valid SMILES string of your ligand
Link to a reference of your ligand, i.e., CCD, PubChem, etc.
Name/composition of the (chemical) sample buffer during grid preparation
Concentration of the (supra)molecule in the sample, in mg/ml
Which cryogen was used for vitrification
Environmental humidity just before vitrification, in %
Environmental temperature just before vitrification, in K
Type of material the support film is made of
Type of pretreatment of the grid, i.e., glow discharge
Pressure of the chamber during pretreatment, in Pa
Atmospheric conditions in the chamber during pretreatment, i.e., addition of specific gases, etc.
List of molecule associated with the sample
List of ligands associated with the sample
What type of higher order structure your sample forms - if any.
The tilt axis angle of a tomography series
The min, max and increment of the tilt angle in a tomography session. Unit is degree.
Type of organization, academic, commercial, governmental, etc.
Role of the author, for example principal investigator
ORCID of the author, a type of unique identifier
List of grants associated with the project
List of authors associated with the project
Minimal value of a given dataset property
Maximal value of a given dataset property
The width of a given item - unit depends on item
The height of a given item - unit depends on item
List of custom descriptors for user-defined key-value pairs describing how movies were obtained or any related information
value of a given field in respect to its SI unit
Describe the data acquisition parameters
Describe the instrument used to acquire the data
cryo electron tomography dataset, with a focus on a single protein (complex) & subtomogram averaging
General acquisition covering materials science and other use cases. For specialized techniques, use the appropriate subclass (AcquisitionSpa for single particle, or tomography subclasses).
A device used to filter for electrons with specific energy.
Optional optics used to correct for instrument limitations.
Used to modulate the phase of the electron wave.
Special device used to correct instrument inherent spherical aberration.
Special device used to correct instrument inherent chromatic aberration.
Instrument values, mostly constant across a data collection.
Unifying class to describe the full sample.
More detailed information about individual molecules.
Details on the grid used in the experiment.
Overarching category for authors and grants
Details on the person performing the experiment.
Any type, used as the base for type-narrowing.
A series of numbers constructed from min, max, and increment
an axis-aligned 2D bounding box (float units)
if a value has a unit, it should be given as a unit value pair.
unit value extended to have two additional fields si_value and si_unit
List of custom descriptors for user-defined key-value pairs describing how micrographs were obtained or any related information