ComPlat / chemotion_ELN

Electronic Lab Notebook
https://www.chemotion.net
GNU Affero General Public License v3.0
126 stars 53 forks source link

Add purity to chemical import feature and XLSX template #1644

Open tilfischer opened 11 months ago

tilfischer commented 11 months ago

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.

Screenshot 2023-11-29 135250

Screenshot 2023-11-29 135337-2

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 commented 9 months ago

push

tilfischer commented 4 months ago

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 commented 1 month ago

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 commented 1 month ago

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

tilfischer commented 1 month ago

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 commented 1 month ago

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 commented 3 weeks ago

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 commented 1 week ago

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