diff --git a/.github/workflows/localisation.yml b/.github/workflows/localisation.yml index d0535179..316e9a33 100644 --- a/.github/workflows/localisation.yml +++ b/.github/workflows/localisation.yml @@ -29,7 +29,7 @@ jobs: java-version: "17" - name: Install dependencies - run: npm ci || npm install + run: npm ci - name: Write translations run: npm run write-translations diff --git a/docs/10_domains/60_synthetic_chemistry.mdx b/docs/10_domains/60_synthetic_chemistry.mdx index 56e67019..c055d04b 100644 --- a/docs/10_domains/60_synthetic_chemistry.mdx +++ b/docs/10_domains/60_synthetic_chemistry.mdx @@ -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): -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 */} @@ -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. diff --git a/docs/40_smartlab/00_smartlab.mdx b/docs/40_smartlab/00_smartlab.mdx index 2e289688..109b8c95 100644 --- a/docs/40_smartlab/00_smartlab.mdx +++ b/docs/40_smartlab/00_smartlab.mdx @@ -13,14 +13,14 @@ import useBaseUrl from "@docusaurus/useBaseUrl"; A smart lab represents a holistic approach to [data management](/docs/data_guide) in chemistry with seamless data flows. What does this mean? It means that all steps within a researcher's [workflow](/docs/domain_guide) across the [research data lifecycle](/docs/data_life_cycle) are interconnected in a digital way. The key difference to a [Laboratory Management System (LIMS)](https://en.wikipedia.org/wiki/Laboratory_information_management_system) is that the Smart Lab's main focus is the realisation of the [FAIR data principles](/docs/fair). For example, a researcher plans and [documents](/docs/data_documentation) their experiment in an [electronic lab notebook (ELN)](/docs/eln). Any experimental data from devices such as spectrometers are then directly ingested by the ELN via [Application Programming Interfaces (APIs)](https://en.wikipedia.org/wiki/API). -The ELN then ideally assigns all the necessary [metadata](/docs/metadata) automatically and appropriately for a corresponding workflow and converts proprietary [data formats](/docs/format_standards) to open data formats. The ELN structures the (meta)data and experimental descriptions in a meaningful and sustainable way which is both human- and machine-readable (e.g., via the use of [machine-readable chemical structures](/docs/machine-readable_chemical_structures). When the researcher chooses to [publish](/docs/data_publishing) or [archive](/docs/data_storage) their data, it is then ingested seamlessly by a data [repository](/docs/repositories) or archive without much further work as the ELN has already appropriately prepared the dataset to meet a repository’s or archive’s [requirements](/docs/choose_repository). +The ELN then ideally assigns all the necessary [metadata](/docs/metadata) automatically and appropriately for a corresponding workflow and converts proprietary [data formats](/docs/format_standards) to open data formats. The ELN structures the (meta)data and experimental descriptions in a meaningful and sustainable way which is both human- and machine-readable (e.g., via the use of [machine-readable chemical structures](/docs/machine-readable_chemical_structures)). When the researcher chooses to [publish](/docs/data_publishing) or [archive](/docs/data_storage) their data, it is then ingested seamlessly by a data [repository](/docs/repositories) or archive without much further work as the ELN has already appropriately prepared the dataset to meet a repository’s or archive’s [requirements](/docs/choose_repository). In this section, key components of the smart lab will be introduced to you. ## Get started: diff --git a/docs/40_smartlab/15_choose_eln.mdx b/docs/40_smartlab/15_choose_eln.mdx index cf8f00e7..0e0273e6 100644 --- a/docs/40_smartlab/15_choose_eln.mdx +++ b/docs/40_smartlab/15_choose_eln.mdx @@ -14,25 +14,25 @@ Therefore, choosing the right ELN is crucial for a successful implementation of :::caution Needs assessment -- Analysing current situation (budget, IT resources, software environment) -- Definition of important features -- ELN concept (generic, discipline-specific) -- Drawing on experiences of other research Institutions - ::: +- Analysing current situation (budget, IT resources, software environment) +- Definition of important features +- ELN concept (generic, discipline-specific) +- Drawing on experiences of other research Institutions + ::: :::info Testing the selected products -- Demo versions or free trial access for individual users -- Testing no more than 2-3 ELNs -- In-depth testing using real-life use cases from the lab - ::: +- Demo versions or free trial access for individual users +- Testing no more than 2-3 ELNs +- In-depth testing using real-life use cases from the lab + ::: :::tip Introducing the chosen ELN -- Run training courses, training material -- Designate contact persons from the test team -- Continuous mentoring - ::: +- Run training courses, training material +- Designate contact persons from the test team +- Continuous mentoring + ::: ### Criteria for selecting an ELN @@ -62,21 +62,21 @@ There are a plethora of ELNs available and it is not always easy to figure out w ### Testing an ELN -Fortunately, you do not always have to install a separate instance to test ELN. At [link](https://demo.chemotion.scc.kit.edu/), the Chemotion team hosts a constantly growing number of test installations of various ELNs that you can try out free of charge. +Fortunately, you do not