Add purity to chemical import feature and XLSX template

[tilfischer]

• I am an ELNer user and ELN admin

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:

1. The template does not take information on purity, concentration, density, melting point, boiling point and refractive index. Would be very unfortunate if this information would get lost, hence, these should be added to the import feature as well as the XLSX template. There is an import sample feature described in the Chemotion documentation here, which eats melting point and boiling point but does not like density and the refractive index.
2. What is the meaning of the residue type column?
3. Minor importance to me: A column for barcode is missing in the XLSX template. Note: I do not know much about the barcode system in Chemotion ELN, but, to my knowledge, it has 9 digits, while other barcodes might have 8 digits similar to EAN-8.
4. The chemical import template XLSX asked for sample name, which is added to "Name" in every sample, while on the top left it shown the sum formular and a name possibly generated from the SMILES. For tetrabutylammonium hydroxide is generated the IUPAC name tetrabutylazanium hydroxide. Is there any possibility to also have the name providede in the template as sample name on the top left? This could be an feature just enabled for samples with the checkbox "Inventory" checked.
5. There is a chemical with SMILES CC1CCC(=O)C1=O, which was imported fine besides the chemical structure picture, while the structure looks fine, if opened with ketcher.

If I press save in ketcher, the preview picture of the chemical structure looks fine again.

Any hints on that?

Best as ever, Tillmann

[tilfischer]

push

[tilfischer]

push

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

[tilfischer]

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

[adambasha0]

Hi @tilfischer, can you please elaborate on point 4 about name in chemical import template, with an example.

[tilfischer]

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

[adambasha0]

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

[tilfischer]

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

[adambasha0]

Dear @tilfischer,

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. The residue_type is related to polymer samples (sample type), so it is not necessarily a must-column in the template.

Best, Adam