ComPlat / chemotion_REPO

Repository for samples, reactions and related research data
https://www.chemotion-repository.net
GNU Affero General Public License v3.0
12 stars 2 forks source link

user should be allowed to specify solvents and concentrations applied for analyses #36

Open tilfischer opened 1 year ago

tilfischer commented 1 year ago

For NMR spectra processed with Chemspectra or NMRium users may reference on the internal standard added or a secondary standard such as the residual solvent signal of the solvent applied. For Chemspectra this information is saved in the ...peak.jdx with Chemspectras own label data records (LDRs) ##$CSSOLVENTNAME= and ##$CSSOLVENTVALUE=.

For other NMR spectra not processed with Chemspectra e.g. 2D NMR data and IR and UV/VIS there is currently no information on solvent applied available in a structured manner. Although both LDRs mentioned above are written for ...peak.jdx of IR and UV/VIS datasets submitted, these do not contain any values.

One possibility to the user is to add data on solvents used to "Description", but this field could contain anything which describes an analysis. Especially machine might struggle to get the data from there.

A field for solvent should be added to every analysis added and may provide a controlled list of solvents but also "other" to add free text for any other solvent or solvent mixtures. Also solid solvents such as KBr, regularly used for the preparation of IR samples, should be covered in a controlled list. This information could than also be written to the ...peak.jdx files.

The second most important information for many measurements is the concentration. A field for concentrations should be added to every analysis added. For quantitative UV/VIS spectroscopy, concentration is required to calculate molar extinction coefficient, while for routine NMR concentration is of less importance and often only roughly know.

Beside of having additional fields to be filled by the users, I also agree that there are other ways to get this data. It might be read from the vendor data formats, if this information was added but not separately written to the ELN. However, there are a lot vendor formats out there and often there is no specification of these formats available. Both information might also be available from data in JCAMP-DX format with LDR ##CONCENTRATIONS= for concentrations and, since JCAMP-DX v5.01, from the optional LDR ##.SOLVENT NAME=. However, software used to write JCAMP-DX files does not necessarily write these LDRs or these LDRs were not even implemented and the same trouble with user interaction as mentioned with the vendor files above might occur.

nicolejung commented 1 year ago

-> these points will be part of the metadata schemes for the individual measurement types