always have to install a separate instance to test ELN. The Chemotion team hosts a constantly growing number of [test installations](https://demo.chemotion.scc.kit.edu/) of various ELNs that you can try out free of charge. ### Set up your own ELN There are several ways to set up an electronic lab notebook (ELN) for your team: -- Run an ELN instance on a local server. For example, Chemotion, NFDI4Chem's favourite ELN, can be installed on a server in your data centre or institute. This allows your team to work completely independently: you can customise the ELN, add device connections as needed, and manage users yourself. You can use a Docker container to easily set up your local instance. Alternatively, you can build it from scratch for full flexibility. Click here for a detailed technical description. -- Use an ELN instance hosted in the cloud. "ELN as a service is a convenient way to test the functionality first. This option is also interesting for smaller teams who are concerned about the effort involved in setting up an ELN on a local server. NFDI4Chem is in the process of setting up Chemotion and some other open source solutions as an ELN as a service. To find out more about when this will be available, please get in touch. +- Run an ELN instance on a local server. For example, Chemotion, NFDI4Chem's favourite ELN, can be installed on a server in your data centre or institute. This allows your team to work completely independently: you can customise the ELN, add device connections as needed, and manage users yourself. You can use a Docker container to easily set up your local instance. Alternatively, you can build it from scratch for full flexibility. Click here for a detailed technical description. +- Use an ELN instance hosted in the cloud. "ELN as a service is a convenient way to test the functionality first. This option is also interesting for smaller teams who are concerned about the effort involved in setting up an ELN on a local server. NFDI4Chem is in the process of setting up Chemotion and some other open source solutions as an ELN as a service. To find out more about when this will be available, please get in touch. ### Contact Us You can contact us at any step of the process: -- whether you want to know more about ELNs, need a demonstration of an ELN, a test installation of an ELN or are simply thinking about one. -- if you want to install an ELN, need help with IT issues etc. -- want additional features in a running instance etc. +- whether you want to know more about ELNs, need a demonstration of an ELN, a test installation of an ELN or are simply thinking about one. +- if you want to install an ELN, need help with IT issues etc. +- want additional features in a running instance etc. Just send an email to [Link](mailto:helpdesk@nfdi4chem.de) with your questions or requests. diff --git a/docs/40_smartlab/20_chemotion_eln.mdx b/docs/40_smartlab/20_chemotion_eln.mdx deleted file mode 100644 index ef207339..00000000 --- a/docs/40_smartlab/20_chemotion_eln.mdx +++ /dev/null @@ -1,56 +0,0 @@ ---- -title: "Chemotion ELN" -slug: "/chemotion_eln" -id: "chemotion_eln" ---- - -import VideoPrivacy from "video-privacy"; -import useBaseUrl from "@docusaurus/useBaseUrl"; - -# Chemotion ELN - -[NFDI4Chem](https://www.nfdi4chem.de/) will support those ELNs that are relevant for documentation of chemical research activities. This support will include hosting one ELN instance for each of the relevant ELNs at KIT for teaching and training purposes. This service was established in 2022 to allow all scientists to compare ELNs and their functionalities. [Comparing and testing different ELNs](/docs/choose_eln) is a prerequisite for making the right choice. Furthermore, NFDI4Chem organises various seminars with the goal of giving a first impression of different ELNs. These seminars are a good opportunity for ELN providers to demonstrate their ELN's usefulness and possible applications. For past and forthcoming seminars, please see the [Stammtisch event page](https://www.nfdi4chem.de/index.php/event/stammtisch-chemotion/). - -## Chemotion ELN - -Chemotion is the ELN reference instance in NFDI4Chem. The Chemotion ELN is developed by several software developers at different NFDI4Chem sites. The ELN development started at the [Karlsruhe institute of Technology (KIT)](https://www.kit.edu/) in Karlsruhe as part of a DFG-funded project. The extension of the software was and is further supported by the [State Ministry of Baden-Wuerttemberg for Sciences, Research and Arts](https://mwk.baden-wuerttemberg.de/), the Karlsruhe Institute of Technology, and the [German Research Foundation (DFG)](https://www.dfg.de/). - -The Chemotion ELN was designed for chemists and adapted to the special requirements of chemical laboratory work and documentation. It therefore serves as a digitalization instrument for work in chemistry, developed to overcome the current limitations of the existing systems. To reach this goal, the development, improvement, and extension of the ELN is a community effort. - -The ELN is also used in other disciplines beyond chemistry as it offers a broad generic functionality to meet the needs of scientists working in interdisciplinary environments. These generic functions are still being extended and adapted. The latest generic extension (from November 2023) is [LabIMotion](https://www.chemotion.net/docs/labimotion), which allows completely non-chemical functionalities to be used by