CHEMeDATA six key formal concepts

CHEMeDATA proposes to define six key formal concepts (objects) for the annotation of chemistry data.

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• 1 Substance
• 2 Chem. Equation formalize the transformation of reactants Substance(s) into products Substance(s)
• 3 Sample include Substances
• 4 Process transforms a Sample into another Sample. Reaction, extraction, purification, etc. are Process’s.
• 5 Analytical data provides information about a Sample
• 6 Assignment combines one (or a set of) Analytical data with properties of the other concepts.

Comments and suggestions are welcome!

The following is a draft

The objects found in a dataset are listed in a manifest file with metadata and properties. A selection of objects and key metadata and properties can be registered with the DOI of the data set using the datacite “subject” field to make them “Findable”.

• Substance
  • Formula (XnYm)
  • properties
    • atom list
    • connection table (+ bond types?)
    • InChi
    • 2D
    • 3D structure(s) (may have multiple conformations/mesomers)
    • etc.
  • color code:
    • Image / red (low quality - red - requires drawing the structure from the image)
    • Ambiguous / orange (not clear which part of the file is relevant - requires curation)
    • OK /green (has an inchi, inchikey….)
• Sample
  • Types:
    • (s) Solution sample : Simple solution with a single pure solvent
    • (m) Solution sample in a mixture of solvents: Mixture of solvents
    • (w) Water solution : for water solution with buffer, salt, etc.
    • (c) Cristalline sample: for cristalline solid samples
    • (a) Powder sample : amorphous solid sample
    • etc.
  • properties
    • composition (Substances, quantity)
    • MInChI
    • etc.
  • color code:
    • No description / red
    • OK / green
  • loosely related:
    • sampling nature, iSample, IGSN
• Chem Equation formalize the transformation of reactants Substance(s) into products Substance(s)
  • Specify the cathegory of the reaction?
  • Properties
    • category (name…)
    • reactants (Substance, stochiometry)
    • products (Substance, stochiometry)
    • conditions (…)
    • Rinchi
  • Color code:
    • No equation or image/ red
    • Ambiguous / orange (not clear which part of the file is relevant - requires curation)
    • OK / green (has an Rinchi, inchi of reactant…)
• Process transforms a Sample into another Sample
  • categories
    • 
    • Chromoatography (HPLC, etc.)
    • Purification? (Recristallisation, etc.)
    • Reaction (RInChi),
    • Plant extraction?
    • etc. to be worked on!
  • Properties
    • Category (name…)
    • Conditions
    • Initial Sample
    • Final Sample
    • Chem Equation (for reactions only)
• Analysis provides information about a Sample
  • Spectroscopy
    • NMR
    • IR
    • Ms…
  • Non-spectroscopy
    • Melting point
    • etc.
  • Properties
    • Sample
    • Temperature
  • color code:
    • No mimimal property present / red
    • Missing essential property / red
    • image / orange-red
    • propriatary format / orange-red
    • (no green - not other categories otherwise becomes Assignment)
• Assignment combines one (or a set of) Analysis with one (or more) property of the other 5 object types
  • NMR
  • IR
  • Ms ? categories…
  • etc.
  • color code for assignmentNMRspectra:
    • no spectral analysis / orange (no peak picking, no extraction of chemical shifts…)
    • OK / green (OK has assignmentNMRdata)
  • color code for assignmentNMRdata:
    • No assignement / orange (has list of peaks otherwise would not exists, but no assignment of peaks to part of the substance)
    • OK / green (has assignement of all reasonably assignable peaks)
    • Validation / gold (has validation)

Goal 1: Provide a linked-data consolidation of the CHEMeDATA format

Move from the NMR-only assignment format of the NMReDATA initiative (based on .sdf files) towards linked data.

Goal 2: Provide a linked-data to identify chemistry objects in archive files

work-in-progress owl file

https://chemedata.github.io/ontologies/chemedata/playground/chemedata.owl

Exported OWLDoc can be found in the chemedata/playground folder.

Diverging implementation

https://webprotege.stanford.edu/#projects/2a6dbe88-eb6e-4a36-a617-629279bd3166/

Please contact us (post issue) if you are interested.