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940aa0b
remove first paragraph to focus on Chemotion; add info box to link ch…
nap84 Apr 23, 2025
5547ce0
text fixes, add workshop info
nap84 Apr 23, 2025
3c6aa83
started new structure
nap84 Jun 23, 2025
11ce8d5
test
FabianFink Jun 23, 2025
1348252
General changes in the structure
FabianFink Jun 27, 2025
6020e17
Further general changes
FabianFink Jun 27, 2025
db01aaf
Section "Planning" finished
FabianFink Jun 27, 2025
ed94c75
Section "Experiment" finished
FabianFink Jun 27, 2025
8e126c5
Section "Data Generation" finished
FabianFink Jun 27, 2025
8e3ca73
Section "Data Collection" finished
FabianFink Jun 27, 2025
f9bc30d
Section "Analysis" finished
FabianFink Jun 27, 2025
cfa9da3
Section "Data Publication" finished by merging existing Repo information
FabianFink Jun 27, 2025
9bb2f62
Merge pull request #454 from FabianFink/eln-chemotion
jliermann Jun 30, 2025
75a7a66
Merge remote-tracking branch 'origin/main' into eln-chemotion
jliermann Jun 30, 2025
c79fe27
add chemotion eln logo
nap84 Jul 3, 2025
29ab025
fix: image placement
nap84 Jul 4, 2025
aa7eacf
add section header
nap84 Oct 21, 2025
d53dc3a
establish structure
nap84 Oct 21, 2025
81073cc
planning subpage
nap84 Oct 21, 2025
7b8331e
rename
nap84 Oct 22, 2025
6f821c1
create experiments sub page
nap84 Oct 22, 2025
dcb8eea
add placeholder img
nap84 Oct 22, 2025
8bdc0d4
add sub page link
nap84 Oct 22, 2025
bbdc4b0
add data gen sub page
nap84 Oct 22, 2025
8920db6
add data collection subpage
nap84 Oct 22, 2025
625ee8a
fix slug typo
nap84 Oct 22, 2025
db90bc1
add data analysis subpage
nap84 Oct 22, 2025
d069da0
edit title and id
nap84 Oct 22, 2025
e33cc92
add data publication subpage
nap84 Oct 22, 2025
2d52e3a
add links to subpages
nap84 Oct 22, 2025
88eab3c
fit titled to our data life cycle article; add comment
nap84 Oct 22, 2025
01d4551
rename rename
nap84 Oct 22, 2025
e7805ce
combine to data collection
nap84 Oct 22, 2025
9da76fa
add comment on data processing
nap84 Oct 22, 2025
72bf738
language edits
nap84 Oct 22, 2025
a96c088
add labimotion logo
nap84 Oct 22, 2025
9280243
proofread, edits, add comment
nap84 Oct 22, 2025
b34bbb7
rename to fix type
nap84 Oct 22, 2025
1aae191
camel script
nap84 Oct 22, 2025
7851e3a
rename to fit lifecycle
nap84 Oct 22, 2025
6d0582b
rename with camel script
nap84 Oct 22, 2025
c8f283a
proofread, edit
nap84 Oct 22, 2025
8a32a9b
proofread and edits
nap84 Oct 22, 2025
977d304
add nmrium logo
nap84 Oct 22, 2025
9bec154
fix nmrium logo alt text
nap84 Oct 22, 2025
903dba6
add repo logos
nap84 Oct 22, 2025
d670d70
add repo article and choose repo article links
nap84 Oct 22, 2025
2b60781
edit, add logo
nap84 Oct 22, 2025
253d923
Merge branch 'eln-chemotion-sepPages' into eln-chemotion
nap84 Oct 22, 2025
99e80c5
add some ideas for images
nap84 Nov 10, 2025
dd418f0
outline new changes that need to be made
nap84 Nov 13, 2025
4796996
add getting started points
nap84 Nov 13, 2025
590eedb
fix typo
nap84 Nov 13, 2025
5630017
review and integration of sharing/literature in Experiment Design
FabianFink Nov 13, 2025
99b9dd4
fix: improve anchor link
jliermann Nov 13, 2025
dc57d1e
Merge remote-tracking branch 'origin/main' into eln-chemotion
jliermann Nov 13, 2025
508a44e
add mailing list
nap84 Nov 17, 2025
8348ca1
chore: update dependencies
nap84 Nov 19, 2025
b5e8808
add and remove images
nap84 Nov 19, 2025
89ab3d9
add: data lifecycle img and icons
nap84 Nov 19, 2025
4742167
add banner image
nap84 Nov 19, 2025
5097287
fix: review and edit
nap84 Nov 19, 2025
c62ccc4
add: chemotion DoE banner img
nap84 Nov 19, 2025
54b1e93
add: alt text
nap84 Nov 19, 2025
9e9a697
add: banner image
nap84 Nov 19, 2025
1a7c5d3
add: bammer image file for experiment
nap84 Nov 19, 2025
8edd434
add: data collection banner
nap84 Nov 19, 2025
e27fb74
add: banner image
nap84 Nov 19, 2025
a755799
change: nmrium logo placement
nap84 Nov 19, 2025
a6f4218
add: publish banner
nap84 Nov 19, 2025
447983d
fix: improvelogo placement (attempted)
nap84 Nov 19, 2025
1f3feda
placeholder comment
nap84 Nov 19, 2025
b7bebec
fix: ajust numbering
nap84 Nov 19, 2025
daa6f9c
revert: renumber files
nap84 Nov 19, 2025
60e8c24
fixed incorrect link
FabianFink Nov 21, 2025
21129e8
Merge pull request #472 from FabianFink/eln-chemotion
jliermann Nov 25, 2025
5da4aff
Update 10_chemotion_eln.mdx
Ted-Bender Dec 2, 2025
5b63670
