LinkML schema for electron microscopy sample and author-related metadata, broadly following the EMDB standard with some additions.
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
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.
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
Unifying class to describe the full sample.
More detailed information about individual molecules.
Details on the grid used in 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