Capture quantification of compounds

Notes of chenomx meeting:
 Make constraints with regard to allowed data formats, e.g. jcamp made
the error to allow for multiple encodings, e.g. fid file compressions.
This makes parsing a nightmare.

2 main use cases for chenomx:
fit/process an existing nmrML spectrum using chenomX: nmrML as input
nmrML as output (from cnx format)(instead of current verbose JCAMP), but
this is currently limited as chenomix does not capture all that is
currently required by nmrML.
This also includes using the chenomix parsers for varian and bruker
formats to generate nmrML formats.

mnrML already capture a great deal of acquisition parameters that will
not be used by processing software. So make less mandatory ? We created
a spreadsheet to indicate what .cnx file would capture. (This part of
missing infor COULD be as welll stored within a cnx file.)
we were hence discussing to shift more such constraints (e.g.
mandatoryness of contact details) from the XSD into the
validation/mapping file shell.

Peak assignment should be able to assign up to 60 compounds to a
spectrum
(group as clusters with information loss, we view a spectrum as a set of
lorenzian peaks)

compound name, concentration (mM), … → peak descriptions

Spectral Processing info is difficult to capture as its dept on
algorithms, but chenomix does it (iProcessing history,incl roll back
funct). But you will never be able to absolutely reproduce all from this
specification. but capturing the terms (with (like in chenomix
processing history) or without concrete parameters), e.g. line
broadening (Hz), zerofilling, baseline correction (parameter:14
breakpoints or automatic: linear/drift vs spline), shim correction
(linewith (Hz), phase correction, … is o.k. for information purposes
(not reproducability by third party).

optional process tag (for spectrum): processing parameter / algorithm
(in CV) + software used for that (CV) + optional parameters (free text
accompanying the CV term, probably in mapping file.

[put screenshot of chenomx spectrum details]

SpectrumList: Do we want the users to be able to store multiple nmr
spectra ? E.g. capturing multiple precessing steps ? We like to have
only 2 spectra, e.g. the raw and the annotated/processed one.
 if many: how associate processing steps to spectrum?

We discussed removing all processing parameters  from the XSD into the
CV, e.g. water supression , post acquisition solvent suppression method,
calibration reference shift  to be more consistent. This will however
shift the workload of validation into the mappng file realm.
What were the reasons to have these in XSD ? Due to C Ludwig request?
due to 2D and J res spectral processing ?

CV error? Apodization equivalentTo ... by window function

Confidence levels for assignments ? Only available from Humans, but we
need it for further statistics, e.g. Metaboanalyst. Use Sumner
Confidences for Identification, or is it too generic or MS centric. What
confidence for concentration ?

Compound IDs are taken from a resurce with best coverage and most
outlinks e.g. PubChem , chebi or inchi.

What to make mandatory in XSD ? Many papameters that are mandatory at
the moment, like Temperature, are not captured/used in Chenomx software.
Make these optional in order to avoid retrogradly converted .nmrML files
be invalid ?

Chenomx wants free version of nmr suite to be able to convert jeol,
bruker and varian into nmrML, the full version will allow to process and
annotate further and maybe make it fully MSI compliant ?

ComputedConcentration terms CV:
Library based computed concentration
Lorenzian (-Integration) (Modeled Area) Estimated Concentration
Measured Area (Integration) based Concentration
time-domain amplitude computed concentration

If a molecule/compound is not yet in any molecule dtb just the cml
representation is specified.
What term to use ? Molecule or Compound.

Chenomx is kindly allowing us to leverage on a few of their test nmr
examples to test our nmrML parsers. Just keep them private.