Update 20_chemotion_eln_experimentDesign.mdx
Ted-Bender Dec 2, 2025
417752b
Update 70_chemotion_eln_dataPublication.mdx
Ted-Bender Dec 2, 2025
2e0b258
add: reply
nap84 Dec 5, 2025
5608114
add: info on autogen SI (first draft)
nap84 Dec 5, 2025
ca0800b
modify: move paragraph to another section
nap84 Dec 5, 2025
7090b40
remove: comment
nap84 Dec 8, 2025
3b26bba
chore: add lifecycle as svg
jliermann Dec 8, 2025
0c194fb
Merge remote-tracking branch 'origin/main' into eln-chemotion
jliermann Dec 8, 2025
00f45e6
fix: remove unnec. nodes
jliermann Dec 8, 2025
ffd1015
fix: new export
jliermann Dec 8, 2025
74f56a8
refactor: group and add ids
jliermann Dec 8, 2025
261facf
add: intro sentence data re-use
nap84 Dec 8, 2025
3deea34
modify: file name
nap84 Dec 8, 2025
9c58ff8
modify: alt text
nap84 Dec 8, 2025
5adfdeb
fix: typo in alternative text
nap84 Dec 8, 2025
c42b4f8
feat: first prototype for lifecycle
jliermann Dec 8, 2025
1cb7886
Merge branch 'eln-chemotion' of https://github.com/NFDI4Chem/knowledg…
jliermann Dec 8, 2025
a41ad3e
feat: replace chemotion icons with svg, improve layout
jliermann Dec 8, 2025
6946a24
chore: include lockfile in git tracking
jliermann Dec 9, 2025
1286ba8
refactor: preferably use npm ci for localisation workflow
jliermann Dec 9, 2025
3594fa2
chore: upgrade packages
jliermann Dec 9, 2025
edf49aa
Merge remote-tracking branch 'origin/main' into eln-chemotion
jliermann Dec 9, 2025
c36d2e9
refactor: streamline svg
jliermann Dec 9, 2025
37c04f3
refactor: remove all matrix declarations, explicit coordinates
jliermann Dec 9, 2025
81b5992
feat: add ChemotionIcon component for consistent icon rendering
jliermann Dec 9, 2025
13ec56b
feat: implement translation for text elements in ChemotionLifecycle c…
jliermann Dec 9, 2025
43c1d83
fix: hover styles not applied when hovering over arrows
jliermann Dec 9, 2025
d5d442f
fix: update hover fill color to use CSS variable for consistency
jliermann Dec 9, 2025
ec81a5b
feat: reorganize page and add short text about re-use
jliermann Dec 9, 2025
68afffa
refactor: restructure Chemotion ELN documentation
jliermann Dec 9, 2025
612d29a
fix: update links in synthetic chemistry documentation for consistency
jliermann Dec 9, 2025
0b04411
fix: links
jliermann Dec 9, 2025
863a360
fix: update links in data publishing documentation for consistency
jliermann Dec 9, 2025
4d33a1e
fix: links
jliermann Dec 9, 2025
13eabc2
chore: rename
jliermann Dec 9, 2025
c52b046
feat: add screenshots as individual pngs
jliermann Dec 10, 2025
819ae90
refactor: improve layout
jliermann Dec 10, 2025
13b03b1
feat: allow custom float direction
jliermann Dec 10, 2025
1fd8b12
feat: add responsive ChemotionCarousel component with custom dots and…
jliermann Dec 10, 2025
bad61d1
feat: showcase ChemotionCarousel
jliermann Dec 10, 2025
7f4c580
feat: add box-shadow to ChemotionCarousel
jliermann Dec 10, 2025
a227d6c
refactor: improve optional staging parameters
jliermann Dec 10, 2025
7026ef0
fix: syntax error
jliermann Dec 10, 2025
55437d7
refactor: improve optional staging parameters
jliermann Dec 10, 2025
d046546
fix: correct sidebar position in Chemotion ELN documentation
jliermann Dec 10, 2025
8631285
chore: upgrade dependency tree
jliermann Dec 11, 2025
7658054
feat: improve appearance of carousel component
jliermann Dec 11, 2025
b9c1382
fix: limit vertical size of lifecycle image
jliermann Dec 11, 2025
e62e5cc
fix: improve styling of carousel
jliermann Dec 11, 2025
2d4f403
feat: make image width and margin configurable in ChemotionIcon compo…
jliermann Dec 11, 2025
78db798
fix: remove redundant attributes from text elements in ChemotionLifec…
jliermann Dec 11, 2025
d6dd06b
chore: add banners to chemotion pages
jliermann Dec 11, 2025
9cd5ca4
refactor: prepare float image component for broader use
jliermann Dec 11, 2025
b66bed1
refactor: replace ChemotionIcon with FloatImage for improved flexibility
jliermann Dec 11, 2025
6225ce2
fix: correct alt texts
jliermann Dec 11, 2025
0534eb2
fix: broken anchors
jliermann Dec 11, 2025
f8c964a
fix: rolling back unneeded id
jliermann Dec 11, 2025
e8eb07c
fix: url case
jliermann Dec 11, 2025
2f0dd66
refactor: change CustomDots to a regular function for consistency and…
jliermann Dec 11, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/localisation.yml
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ jobs:
java-version: "17"