designing new modules. - -Chemotion ELN offers a specific function that facilitates the [publication of research data](/docs/data_publishing): it supports the transfer of data from a user's ELN account to a research data repository. This function reduces the scientists' effort in allowing access to research data, which is required by many funding agencies and helpful for the publication of scientific text publications. Currently, the ELN supports the transfer of data to the [Chemotion repository](https://www.chemotion-repository.net/welcome). Additionally, Chemotion Repository is connected to other databases (e.g. [PubChem](https://pubchem.ncbi.nlm.nih.gov/)) and repositories (e.g. [NMRShiftDB2](https://nmrshiftdb.nmr.uni-koeln.de/), soon to be superseded by [nmrXiv](https://nmrxiv.org/)), to ensure best visibility and a user-friendly search of original research data. The NFDI4Chem team is working on establishing connections to further repositories, in particular, the repositories supported and recommended by NFDI4Chem. - -A short introduction to the Chemotion ELN as well as the connection to the Chemotion repository is demonstrated in this video: - - - - - -### Documentation, information, and contact - -Chemotion ELN and its functions were described in various publications (see [below](#sources-and-further-information)). For users, developers, and admins, a documentation is available via the project's [website](https://www.chemotion.net/docs). Chemotion ELN is an Open Source development; the source code is available on [GitHub](https://github.com/ComPlat/chemotion_ELN). - -## Sources and further information - -- [Chemotion mailing list for Users and Admins](https://www.lists.kit.edu/sympa/subscribe/chemotion_eln) -- [Chemotion ELN: an Open Source electronic lab notebook for chemists in academia](https://doi.org/10.1186/s13321-017-0240-0) -- [Chemotion-ELN part 2: adaption of an embedded Ketcher editor to advanced research applications](https://doi.org/10.1186/s13321-018-0292-9) -- [CHEMSCANNER: extraction and re-use(ability) of chemical information from common scientific documents containing ChemDraw files](https://doi.org/10.1186/s13321-019-0400-5) -- [Chemotion ELN documentation](https://chemotion.net/docs/eln) -- [Chemotion ELN on Github](https://github.com/ComPlat/chemotion_ELN) diff --git a/docs/40_smartlab/41_chemotion_eln/10_chemotion.mdx b/docs/40_smartlab/41_chemotion_eln/10_chemotion.mdx new file mode 100644 index 00000000..3d43c5da --- /dev/null +++ b/docs/40_smartlab/41_chemotion_eln/10_chemotion.mdx @@ -0,0 +1,195 @@ +--- +title: "Chemotion ELN" +slug: "/chemotion" +sidebar_position: "99" +--- + +# Chemotion ELN + +import VideoPrivacy from "video-privacy"; +import useBaseUrl from "@docusaurus/useBaseUrl"; + +import styles from "@site/src/css/video.module.css"; + +import FloatImage from "@site/src/components/commons/FloatImage"; + +import ChemotionLifecycle from "@site/src/components/chemotion/ChemotionLifecycle"; + + + +:::info +To find out about choosing an ELN, head to the [Choose the right ELN +article](/docs/choose_eln) and test demo instances [here](https://demo.chemotion.scc.kit.edu/). +::: + +:::tip +Want to dive right in? Check out the [Getting Started](#getting_started) section! +::: + +The Chemotion ELN has been specifically designed for chemists, taking into account the unique requirements of chemical laboratory work and documentation. It serves as a powerful digitalization tool for chemistry, aimed at creating seamless workflows throughout the [reseach data life cycle](/docs/data_life_cycle). Achieving this vision is a collaborative effort involving continuous development, enhancement, and expansion of the ELN. + +To get an overview on how and with which tools Chemotion ELN supports you throughout the whole [reseach data life cycle](/docs/data_life_cycle), have a look at the sections below and find out more detailed information about the single steps by clicking the link in the respective section. + +## Data Life Cycle Support + +--- + + + +### Experiment Design {#experiment_design} + +Chemotion assists in experiment design and planning research by offering embedded _structure editors_, reading and generating _chemical identifiers_, and pulling information from relevant _databases_. + +[Find out more](/docs/chemotion_experimentDesign) + +--- + + + +### Experiment {#experiment} + +During experiments, Chemotion supports researchers with _automated calculations_, _structured documentation_, and a _concise overview_ of experimental information. + +[Find out more](/docs/chemotion_experiment) + +--- + + + +### Data Collection and Processing {#collection_processing} + +For seamless workflows, _analytical devices_ can be connected and directly accessed within the Chemotion ELN. Besides this connection, data from these devices can be automatically transferred, file formats are converted, and metadata is mapped. + +[Find out more](/docs/chemotion_dataCollection) + +--- + + + +### Analysis {#analysis} + +Analyses can be performed directly in the Chemotion ELN by utilizing one of the embedded _spectra editors_. + +[Find out more](/docs/chemotion_analysis) + +--- + + + +### Data Publication {#publication} + +The Chemotion ELN is connected to several _data repositories_. Incorperated publishing workflows allow for simple and fast publication of research data. + +[Find out more](/docs/chemotion_dataPublication) + +--- + + + +### Data Re-Use {#reuse} + +Chemotion ELN enables