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Restructure calibration compound #4

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NRayya opened this issue Jan 22, 2024 · 3 comments · Fixed by #45 · May be fixed by #19
Closed
6 tasks done

Restructure calibration compound #4

NRayya opened this issue Jan 22, 2024 · 3 comments · Fixed by #45 · May be fixed by #19
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@StroemPhi @NRayya
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NRayya commented Jan 22, 2024 •
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  • We should have the hierarchy:

    • calibration compound
      • chemical shift calibration compound
        • chemical shift reference compound
      • concentration calibration compound

  • Enhance definitions:

    • calibration compound: A molecular entity that is used as a calibration compound in nuclear magnetic resonance (NMR) spectroscopy.
    • chemical shift calibration compound: A molecular entity that is used as a chemical shift calibration compound in nuclear magnetic resonance (NMR) spectroscopy.
    • chemical shift reference compound: A molecular entity that is used as a chemical shift reference compound in nuclear magnetic resonance (NMR) spectroscopy.
    • concentration calibration compound: A molecular entity that is used as a concentration calibration compound in nuclear magnetic resonance (NMR) spectroscopy.
    • calibration compound role: A compound that produces one or more peaks used to calibrate the NMR spectrometer and/or the spectrum.
    • chemical shift calibration compound role: A compound that produces one or more peaks used for chemical shift calibration.
    • chemical shift reference compound role: A compound that produces the peak used as reference frequency in the δ chemical shift scale.
    • concentration calibration compound role: A compound of a known concentration that produces one or more peaks used to calibrate a spectrum for quantification.

  • Remove its synonyms of reference compound: "reference compound, reference standard".

  • Rename chemical shift standard to chemical shift reference.

  • Remove children of concentration compound.

  • calibration compound and its children should be defined similarly to 'NMR solvent' according to the roles they bear.

    • For chemical shift standard this can be done by reusing CHEBI:'NMR chemical shift reference compound'.
@NRayya NRayya changed the title Rename chemical shift standard Restructure calibration compound Feb 21, 2024
@NRayya NRayya self-assigned this Feb 21, 2024
@NRayya NRayya added the approved Decision regarding this issue was already taken during task force meeting label Feb 21, 2024
@StroemPhi StroemPhi mentioned this issue Mar 19, 2024
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@NRayya NRayya added discussion This issue still needs discussion before resolving and removed approved Decision regarding this issue was already taken during task force meeting labels Mar 19, 2024
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NRayya commented Mar 20, 2024

  • Every shift reference can be used as calibration compound.
  • There are no solvents that are used as shift references but as calibration compound.
  • Chemical shift reference in NMR is always 0, while calibration compound can have different ppm.

@NRayya NRayya mentioned this issue Mar 20, 2024
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NRayya commented Mar 21, 2024

Nuclei in nmrCV that didn't get a reference compound from IUPAC:

  • 2H

@NRayya NRayya mentioned this issue Mar 21, 2024
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NRayya commented Mar 21, 2024

What I have done so far in calibration

  1. Enhance calibration compound annotations. We still need a precise definition --> done in be66814 & f169762
  2. Enhance chemical shift standard annotations. We still need a precise definition and to clean old nmrCV entries --> done in d208f75
  3. Add new classes for grouping the references by the nuclei according to IUPAC recommendations in addition to enhancing the annotations of existing ones --> done in 113a2a0
  4. Obsolete old nmrCV references in favour of imported CHEBI equivalent --> done in 75f3de3
  5. Move imported CHEBI references under the corresponding grouping parents. We still need to refresh CHEBI:229458 import --> done in 04bc1d7
  6. Obsolete old nmrCV references that are not recommended by IUPAC. These entities are still imported from IUPAC by having the role NMR chemical shift reference compound. We need to figure their actual roles and clean them in CHEBI. --> done in e68e974

@NRayya NRayya added approved Decision regarding this issue was already taken during task force meeting and removed discussion This issue still needs discussion before resolving labels Aug 21, 2024
@NRayya NRayya mentioned this issue Sep 10, 2024
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4 restructure calibration compound nmrML/nmrCV
Restructure calibration compound nmrML/nmrCV
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@StroemPhi @NRayya