- name: Install dependencies
run: npm install
run: npm ci || npm install

- name: Write translations
run: npm run write-translations
Expand Down
2 changes: 1 addition & 1 deletion .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ npm-debug.log*
yarn-debug.log*
yarn-error.log*
yarn.lock
package-lock.json
# package-lock.json
# config for staging
docusaurus.config.js
.Rproj.user
Expand Down
30 changes: 15 additions & 15 deletions docs/10_domains/60_synthetic_chemistry.mdx
Original file line number Diff line number Diff line change
Expand Up @@ -16,43 +16,43 @@ During the synthesis of a desired compound, all steps, such as planning, realisa

## Data Types

In synthetic chemistry different types of research data can be obtained. In general, this data is not limited to characterisation of synthesised products. A typical experiment starts with its design and planning, followed by carrying out the procedure in a laboratory setting. During realisation of an experiment, observations, experimental conditions, and yields are documented. Ideally, this manually collected research data is recorded digitally in an [Electronic Lab Notebooks (ELN)](/docs/eln/).
In synthetic chemistry different types of research data can be obtained. In general, this data is not limited to characterisation of synthesised products. A typical experiment starts with its design and planning, followed by carrying out the procedure in a laboratory setting. During realisation of an experiment, observations, experimental conditions, and yields are documented. Ideally, this manually collected research data is recorded digitally in an [Electronic Lab Notebooks (ELN)](/docs/eln).