easy _sharing_ of data and entries with collaborators. Additionally, both your own data as well as those of group members can be reused for new experiments. + +--- + +## LabIMotion + +In addition to its primary focus on chemistry, the ELN is also utilized in various other disciplines due to its versatile functionality that caters to the needs of scientists operating in interdisciplinary environments. These generic elements are continually being refined and adapted. The latest extension, introduced in November 2023, is [LabIMotion](https://www.chemotion.net/docs/labimotion), which enables users to incorporate entirely non-chemical functionalities by designing new modules. + +## Chemotion Introductory Video + +A short introduction to the Chemotion ELN as well as the connection to the Chemotion repository is demonstrated in this video: + + + + + +## Documentation, Information, and Contact + +Chemotion ELN and its functionalities are described in various publications (see [below](#sources)). For users, developers, and admins, a documentation is available via the project's [website](https://www.chemotion.net/docs). Chemotion ELN is an Open Source development; the source code is available on [GitHub](https://github.com/ComPlat/chemotion). + +Chemotion is the ELN reference instance in [NFDI4Chem](https://www.nfdi4chem.de/). The software is developed by several developers at different NFDI4Chem sites. The development started at the [Karlsruhe institute of Technology (KIT)](https://www.kit.edu/) as part of a DFG-funded project. The extension of the software was and is further supported by the [State Ministry of Baden-Wuerttemberg for Sciences, Research and Arts](https://mwk.baden-wuerttemberg.de/), the Karlsruhe Institute of Technology, and the [German Research Foundation (DFG)](https://www.dfg.de/). + +NFDI4Chem offers hands-on workshop and Q&A sessions for Chemotion ELN and the LabIMotion extension. Visit the [workshop overview page](https://www.nfdi4chem.de/workshops/) for more information. + +### Getting Started {#getting_started} + +#### Newcomers + +There are various ways for newcomers to begin using Chemotion and get to know the software: + +- Check out the [Chemotion Docs](https://chemotion.net/docs): instructions on both the Chemotion ELN and the Chemotion Repo +- Check out the official [Chemotion Demo Instance](https://demo.chemotion.ibcs.kit.edu/). +- Check out the [Chemotion Tutorial Videos](https://chemotion.net/docs/eln/videos): familiarize yourself with the user interface and the features +- Attend an online [Live Demo & Q&A Session](https://www.nfdi4chem.de/event/chemotion-demo-qa-session/) +- Attend a [Chemotion ELN Hands-on Workshop](https://www.nfdi4chem.de/event/chemotion-eln-hands-on-workshop/) +- Sign up for the [chemotion mailing list for users and admins](https://www.lists.kit.edu/sympa/subscribe/chemotion) to stay up to date + +#### Establishing Chemotion ELN in your Group + +- Before you start rolling out Chemotion ELN in your research group, setup a sharing policy. See [Sharing is Caring: Guidelines for Sharing in the Electronic Laboratory Notebook (ELN) Chemotion as applied by a Synthesis-oriented Working Group](https://doi.org/10.1002/cmtd.202200026) for guidance. +- Install [ChemConverter profiles](https://chemotion.net/docs/services/chemconverter/profiles) for any file types that need conversion. +- Establish internal processes for data publication, such as [approval workflows for groups leads](https://chemotion.net/docs/repo/workflow/group_lead_review). See also the [workflow for publishing to the Chemotion Repo](https://chemotion.net/docs/repo/workflow). +- Clearly communicate the above policies and workflows to new group members during the onboarding process. +- Establish clear offboarding policies and workflows to ensure the necessary measures are [taken to revoke access](https://chemotion.net/docs/eln/admin/user_management#de-activating-vs-un-locking-an-account) and ensure others in the group maintain access, where needed. +- Setup your chemical [Inventory](https://chemotion.net/docs/eln/ui/inventory) for your group and ensure correct access to it. You can [import and export](https://chemotion.net/docs/eln/ui/inventory#import-and-export-chemicals) chemical lists, as well. +- Setup [LabIMotion templates](https://chemotion.net/docs/labimotion/design-principles) to expand and customize the ELN to fit your needs. You may also visit a [LabIMotion Online Hands-on Workshop](https://www.nfdi4chem.de/event/labimotion-online-hands-on-workshop/) to familiarize yourself with this feature. + +### Publications, Sources, and Further Information {#sources} + +- [Chemotion ELN: an Open Source electronic lab notebook for chemists in academia](https://doi.org/10.1186/s13321-017-0240-0) +- [Chemotion-ELN part 2: adaption of an embedded Ketcher editor to advanced research applications](https://doi.org/10.1186/s13321-018-0292-9) +- [CHEMSCANNER: extraction and re-use(ability) of chemical information from common scientific documents containing ChemDraw files](https://doi.org/10.1186/s13321-019-0400-5) +- [Chemotion ELN documentation](https://chemotion.net/docs/eln) +- [Chemotion ELN on Github](https://github.com/ComPlat/chemotion) diff --git a/docs/40_smartlab/41_chemotion_eln/20_chemotion_experimentDesign.mdx b/docs/40_smartlab/41_chemotion_eln/20_chemotion_experimentDesign.mdx new file mode 100644 index 00000000..17e8b63f --- /dev/null +++ b/docs/40_smartlab/41_chemotion_eln/20_chemotion_experimentDesign.mdx @@ -0,0 +1,38 @@ +--- +title: "Experiment Design" +slug: "/chemotion_experimentDesign" +--- + +# Chemotion ELN: Experiment Design + +import useBaseUrl from "@docusaurus/useBaseUrl"; +import ChemotionCarousel from "@site/src/components/chemotion/ChemotionCarousel"; + + + +In the Chemotion ELN, various entry types can be generated for planning various experimental setups. Generally, all entry types offer the possibility to draw chemical structures directly within the ELN. This is realized by embedded structure editors: _ketcher-rails_ and _Ketcher 2_ are integrated as default structure editors, while _ChemDraw JS_ and _Marvin JS_ can be integrated when the needed licences are available. + +All structure editors directly convert the chemical structures into common chemical identifiers such as [_InChI_](https://www.inchi-trust.org/) and notations such as [_SMILES_](https://doi.org/10.1021%2Fci00057a005) code and automatically generate a MOL file of the chemical structure. Conversely, chemical structures can be generated in the ELN by importing the codes and files mentioned above as well as by [_CAS numbers_](https://www.cas.org/cas-data/cas-registry). + +The Chemotion ELN directly pulls information from and links entries to databases such as [_PubChem_](https://pubchem.ncbi.nlm.nih.gov/) and [_CAS SciFinder_](https://www.cas.org/solutions/cas-scifinder-discovery-platform/cas-scifinder). Thus, the planning of experiments is facilitated as all relevant information is automatically integrated into the ELN entries. + +Furthermore, the Chemotion ELN offers the possibility to link (text) publications directly to the ELN entries as references using [persistant identifiers](/docs/pid) such as DOIs. With this, the ELN allows you to directly connect corresponding literature to experiments so you can cite and reference your own published work, experiments performed by others, or related publications. + +Oftentimes, projects or experiments require collaboration and exchange with other scientists. The Chemotion ELN allows for a simple sharing of ELN entries and corresponding data. Depending on the selected permission and detail levels, collaborators can access and edit shared data in the ELN. If you want to find out more about sharing in the Chemotion ELN and exemplarily sharing guidelines, have a look at this [publication](https://doi.org/10.1002/cmtd.202200026). diff --git a/docs/40_smartlab/41_chemotion_eln/30_chemotion_experiment.mdx b/docs/40_smartlab/41_chemotion_eln/30_chemotion_experiment.mdx new file mode 100644 index 00000000..9486583b --- /dev/null +++ b/docs/40_smartlab/41_chemotion_eln/30_chemotion_experiment.mdx @@ -0,0 +1,32 @@ +--- +title: "Experiment" +slug: "/chemotion_experiment" +--- + +# Chemotion: Experiment + +import useBaseUrl from "@docusaurus/useBaseUrl"; +import ChemotionCarousel from "@site/src/components/chemotion/ChemotionCarousel"; + + + +As relevant information on chemical compounds such as molar mass, density, and purity are stored within the ELN, Chemotion automatically calculates all relevant amounts saving a researcher's time and preventing miscalculations and typos. Furthermore, predefined text snippets and the transfer of reaction information to the description of experiments allow for a fast and facile documentation. + +Due to structured and standardized input fields, the documentation takes place in an uniform and [metadata](/docs/metadata)-enriched way. Thus, entries in the Chemotion ELN always give a full but still concise overview on all experimental information facilitating to conduct and document experiments in the laboratory. diff --git a/docs/40_smartlab/41_chemotion_eln/50_chemotion_dataCollection.mdx b/docs/40_smartlab/41_chemotion_eln/50_chemotion_dataCollection.mdx new file mode 100644 index 00000000..37231cec --- /dev/null +++ b/docs/40_smartlab/41_chemotion_eln/50_chemotion_dataCollection.mdx @@ -0,0 +1,36 @@ +--- +title: "Data Collection and Processing" +slug: "/chemotion_dataCollection" +--- + +# Chemotion: Data Collection and Processing + +import useBaseUrl from "@docusaurus/useBaseUrl"; +import ChemotionCarousel from "@site/src/components/chemotion/ChemotionCarousel"; + + + +Analytical data are typically generated and stored in a fully digital format. However, there is often a disconnect between these data, the associated analytical devices, and the laboratory notebook documenting the experiments. Chemotion ELN addresses this issue by enabling the integration of analytical devices with the ELN through [device integration](https://doi.org/10.1016/j.acax.2019.100007). This feature not only facilitates linking devices to the ELN and experiments but also allows for remote control of the devices. As a result, users can manage device operations, initiate measurements, and monitor progress directly within the ELN from any location. + +When analytical devices are connected to the Chemotion ELN, data is easily transferred to the ELN. The transfer maps generated data to experiment entries by employing the experiment naming conventions. Thus, analytical data are seamlessly connected to experiments. + +In many cases, analytical devices might store data in proprietary file formats. To enable the [FAIR data principles](/docs/fair), Chemotion is able to convert such files to the text-based, open source file format _JCAMP-DX_. This conversion occurs automatically once data has been transferred from the analytical device. The