NMRspec

metamodel version: 1.7.0

version: 0.0.2

This model can be used to semantify NMR spectroscopy research data.

Classes

• MOLfile
• Manufacturer
• MolarConcentration - A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. [Wikipedia:http://en.wikipedia.org/wiki/concentration]
• MolarityMeasurementDatum - A scalar measurement datum that is the result of measuring the molarity (aka volume concentration) of a chemical solution.
• NmrBuffer
• NmrSample
• NmrSampleTube
• NmrSolution - A NMR sollution is the solution made up of the solvent in which the evaluated sample is dissolved in as well as possibly the buffer needed to adjust the pH value.
• NmrSolvent
• NmrSpecRecord - A data item that serves as a container for all relevant information about one NMR spectroscopy assay record. The properties of this class represent the required metadata of an NMR assay, such as: * what kind of assay was performed (e.g. 2D 13C COSY) and what devices where used for that (e.g. spectrometer, magnet, solvent, buffer, ...) * what are the detail infos of the assayed sample (name, formula, structure, concentration, preperation process, ...)
• NmrSpecRecordCollection - This class represents a collection of NMR spectroscopy records. It is to be used when multiple NMR assays were made in order to analyse a given sample.
• NmrSpectrometer
• PhMeasurementDatum - A scalar measurement datum that is the result of measuring the pH value of a chemical solution.
• PhValue
• PulsedNmrAssay
• Temperature
• TemperatureMeasurementDatum - A scalar measurement datum that is the result of measuring temperature.

Mixins

• ChemicalDescriptor - A chemical descriptor is a data item (quantity or value) about a chemical entity that conforms to a specification for how it is calculated, measured or recorded.
• NamedThing - a mixin to be used by any class that has a name and unique id
• Provenance - This is a mixin to be used by any class that is needed as part of an audit trail to ensure the provenance of the metadata.

Slots

• ➞formula
• ➞inchi
• ➞inchikey
• ➞iupac_name
• ➞mol_file
• ➞smiles - The canocical SMILES of a compound (Sample, Solvent or Buffe)
• id
  • Manufacturer➞id
  • MolarConcentration➞id
  • NmrBuffer➞id
  • NmrSampleTube➞id
  • NmrSample➞id
  • NmrSolution➞id
  • NmrSolvent➞id
  • NmrSpecRecord➞id - the URI of a NMR spectroscopy record. If a record does not have an URI, you must use "nmrSPARQL" as prefix and the filename (e.g. "nmrSPARQL:filename1.jdx") and an unresolvable URI will be minted upon ingest by replacing this prefix with the URI of the dataset.
  • NmrSpectrometer➞id
  • PhValue➞id
  • PulsedNmrAssay➞id
  • Temperature➞id
• local_id - This property should be used to provide the local identifier with which something is denoted in a local context (e.g. your lab notebook).
• manufactured_by - a property to be used on any class that represents some form of atrefact, in order to refer to the artefacts maker.
  • NmrSampleTube➞manufactured_by
  • NmrSpectrometer➞manufactured_by
• measured_as
  • MolarConcentration➞measured_as
  • PhValue➞measured_as
  • Temperature➞measured_as
• name - a generic property to provide a string that is used to name a something
  • Manufacturer➞name
  • NmrSolvent➞name
• ➞measured_temperature
• NmrSolution➞buffer - The attribute needed to relate the NMR solution to the buffer it might contain.
• ➞measured_molarity - The attribute needed to relate to the molarity of the NMR solution.
• ➞measured_pH - The attribute needed to relate to the pH of the NMR solution.
• NmrSolution➞sample - The attribute needed to relate the NMR solution to the sample it contains.
• NmrSolution➞solvent - The attribute needed to relate the NMR solution to its solvent.
• ➞assays_sample - This property is used to provide metadata on the assayed NMR sample.
• NmrSpecRecordCollection➞contains_assay_records
• ➞output_of_nmr_assay
• ➞sample_tube
• Provenance➞created_by - the creator of the ressource
• Provenance➞date_created - The date on which the source file was processed according to this schema.
• ➞description
• Provenance➞licence_str - the licence of the ingested raw data as string
• Provenance➞licence_url - the licence of the ingested raw data in machine readable format as URL
• Provenance➞source - This property is used to describe the source of the data as string (e.g. "Chemotion Repository", the file name of a record).
• Provenance➞source_uri - This property can be used to provide the URL or CURIE of the the source file, if it has one.
• PulsedNmrAssay➞acquisition_nuclei - the nuclei to be assayed as specified by the protocol
• PulsedNmrAssay➞assay_date - the date the assay was carried out by someone
• ➞has_dimension
• PulsedNmrAssay➞observed_frequencies
• PulsedNmrAssay➞pulse_program - The pulse program of a PulsedNmrAssay is a required property and must be conform to one of the values defined in the PulseProgram enum class. The possible values there are defined according to common pulse programs, e.g. NMR for basic 1H-NMR, or COSY and COSY-DOSY, etc.
• PulsedNmrAssay➞pulse_program_custom - A custom pulse program specification that is not yet in our list of allowed values for the pulse program parameter.
• PulsedNmrAssay➞solution - the property refering to solution in which the assayed sample is disolved in
• PulsedNmrAssay➞spectrometer
• type
  • NmrSpectrometer➞type - This property represents the type of spectrometer used in the NMR assay as string. Often this information will not be present in the JCAMP-DX file, but it can be parsed from Brucker source files
• unit
  • MolarityMeasurementDatum➞unit
  • PhMeasurementDatum➞unit
  • TemperatureMeasurementDatum➞unit
• value
• website - a generic property to be used in classes that represent something which has a website