The synthesis of a specific product is followed by analysing its properties. Regarding data collection, both manually determined and digital data can be obtained. Observations and results of analytical methods with no digital output (i.e., no data files) can be added manually to the ELN entry of the experiment, which include for example melting/boiling point, optical rotation, TLC Rf values, or refraction index. Digital data are obtained from analytical instruments, e.g., NMR, IR, MS. These data can be uploaded seamlessly from the analytical devices to an ELN and analysed therein. An overview on file extensions, file sizes and converters for several analytical methods is given in the table below. It is recommended to save raw data files in [proprietary file formats](/docs/format_standards/) alongside interoperable [open file formats](/docs/format_standards/) by using converters or the software of the analytical device. If no specific open format is currently available, export as .txt or .csv is recommended.
The synthesis of a specific product is followed by analysing its properties. Regarding data collection, both manually determined and digital data can be obtained. Observations and results of analytical methods with no digital output (i.e., no data files) can be added manually to the ELN entry of the experiment, which include for example melting/boiling point, optical rotation, TLC Rf values, or refraction index. Digital data are obtained from analytical instruments, e.g., NMR, IR, MS. These data can be uploaded seamlessly from the analytical devices to an ELN and analysed therein. An overview on file extensions, file sizes and converters for several analytical methods is given in the table below. It is recommended to save raw data files in [proprietary file formats](/docs/format_standards) alongside interoperable [open file formats](/docs/format_standards) by using converters or the software of the analytical device. If no specific open format is currently available, export as .txt or .csv is recommended.

Overall, [metadata](/docs/metadata/) should always be included when collecting and [storing](/docs/data_storage/) data to allow understanding of the research data in the long term.
Overall, [metadata](/docs/metadata) should always be included when collecting and [storing](/docs/data_storage) data to allow understanding of the research data in the long term.

## ELNs and Other Tools

For effective data management, software tools should be selected in a uniform manner within a project or research group with the aim to [organize](/docs/data_organisation)
and streamline workflows. This involves establishing clear usage guidelines, including metadata templates drawn from minimum information standards for a given method, where available.
These should be outlined in a [data management plan (DMP)](/docs/dmp) for each project. NFDI4Chem provides an [RDMO template](https://rdmo.nfdi4chem.de/) specifically tailored to the needs of chemists.
These should be outlined in a [data management plan (DMP)](/docs/dmp) for each project. NFDI4Chem provides an [RDMO template](https://rdmo.nfdi4chem.de) specifically tailored to the needs of chemists.

If you want your data to comply with the [FAIR principles](/docs/fair/) it can be very tedious and extremely time consuming if you try to apply the FAIR principles to your data retrospectively if your existing workflows involve a large degree of analogue documentation (e.g. paper lab notebooks). The reality is that you need tools to take care of certain aspects of the FAIR principles automatically so you don’t have to apply them manually each time. [Electronic Lab Notebooks (ELNs)](/docs/eln/) are very powerful tools that can help you with this. Depending on what ELN you use, the [metadata](/docs/metadata/) can be automatically assigned in both human and [machine-readable formats](/docs/format_standards/). Furthermore, some ELNs can automatically generate interoperable [open file formats](/docs/format_standards/#chemistry_formats) for your analytical data. Choosing the right ELN can be challenging and this process should be thought about and carried out carefully. You can find out more on [how to choose the right ELN here](/docs/choose_eln/):
If you want your data to comply with the [FAIR principles](/docs/fair) it can be very tedious and extremely time consuming if you try to apply the FAIR principles to your data retrospectively if your existing workflows involve a large degree of analogue documentation (e.g. paper lab notebooks). The reality is that you need tools to take care of certain aspects of the FAIR principles automatically so you don’t have to apply them manually each time. [Electronic Lab Notebooks (ELNs)](/docs/eln) are very powerful tools that can help you with this. Depending on what ELN you use, the [metadata](/docs/metadata) can be automatically assigned in both human and [machine-readable formats](/docs/format_standards). Furthermore, some ELNs can automatically generate interoperable [open file formats](/docs/format_standards/#chemistry_formats) for your analytical data. Choosing the right ELN can be challenging and this process should be thought about and carried out carefully. You can find out more on [how to choose the right ELN here](/docs/choose_eln):