Chemotion tool [_ChemConverter_](https://chemotion.net/docs/services/chemconverter) carries out this process and stores both the proprietary file format and the converted file format within the ELN. + +Generally, Chemotion supports researchers with their data collection by semi-automated metadata mapping. Here, Chemotion identifies and extracts metadata from analytical data files and writes them into the corresponding, standardized input fields. diff --git a/docs/40_smartlab/41_chemotion_eln/60_chemotion_analysis.mdx b/docs/40_smartlab/41_chemotion_eln/60_chemotion_analysis.mdx new file mode 100644 index 00000000..5b96cb13 --- /dev/null +++ b/docs/40_smartlab/41_chemotion_eln/60_chemotion_analysis.mdx @@ -0,0 +1,54 @@ +--- +title: "Analysis" +slug: "/chemotion_analysis" +--- + +# Chemotion: Analysis + +import useBaseUrl from "@docusaurus/useBaseUrl"; +import ChemotionCarousel from "@site/src/components/chemotion/ChemotionCarousel"; +import FloatImage from "@site/src/components/commons/FloatImage"; + + + + + +After the [transfer and potential conversion of analytical +data](/docs/chemotion_dataCollection), the next step is to analyze these raw +data. In Chemotion, this can be done seamlessly using one of the integrated +spectra editors. [_NMRium_](https://www.nmrium.org/) is an online tool designed +for processing both one-dimensional and two-dimensional NMR spectra. In addition +to processing NMR spectra, NMRium allows users to directly link chemical +structures to their corresponding NMR signals, facilitating the creation of +[FAIR](/docs/fair) and machine-readable, actionable analytical data. + +Alternatively, spectra can be analyzed with [_ChemSpectra_](https://doi.org/10.1186/s13321-020-00481-0). This software, developed within Chemotion, supports a wide range of analytical techniques including NMR, IR, MS, UV/VIS, GC, HPLC, CV, XRD, and more. Depending on the specific analytical method employed, ChemSpectra offers various processing options such as peak picking, signal integration, and multiplicity setting. + +Once analyses are completed, the processed analytical data are stored alongside the raw data within ELN entries, establishing a direct connection to the experiments conducted. Since the processed data are saved in open file formats, they remain interoperable and can be easily reused. diff --git a/docs/40_smartlab/41_chemotion_eln/70_chemotion_dataPublication.mdx b/docs/40_smartlab/41_chemotion_eln/70_chemotion_dataPublication.mdx new file mode 100644 index 00000000..ae8d947d --- /dev/null +++ b/docs/40_smartlab/41_chemotion_eln/70_chemotion_dataPublication.mdx @@ -0,0 +1,73 @@ +--- +title: "Data Publication" +slug: "/chemotion_dataPublication" +--- + +# Chemotion: Data Publication + +import useBaseUrl from "@docusaurus/useBaseUrl"; +import ChemotionCarousel from "@site/src/components/chemotion/ChemotionCarousel"; +import FloatImage from "@site/src/components/commons/FloatImage"; + + + + + +{/* prettier-ignore-start */} + +Chemotion ELN provides a dedicated functionality that facilitates the [publication of research data](/docs/data_publishing) by enabling seamless transfer from a user's ELN account to a [research data repository](/docs/repositories). Currently, the ELN supports data transfers to the [_Chemotion Repository_](https://www.chemotion-repository.net/welcome) and [_RADAR4Chem_](https://radar4chem.radar-service.eu/radar/en/home). + +This feature allows researchers to easily transfer their research data, +including semantic metadata, into a repository, thereby reducing their workload +and helping meet the requirements set by funding agencies, while making their +work available to their research community. + +{/* prettier-ignore-end */} + + + +Furthermore, Chemotion ELN is connected to other repositories such as +[_nmrXiv_](https://nmrxiv.org/) to ensure optimal visibility and facilitate +user-friendly searches for original research data. The NFDI4Chem team is +actively working on establishing connections to additional repositories, +particularly those [supported and recommended by +NFDI4Chem](/docs/choose_repository/). This ongoing effort aims to enhance +accessibility and interoperability within the research community. + +Chemotion ELN also provides researchers with the option to automatically generate supplemental information (SI) for their manuscripts. This includes direct references to the published datasets via their DOI. diff --git a/docs/40_smartlab/41_chemotion_eln/_category_.json b/docs/40_smartlab/41_chemotion_eln/_category_.json new file mode 100644 index 00000000..e58bf871 --- /dev/null +++ b/docs/40_smartlab/41_chemotion_eln/_category_.json @@ -0,0 +1,7 @@ +{ + "label": "Chemotion ELN", + "link": { + "type": "doc", + "id": "chemotion" + } +} diff --git a/docs/50_data_publication/00_data_publishing.mdx b/docs/50_data_publication/00_data_publishing.mdx index 86f61e96..36852eed 100644 --- a/docs/50_data_publication/00_data_publishing.mdx +++ b/docs/50_data_publication/00_data_publishing.mdx @@ -46,14 +46,14 @@ There are two main ways to publish research data: Field-specific repositories should be the first choice as these repositories enhance the FAIRness of data on behalf of the submitters. To retain the same level of FAIRness, data publishing in generic repositories requires manual FAIRification. ::: -[Smart Lab](/docs/smartlab) solutions, such as [Chemotion ELN](/docs/chemotion_eln/), can offer built-in workflows to assist researchers in publishing