For Data Files
It is not mandatory to provide all of the following types of analysis (measurement types) to the repository, the selection of the analysis is up to you. Highly recommended is the provision of all data that is needed for proving evidence for the characterized compounds.
The following list contains the file formats that should be available. In many cases, the repository supports with automated processing of files. An example is the processing of zip files to jcamp files and images (alternatively the processing of jcamp files to images). If you provide files that can be processed (in that case zip and/or jcamp), additional files (e.g. images) are not necessary. An exception to this rule is [1].
NMR Spectroscopy
NMR Spectroscopy - 1D data
| Supported files | Ending | Required | Explanation |
|---|---|---|---|
| zip | .zip | Yes | Original data from device - please add this in any case |
| jcamp-dx | .jdx, .dx, .jcamp | No | Please add in addition to zip if the automatically generated one has low quality[1.1] |
| NMRium | .nmrium | No | If NMRium data is available, you can add it additionally to the zip[1.2] |
| Generated files | Ending | Explanation |
|---|---|---|
| jcamp | .peak.jdx | is generated from zip with automated peak picking (not editable) |
| jcamp | .edit.jdx | is generated from jdx including manual editing |
| png | .peak.png | is automatically generated from .peak.jdx |
| png | .edit.png | is automatically generated from .edit.jdx |
| json | .infer.json | is automatically generated from .edit.jdx, data exchange format for NMRshiftDB |
| NMRium | .nmrium | is generated from zip if NMRium editor is selected (not automatically) [1.2] |
[1.2] the automatic processing from zip to jcamp with the embedded software gives sometimes bad results. In those cases, please provide a jcamp file that was processed with a suitable external software to allow the provision of clear, high quality data.
[2.2] NMRium is supported from version 1.5 of Chemotion ELN (March 2023).
NMR Spectroscopy - 2D data
| Supported files | Ending | Required | Explanation |
|---|---|---|---|
| zip | .zip | Yes | Original data from device - please add this in any case |
| jcamp-dx | .jdx, .dx, .jcamp | No | Please add in addition to zip if the automatically generated one has low quality[2.1] |
| NMRium | .nmrium | No | If NMRium data is available, you can add it additionally to the zip[2.2] |
| Generated files | Ending | Explanation |
|---|---|---|
| NMRium | .nmrium | is generated from zip if NMRium editor is selected (not automatically) [2.2] |
[2.1] the automatic processing from zip to jcamp with the embedded software gives sometimes bad results. In those cases, please provide a jcamp file that was processed with a suitable external software to allow the provision of clear, high quality data.
[2.2] NMRium is supported from version 1.5 of Chemotion ELN (March 2023).
Please take care that your files are given with an analysis including the listing of the observed signals. The information is supposed to be given as analyzed signals. Peak lists in form of non-analyzed signals (without coupling constants) are not suitable.
Mass spectrometry data
If you can't provide the supported data file types, please add an image (.jpg, .png). This should be avoided and only used if there is no option to get access to a digital file.
| Supported files (SF) | Ending | Required | Explanation |
|---|---|---|---|
| raw | .zip | (Yes) [3.1] | Original data from device [3.2] |
| MzML | .jdx, .dx, .jcamp | (Yes) [3.1] | |
| jcamp-dx | .jdx, .dx, .jcamp | (Yes) [3.1] | |
| Excel | .xlsx | (Yes) [3.1] | Supported by Converter - please refer to ChemConverter Profiles given below [3.3] |
| CSV | .jdx, .dx, .jcamp | (Yes) [3.1] | Supported by Converter - please refer to ChemConverter Profiles given below [3.3] |
| xy | .xy | (Yes) [3.1] | Supported by Converter - please refer to ChemConverter Profiles given below [3.3] |
[3.1] one of these files should be given.
[3.2] RAW data is supported for selected instruments of ThermoFisher currently.