<ElnFinder subDisc="Synthetic chemistry" />

A tool to help you find the right ELN is the so-called [ELN finder](https://eln-finder.ulb.tu-darmstadt.de/home) which is a searchable online repository for many different ELNs. It is important to note that not one size fits all and that one ELN may be appropriate for one research group, another ELN may be more appropriate for a different research group. Within NFDI4Chem, Chemotion ELN is the reference instance (find out more here in our [knowledge base article overview of Chemotion](/docs/chemotion_eln/)). This means that our developments in automatically applying the FAIR data principles to research data are implemented in Chemotion first.
A tool to help you find the right ELN is the so-called [ELN finder](https://eln-finder.ulb.tu-darmstadt.de/home) which is a searchable online repository for many different ELNs. It is important to note that not one size fits all and that one ELN may be appropriate for one research group, another ELN may be more appropriate for a different research group. Within NFDI4Chem, Chemotion ELN is the reference instance (find out more here in our [knowledge base article overview of Chemotion](/docs/chemotion)). This means that our developments in automatically applying the FAIR data principles to research data are implemented in Chemotion first.

Chemotion is especially suitable for synthetic chemistry as it originally started out as an ELN for synthetic chemistry but has now been extended to a wider array of scientific disciplines through its [LabIMotion extension](https://chemotion.net/docs/labimotion).

## Publishing Data

[Publishing research data](/docs/data_publishing/) is important in order to allow for the reuse of data by other researchers or for machine learning. Especially for machine learning, it is crucial that the data is published in a structured and standardised way. Where can you publish your data? Open access [data repositories](/docs/repositories/) are a good solution to provide your data for reuse by others. Choosing the right repository is crucial and as a general rule of thumb it is better to deposit your data in data-specific or discipline-specific repositories as these enforce more standardisation in how the data are published thus allowing for better machine-readability.
[Publishing research data](/docs/data_publishing) is important in order to allow for the reuse of data by other researchers or for machine learning. Especially for machine learning, it is crucial that the data is published in a structured and standardised way. Where can you publish your data? Open access [data repositories](/docs/repositories) are a good solution to provide your data for reuse by others. Choosing the right repository is crucial and as a general rule of thumb it is better to deposit your data in data-specific or discipline-specific repositories as these enforce more standardisation in how the data are published thus allowing for better machine-readability.

In order to reach as many researchers as possible, choosing the right repository can be crucial (more on this in the [article on choosing the right repository](/docs/choose_repository/)).
In order to reach as many researchers as possible, choosing the right repository can be crucial (more on this in the [article on choosing the right repository](/docs/choose_repository)).

Above you can see a modified version of our decision tree from our guide how to choose the right repository. Here is a table giving an overview of what data fits into what repository:

{/* prettier-ignore-start */}
| Data type | Data format | Suggested Repository | Criteria for selection |
| :---- | :---- | :---- | :---- |
| Nuclear Magnetic Resonance | Bruker XWIN-NMR format (zip), [JCAMP-DX](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/JCAMP-DX/) | [**Chemotion**](https://www.chemotion-repository.net/welcome) | Passing basic checks, curation |
| Nuclear Magnetic Resonance | Bruker XWIN-NMR format, JOEL format NMReData, nmrML, ISA JSON | [**nmrXiv**](https://docs.nmrxiv.org/) | Validations / Minimum information reporting standards |
| Molecules and their properties, identification, reactions and experimental investigations | mass spectrometry: JCAMP-DX, [mzMl](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/mzML/), mzXML (open, visualisable and processable), RAW for selected mass data types (processed and converted in JCAMP-DX), IR and Raman: JCAMP-DX, XRD: JCAMP-DX, UV/VIS: JCAMP-DX, Cyclic voltammetry: JCAMP-DX. \*Chemotion repo offers the option to convert data from different file formats into JCAMP-DX. | [**Chemotion**](https://www.chemotion-repository.net/welcome) | Passing basic checks, curation |
| Inorganic crystal structures | Crystallographic Information File (CIF) | [**ICSD**](https://icsd.fiz-karlsruhe.de/) | Crystal structure data available |
| Organic and metal-organic crystal structures | Crystallographic Information File (CIF) but other supporting file formats accepted | [**CSD**](https://www.ccdc.cam.ac.uk/structures/) | Cell parameters (single crystal), full coordinates (powder), in CIF format |
| Organic, inorganic and metal-organic crystal structure data | primarily Crystallographic Information File (CIF) but other supporting file formats accepted | [**joint CCDC/FIZ Access Structures ServiceD**](https://www.ccdc.cam.ac.uk/structures//) | At least one CIF file must be included in the submission and structure factor data for all structures should be provided (if possible) |
| Nuclear Magnetic Resonance | Bruker XWIN-NMR format (zip), [JCAMP-DX](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/JCAMP-DX) | [**Chemotion**](https://www.chemotion-repository.net/welcome) | Passing basic checks, curation |
| Nuclear Magnetic Resonance | Bruker XWIN-NMR format, JOEL format NMReData, nmrML, ISA JSON | [**nmrXiv**](https://docs.nmrxiv.org) | Validations / Minimum information reporting standards |
| Molecules and their properties, identification, reactions and experimental investigations | mass spectrometry: JCAMP-DX, [mzMl](https://knowledgebase.nfdi4chem.de/knowledge_base/docs/mzML), mzXML (open, visualisable and processable), RAW for selected mass data types (processed and converted in JCAMP-DX), IR and Raman: JCAMP-DX, XRD: JCAMP-DX, UV/VIS: JCAMP-DX, Cyclic voltammetry: JCAMP-DX. \*Chemotion repo offers the option to convert data from different file formats into JCAMP-DX. | [**Chemotion**](https://www.chemotion-repository.net/welcome) | Passing basic checks, curation |
| Inorganic crystal structures | Crystallographic Information File (CIF) | [**ICSD**](https://icsd.fiz-karlsruhe.de) | Crystal structure data available |
| Organic and metal-organic crystal structures | Crystallographic Information File (CIF) but other supporting file formats accepted | [**CSD**](https://www.ccdc.cam.ac.uk/structures) | Cell parameters (single crystal), full coordinates (powder), in CIF format |
| Organic, inorganic and metal-organic crystal structure data | primarily Crystallographic Information File (CIF) but other supporting file formats accepted | [**joint CCDC/FIZ Access Structures ServiceD**](https://www.ccdc.cam.ac.uk/structures/) | At least one CIF file must be included in the submission and structure factor data for all structures should be provided (if possible) |
| Generic data from all disciplines of chemistry, all data that do not fit in the disciplinary repositories | format-independent | [**RADAR4Chem**](https://www.radar-service.eu/de) | Validation against metadata schema |
{/* prettier-ignore-end */}

Expand All @@ -64,4 +64,4 @@ While for some data types & workflows it may be obvious how to comply with the F

Many old devices do not put out open-data formats and some devices have no digital output at all which makes good RDM more challenging though not impossible given the right tools (e.g. Chemotion’s [ChemConverter](https://chemotion.net/docs/services/chemconverter) which automatically generates open file formats from analytical devices which are not capable of outputting them).

One of the biggest challenges to RDM in Chemistry at the moment is the lack of inter-ELN interoperability. This means that it is very challenging if not impossible to transfer data between different ELNs. This makes it especially challenging for interdisciplinary collaborations where collaborating groups use different ELNs. There are, however, efforts underway to establish inter-ELN interoperability such as the [ELN consortium](https://github.com/TheELNConsortium/) of which Chemotion is a member.
One of the biggest challenges to RDM in Chemistry at the moment is the lack of inter-ELN interoperability. This means that it is very challenging if not impossible to transfer data between different ELNs. This makes it especially challenging for interdisciplinary collaborations where collaborating groups use different ELNs. There are, however, efforts underway to establish inter-ELN interoperability such as the [ELN consortium](https://github.com/TheELNConsortium) of which Chemotion is a member.
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