data. If the data is already documented in a structured way in Chemtotion ELN, then the data can also be published in this structured way via [Chemotion Repository](https://www.chemotion-repository.net/). +[Smart Lab](/docs/smartlab) solutions, such as [Chemotion ELN](/docs/chemotion), can offer built-in workflows to assist researchers in publishing data. If the data is already documented in a structured way in Chemtotion ELN, then the data can also be published in this structured way via [Chemotion Repository](https://www.chemotion-repository.net). Further information on repositories, including a list of recommended chemistry-friendly repositories, is provided on our pages on [repositories](/docs/repositories) and guide on [how to choose the right repository](/docs/choose_repository). -A [data availability statement](/docs/data_availability_statement) in the back matter of a manuscript communicates how the data has been shared and how it can be accessed by others. Datasets and scientific publications should be interlinked using [persistent identifiers](/docs/pid/). +A [data availability statement](/docs/data_availability_statement) in the back matter of a manuscript communicates how the data has been shared and how it can be accessed by others. Datasets and scientific publications should be interlinked using [persistent identifiers](/docs/pid). :::danger Notice: -Still confused about how to publish chemistry data? We do provide a consulting and data stewardship service via our [Lead by Example](/docs/lbe_intro/) project. Have a look at Lead by Example [Datasets](/docs/datasets) for inspiration! +Still confused about how to publish chemistry data? We do provide a consulting and data stewardship service via our [Lead by Example](/docs/lbe_intro) project. Have a look at Lead by Example [Datasets](/docs/datasets) for inspiration! ::: ## Sources and further information diff --git a/docs/50_data_publication/25_best_practice.mdx b/docs/50_data_publication/25_best_practice.mdx index 67050e6e..76c6317e 100644 --- a/docs/50_data_publication/25_best_practice.mdx +++ b/docs/50_data_publication/25_best_practice.mdx @@ -13,7 +13,7 @@ On this page, we provide best practices for the publication of data in field-spe ## Best practices for field-specific repositories -For the field-specific repositories [Chemotion Repository](/docs/chemotion_repository) in combination with [Chemotion ELN](/docs/chemotion_eln), the data is collected along the scientific workflows, analytical data files are automatically converted to open formats, controlled vocabularies or ontologies are used to describe data, and analysis data is interconnected to reactions and samples, hence, chemical structures. The entire Chemotion package allows researchers to collect, analyse, process, store, and publish various types of analytical data attached to reactions and samples in one [digital environment](/docs/smartlab). FAIRification of data along this [data life cycle](/docs/data_life_cycle) is mainly handled by Chemotion. During the seamless export from the ELN into the repository, [PIDs](/docs/pid) (in this case [DOIs](https://www.doi.org/)) are assigned to the deposited data. Chemotion Repository [provides](https://www.chemotion.net/docs/repo/doi) DOIs for reactions, samples, analysis data, and collections (Collection DOI). +For the field-specific repositories [Chemotion Repository](/docs/chemotion_repository) in combination with [Chemotion ELN](/docs/chemotion), the data is collected along the scientific workflows, analytical data files are automatically converted to open formats, controlled vocabularies or ontologies are used to describe data, and analysis data is interconnected to reactions and samples, hence, chemical structures. The entire Chemotion package allows researchers to collect, analyse, process, store, and publish various types of analytical data attached to reactions and samples in one [digital environment](/docs/smartlab). FAIRification of data along this [data life cycle](/docs/data_life_cycle) is mainly handled by Chemotion. During the seamless export from the ELN into the repository, [PIDs](/docs/pid) (in this case [DOIs](https://www.doi.org/)) are assigned to the deposited data. Chemotion Repository [provides](https://www.chemotion.net/docs/repo/doi) DOIs for reactions, samples, analysis data, and collections (Collection DOI). Other field-specific repositories such as [CSD and ICSD](/docs/csd_icsd), [Strenda DB](/docs/strenda_db), [SupraBank](/docs/suprabank), [NOMAD](/docs/nomad), and [Chemotion Repository](/docs/chemotion_repository), if used independently from Chemotion ELN, offer built-in workflows for the aggregation of structured data along the submission pathways, aligned with the [FAIR Data Principles](/docs/fair). This greatly facilitates the publication of FAIR data. @@ -54,7 +54,7 @@ For further aspects to consider, we provide a non-exhaustive list of generic bes - **The provenance information of data should be included.**