[3.3] Excel and CSV: some standard versions are supported (see list below) and described in the section ChemConverter- for others, please contact us. You can find all ChemConverter Profiles here
| Ending | metadata converted | Identifier | Link |
|---|---|---|---|
| .xlsx | No | ||
| .csv | No | line1: "long name, units","mass over charge, m/z","intensity, %" | from Finnigan Mat 8230, EI-MS |
| .xy | No | line1: "mass_spectrometry, general_xy" | modified to allow the upload of pure tables without metadata |
The following files are generated after providing one or several supported file formats: For raw, MzMl, jcamp-dx:
| Generated files | Ending | Explanation |
|---|---|---|
| jcamp | .peak.jdx | is generated from zip with automated peak picking (not editable) |
| jcamp | .edit.jdx | is generated from jdx including manual editing |
| json | .infer.json | is automatically generated from .edit.jdx, data exchange format |
| png | .peak.png | is automatically generated from .peak.jdx |
| png | .edit.png | is automatically generated from .edit.jdx |
If the added file is .xy, then the following data file types are generated:
| Generated files | Ending | Explanation |
|---|---|---|
| BagIt | .zip | is generated from uploaded Excel, CSX or Text-File |
| jcamp | bagit.jdx | is generated from the supported file formats |
| jcamp | bagit.peak.jdx | is generated from zip with automated peak picking (not editable) |
| png | bagit.png | is automatically generated from .peak.jdx |
IR spectroscopy data
If you can't provide the supported data file types, please add an image (.jpg, .png). This should be avoided and only used if there is no option to get access to a digital file.
| Supported files | Ending | Required [4.1] | Explanation |
|---|---|---|---|
| jcamp-dx | .jdx, .dx, .jcamp | Yes | |
| Excel | .xlsx | Yes | Supported by ChemConverter - please refer to profiles given below [4.2] |
| CSV | .csv | Yes | Supported by ChemConverter - please refer to profiles given below [4.2] |
[4.1] One of the files in this list should be given.
[4.2] Excel and CSV: some standard versions are supported (see list below) and described in the section ChemConverter- for others, please contact us. You can find all ChemConverter Profiles here
| Ending | metadata converted | Identifier | Link |
|---|---|---|---|
| .xlsx | No | ||
| .csv | No |
| Generated files | Ending | Explanation |
|---|---|---|
| jcamp | .jdx | is generated from the supported file formats |
| jcamp | .peak.jdx | is generated from zip with automated peak picking (not editable) |
| jcamp | .edit.jdx | is generated from jdx including manual editing |
| png | .peak.png | is automatically generated from .peak.jdx |
| png | .edit.png | is automatically generated from .edit.jdx |
UV VIS spectroscopy data
If you can't provide the supported data file types, please add an image (.jpg, .png). This should be avoided and only used if there is no option to get access to a digital file.
| Supported files | Ending | Required [5.1] | Explanation |
|---|---|---|---|
| jcamp-dx | .jdx, .dx, .jcamp | Yes | but only if ##DATA TYPE= UV-VIS or UV/VIS SPECTRUM [5.3] |
| Excel | .xlsx | Yes | Supported by ChemConverter - please refer to profiles given below [5.2] |
| CSV | .csv | Yes | Supported by ChemConverter - please refer to profiles given below [5.2] |
| TEXT | .txt | Yes | Supported by ChemConverter - please refer to profiles given below [5.2] |
[5.1] One of the files in this list should be given.
[5.2] Excel, CSV, Text: some standard versions are supported (see list below) and described in the section ChemConverter- for others, please contact us. You can find all ChemConverter Profiles here
| Ending | metadata converted | Identifier | Link/comments |
|---|---|---|---|
| .txt | No | line1 "UV_spectrometry, general" | |
| .csv | No | ||
| .txt | No | line2 "601" | UV-VIS Horiba Duetta - KIT CN |
| Generated files | Ending | Explanation |
|---|---|---|
| BagIt | .zip | is generated from uploaded Excel, CSX or Text-File |
| jcamp | bagit.jdx | is generated from the supported file formats |
| jcamp | bagit.peak.jdx | is generated from zip with automated peak picking (not editable) |
| png | bagit.png | is automatically generated from .peak.jdx |
Fluorescence spectroscopy data
I.a. jcamp-dx data with "##DATA TYPE= FLUORESCENCE SPECTRUM". Currently work in process. [5.3] In the meantime you could edit your files to match "##DATA TYPE= UV-VIS or UV/VIS SPECTRUM".
XRD spectroscopy data
Status: in test phase - please contact us for questions: we can assist you to get your data represented.