Enums

• Dimension - The dimensionality of the produced spectrum.
• MolarityUnit - Enums of needed units aligned with UO. WIP:needs to be expanded
• NmrManufacturers - Controlled list of manufacturers of NMR lab devices.
• PhValueUnit
• PulseProgram - Enum of the most commonly used pulse sequences that specify the type of pulsed NMR. Based on a mix of Bruker specs (https://pharm.ucsf.edu/sites/pharm.ucsf.edu/files/Pulse%20Program%20Catalog%201%20%281D%20and%202D%20Experiments%29.pdf), IUPAC specs (http://www.jcamp-dx.org/protocols/NMR%20Pulse%20Sequences%20PAC%2079(11)%20pp1748-1764%202001.pdf) and JEOL specs (https://www.uh.edu/nsm/chemistry/resources/nmr/ECAXSII_Advanced_Mode_Tutorial_Manual.pdf)
• TemperatureUnit

Subsets

Types

Built in

• Bool
• Decimal
• ElementIdentifier
• NCName
• NodeIdentifier
• URI
• URIorCURIE
• XSDDate
• XSDDateTime
• XSDTime
• float
• int
• str

Defined

• Boolean (Bool) - A binary (true or false) value
• Date (XSDDate) - a date (year, month and day) in an idealized calendar
• DateOrDatetime (str) - Either a date or a datetime
• Datetime (XSDDateTime) - The combination of a date and time
• Decimal (Decimal) - A real number with arbitrary precision that conforms to the xsd:decimal specification
• Double (float) - A real number that conforms to the xsd:double specification
• Float (float) - A real number that conforms to the xsd:float specification
• Integer (int) - An integer
• Ncname (NCName) - Prefix part of CURIE
• Nodeidentifier (NodeIdentifier) - A URI, CURIE or BNODE that represents a node in a model.
• Objectidentifier (ElementIdentifier) - A URI or CURIE that represents an object in the model.
• String (str) - A character string
• Time (XSDTime) - A time object represents a (local) time of day, independent of any particular day
• Uri (URI) - a complete URI
• Uriorcurie (URIorCURIE) - a URI or a CURIE