Open tilfischer opened 11 months ago
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Bullet point No. 1 is important for a group which already has an ELN with inventory, to move their inventory to Chemotion ELN as part of the transition to Chemotion ELN.
Best, Tillmann
Dear All,
checked the template again. From what was listed above, purity, concentration/molarity and refractive index is not listed in the template provided here. As soon as this information can be provided for excel based import, someone needs to map and the group may start using Chemotion ELN.
Best, Tillmann
Hi @tilfischer, can you please elaborate on point 4 about name in chemical import template, with an example.
Dear Adam,
On No. 4: The import sheet contains columns for name and molecule name, hence, its not an issue anymore. Possibly, I haven't seen this a year ago. Anyhow, thanks for asking!
On No 2: What does the "residue type" column means provided in the XLSX import template in column A?
On No 1 (and most important to me): I went again though the export sheet, import sheet and what is available looking on the Chemotion UI (including inventory tab).
property export | comment property export | property(ies) import | available in import XLSX | comment property import |
---|---|---|---|---|
name | sample name; molecule* name | yes | ||
empircal formula | actually is sum formula | sum formula | yes | |
CAS number | Sample:CAS | no | ||
purity/concentration** | concentration has solvent | Sample_Properties:Purity; Sample_Properties:Molarity; Sample_Properties:Solvents (CV) | no, yes for last one | as weight percentag in 0 to 1; as Molarity |
Responsible person | Sample_Inventory:Person | no | is name | |
stereo-SMILES | canonical smiles | yes | ||
MW | no unit, actually in g/mol in UI | molecular* mass | yes | in g/mol, only for decoupled samples |
amount*** | target amount; target unit; real amount; real unit | yes | ||
storage | Sample_Inventory:Host location:building; Sample_Inventory:Host location:room, Sample_Inventory:Host location:cabinet; Sample_Inventory:Host localtion:room | no | ||
supplier | Sample_Inventory:Vendor | no | ||
density (20°C) | no unit, actually in g/cm3 in UI | density | yes | |
melting point | no unit, actually in °C in UI | melting pt | yes | |
boiling point | at atm or pressure is given | boiling pt | yes | |
refractive index | Sample_Properties:Refractive Index | no | ||
comment on chemical | Sample_Inventory:Important notes | no | one might argue for Sample_Properties:Description |
What happens with chemical having more than one CAS number? To my knowledge, there is only one number and legacy numbers. Unfortunately, also old numbers are still in used i.e. are printed to bottle sitting on the shelf, waiting for researchers.
This is molecule-centric. The more generic alternative imho would be "chemical substance name" and "molar mass". With the decoupled mode, inventory samples which cannot be represented with SMILES and/or InChI can be added. I must admit that I do not like the idea to call everything "molecule". While NFDI4Chem focuses on molecules, we still should try to stay interoperable and allow any other types of compounds to be represented. This will get ab bit tricky (and time consuming) as this columns has information such as purity (e.g. 93 % (yes, with space)) or concentration (e.g. 80% in Toluene (w/w), 3 mol/L in DCM). These filed contain information such as "20 g / 20 g" (amount = 20 g, still available = 20 g) or "30 mL / 1000 mL" (amount 1000 mL, still available 30 mL).
Test data will be sent via another channel.
Best, Tillmann
Dear Tillmann,
1- import of samples properties of refractive index and flash point, and fix for importing amount field in inventory tab for chemicals will come in the next release 2- please have a look at the documentation on chemotion saurus for import of chemicals (https://www.chemotion.net/docs/eln/ui/inventory?_highlight=import#import-chemicals), all fields including CAS number in inventory tab can be imported except for a description and important notes fields
3- currently ELN allows only the import of one CAS number for a sample.
4- for the purity/concentration field, only digits (decimals) can be easily imported, but any neighbouring words/characters will have to be ignored. Residue type column is not a must column for the import, so it can be deleted.
please note that the import of samples as a normal sample, is different from import of chemicals as inventory samples. Both features intersect, but users need to follow the documentation on Chemotion Saurus to handle each case individually.
let me know if something else is needed with respect the import process for your department and the feature in general.
Best, Adam
Dear Adam,
Thank you Adam and anybody else who was involved! Also thank you for pointing me on the other import template for chemicals (import_chemicals_template.xlsx).
Will the import sheet available at the end of page https://www.chemotion.net/docs/eln/ui/inventory also be updated following the next release? I checked the columns again and could not spot empirical formula / chemical formula, purity, molecular weight / molar mass, refractive index, melting point, boiling point and density.
Again, was is the "residue type" column made for?
Best, Tillmann
Dear Tillman,
Thank you. and yes the new up-to-date import sheet will be available. empirical formula / chemical formula, and molecular weight will not be supported. While purity, refractive index, melting point, boiling point and density will be supported. I will forward your question about residue_type to Nicole, as I am not sure about it.
Best, Adam
Description
I just imported some chemicals exported from another chemical inventory to an inventory in Chemotion ELN. Did the excel based mapping of the exported inventory to the import_chemicals_template.xlsx provided in the Chemotion documentation here. Thank you for that feature! Nevertheless, I want to report some issues and have some questions:
If I press save in ketcher, the preview picture of the chemical structure looks fine again.
Any hints on that?
Best as ever, Tillmann