Cyclic voltammetry data
If you can't provide the supported data file types, please add an image (.jpg, .png). This should be avoided and only used if there is no option to get access to a digital file. Data file types are dependent from your devices software / manufacturer. Please look at the table below.
| Supported files and manufacturer | Ending (case sensitive) | Required | Explanation |
|---|---|---|---|
| Gamry Framework DTA | .DTA | Yes | Supported by ChemConverter - please refer to profiles given below |
| PalmSens PSTrace | .pssession | Yes | Supported by ChemConverter - please refer to profiles given below |
| Metrohm Nova | .txt | Yes | Supported by ChemConverter - please refer to profiles given below |
IKA's csv files are currently in testing state.
| Ending | metadata converted | Identifier | Link/comments |
|---|---|---|---|
| .DTA | Yes | line3 TITLE == "Cyclic" | |
| .pssession | Yes | title == "Cyclic Voltammetry" | |
| .txt | No | column_00 == Potential applied (V) & column_02 == "WE(1).Current (A)" |
Elemental Analysis
| Supported files | Ending | Required | Explanation |
|---|---|---|---|
| PNG or JPEG | .png, .jpg | Yes | Files are not processed - coming soon |
Crystal structures
| Supported files | Ending | Required | Explanation |
|---|---|---|---|
| CIF | .cif | Yes | Files are not processed - coming soon |
| PNG | .png | Yes | Files are not processed - coming soon |
Circular dichroism spectroscopy (CD spectrometry)
Status: in test phase - please contact us for questions: we can assist you to get your data represented.
Adsorption and desorption
AIF Files
Status: in test phase - please contact us for questions: we can assist you to get your data represented.
Stefan Bräse group: advices in brief
| Method | device | to be provided | processing | Explanation |
|---|---|---|---|---|
| 1D NMR | all | Zip (+jcamp) [SB1] | Yes | jcamp needed if quality of processed file too low |
| 2D NMR | all | Zip (+jcamp) [SB1] | No | |
| mass | ThermoFisher (CS) | .raw | Yes | |
| mass | Advion Expression-L (CN) | .cdf | Yes | aut. conversion .datx -> .cdf |
| IR | Bruker Alpha (CS, CN) | .dx | Yes | aut. conversion .0 (OPUS) -> .dx |
| Raman | Bruker Multiram (CN) | .dx | tbd | aut. conversion .0 (OPUS) -> .dx |
| UV-Vis | Horiba (CN) | .txt | Yes | manual conversion .ezspec_data -> .txt |
| UV-Vis | Analytik Jena Specord 50 (CS) | .csv | tbd | aut. conversion .auv -> .csv |
| EA | EA (CS) | .png | No | |
| X-ray | all | .cif + png | No | |
| GC-FID/MS | Shimadzu GC/MS (CN) | .cdf (AIA(Andi)) | No | aut. conversion .gcd -> .cdf and .txt (ASCII); |
| GC-BID | Shimadzu GC-BID 2030 (CN) | .cdf (AIA(Andi)) | No | aut. conversion .gcd -> .cdf and .txt (ASCII); |
| TGA | TA Instruments (CN) | .xls | No | manual conversion .tri -> .xls |
| LC/MS | Agilent IQ (CN) | .cdf, .ms (AIA-Format), .dx (CDS2 raw-Format) | No | aut. conversion .sirstl -> .cdf, .ms and .dx |
| Polarimeter | Anton Paar MCP4100 (CN) | No | ||
| DSC | TA Instruments (CN/SML) | .xls | No | manual conversion .tri -> .xls |
[SB1] please ensure that the zip is the originally provided one. Don't collect data as zip on our own, don't add other data than the provided ones to the original file folder, please don't add mestre file to the zip. Please use the data provided by the instrument (eventually generate the zip from the obtained folder- without other changes).
Sonja Herres-Pawlis group: advices in brief
| Method | device | to be provided | processing | Explanation/comment |
|---|---|---|---|---|
| 1D NMR | all | Zip (+jcamp) | Yes | jcamp needed if quality of processed file too low |
| 2D NMR | all | Zip (+jcamp) | No | |
| mass | UHR-TOF Bruker Daltonik maXis II | .xy | Yes | file needs adaptation before upload![SHP1] |
| IR | Perkin Elmer BX FT-IR | .jdx | Yes | supported |
| UV-Vis | JASCO V770 | .dx | ||
| UV-Vis | CARY60 | .csv | Yes | supported, type "a" not added yet |
| EA | EA | .png | No | |
| X-ray | all | .cif + png | No | |
| CV | .mnova | Yes |
[SHP1] According to Table "mass spectrometry", the file needs to be opened and a new line on the top of the file has to be inserted: line1:
"mass_spectrometry, general_xy"
This additional line allows to identify the file and enables conversion.