Part of that [provenance information](/docs/provenance) is part of the dataset's metadata and should be added via the metadata editor of the repository. All information which previously would have typically been included in the supplemental PDF section on general information and protocols, e.g. information on methods and instruments used, are provenance information and should be added to a README file, as long as no domain-specific metadata schema is available. This README could be a text file, or written in Markdown, while also a human-readable rendered representation as HTML could be provided. :::danger Notice: -Does that sound like a lot of manual work? Avoid extra work by using a [smart lab](/docs/smartlab) digital environments for collecting, processing, analysing, and publishing research data, such as [Chemotion ELN](/docs/chemotion_eln) in combination with [Chemotion Repository](/docs/chemotion_repository)! Plus, you may omit the preparation of supplementary PDFs and use the saved work time to prepare your dataset for publication! +Does that sound like a lot of manual work? Avoid extra work by using a [smart lab](/docs/smartlab) digital environments for collecting, processing, analysing, and publishing research data, such as [Chemotion ELN](/docs/chemotion) in combination with [Chemotion Repository](/docs/chemotion_repository)! Plus, you may omit the preparation of supplementary PDFs and use the saved work time to prepare your dataset for publication! ::: ### Best practice examples for generic repositories diff --git a/docs/60_topics/63_data_description_annotation/20_ontology.mdx b/docs/60_topics/63_data_description_annotation/20_ontology.mdx index d13ee2ae..4a0fc719 100644 --- a/docs/60_topics/63_data_description_annotation/20_ontology.mdx +++ b/docs/60_topics/63_data_description_annotation/20_ontology.mdx @@ -4,6 +4,7 @@ slug: "/ontology" --- import VideoPrivacy from "video-privacy"; +import styles from "@site/src/css/video.module.css"; import useBaseUrl from "@docusaurus/useBaseUrl"; :::info Summary: @@ -13,22 +14,23 @@ The term ontology, as used in our context, refers to a formally specified concep ## Introduction - + ![Ontology-based RDM](/img/topics/Graphical_Abstract_Ontologies4Chem_2021.svg) @@ -48,65 +50,64 @@ Here we can see that these ontologies have different scopes, which means they on This tabular overview lists the suitable ontologies with regard to: -- their general research domain, -- their open access licence, -- the possibility of reusing them in a modular way (whereas a BFO alignment and OBO compatibility indicates an increased possibility), -- and, their use in known applications. - -|Ontology |Domain |Licence |Modularity |Used in | -|----------|-------------------------------|------------------------|----------------------------------------------------------|----------------------------------------------------------------------------------------------------------| -|[ChEBI] |chemistry |[CC-BY 4.0] |BFO & OBO based |YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB | -|[CHIRO] |chemistry |[CC0 1.0] |BFO & OBO based |unknown | -|[ChemOnt] |chemistry |custom OA licence |subsumable under BFO's _material entity_ |YMDB, HMDB, T3DB, ECMDB, DrugBank,PubChem, ChEBI, LIPID MAPS, MoNA | -|[CHEMINF] |chemistry |[CC-BY 3.0] |BFO & OBO based |PubChem, Open PHACTS | -|[CHMO] |chemistry |[CC-BY 4.0] |BFO & OBO based |Chemotion, Allotrope™ | -|[MOP] |chemistry |[CC-BY 4.0] |BFO & OBO based |RXNO | -|[RXNO] |chemistry |[CC-BY 4.0] |BFO & OBO based |NameRXN, Wikipedia, Chemotion | -|[OntoKin] |chemistry |[MIT] |OntoCAPE upper level & modules |J-Park Simulator | -|[AFO] |chemistry |[CC-BY 4.0] |BFO classes & relations, many AFO- some custom OBO-modules|Allotrope™ | -|[PROCO] |chemistry |[CC-BY 4.0] |BFO/AFO & OBO based |Allotrope™ | -|[MS] |chemistry |[CC-BY 4.0] |BFO & OBO mapping possible |mzML | -|[nmrCV] |chemistry |[Public Domain Mark 1.0]|BFO & OBO mapping possible |MetaboLights, HMDB | -|[BFO] |upper level (classes only) |[CC-BY 4.0] |OBO backbone |>300 ontologies & >50 organizations, PubChem | -|[RO] |upper level (relations) |[CC0 1.0] |BFO & OBO based |Monarch Initiative, OBO Foundry, Gene Ontology, PubChem | -|[IAO] |information artefacts |[CC-BY 4.0] |BFO & OBO based |OBO Foundry, Allotrope™, PubChem, ISA tools | -|[OBI] |biomedicine |[CC-BY 4.0] |BFO & OBO based |OBO Foundry, Allotrope™, PubChem | -|[UO] |scientific units |[CC-BY 4.0] |BFO & OBO based |OBO Foundry, UOM, PubChem | -|[QUDT] |scientific units |[CC-BY 4.0] |BFO & OBO based mapping possible |openPHACTS | -|[PATO] |phenotypic & physical qualities|[CC-BY 3.0] |BFO & OBO based |OBO Foundry, Allotrope™ | -|[SIO] |upper level |[CC-BY 4.0] |BFO alignment |PubChemRDF, Bio2RDF, SADI Semantic Web Services, DisGeNET, EBI's Gene Expression Atlas, Graph4Code project| -|[EDAM] |life-sciences & data management|[CC-BY 4.0] |BFO & OBO mapping possible |EMBOSS, Bio-jETI | -|[OntoCAPE]|upper level & engineering |[GNU GPLv2] |provides upper level concepts |J-Park Simulator | - -[ChEBI]: https://www.ebi.ac.uk/ols/ontologies/chebi -[CHIRO]: https://terminology.nfdi4chem.de/ts/ontologies/chiro -[ChemOnt]: http://classyfire.wishartlab.com/downloads -[CHEMINF]: https://terminology.nfdi4chem.de/ts/ontologies/cheminf -[CHMO]: https://terminology.nfdi4chem.de/ts/ontologies/chmo -[MOP]: https://terminology.nfdi4chem.de/ts/ontologies/mop -[RXNO]: https://terminology.nfdi4chem.de/ts/ontologies/rxno -[OntoKin]: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl -[AFO]: https://www.ebi.ac.uk/ols/ontologies/afo -[PROCO]: http://purl.obolibrary.org/obo/proco.owl -[MS]: https://terminology.nfdi4chem.de/ontologies/ms -[nmrCV]: https://terminology.nfdi4chem.de/ontologies/nmrcv -[BFO]: https://terminology.nfdi4chem.de/ontologies/bfo -[RO]: https://terminology.nfdi4chem.de/ts/ontologies/ro -[IAO]: https://terminology.nfdi4chem.de/ts/ontologies/iao -[OBI]: https://terminology.nfdi4chem.de/ts/ontologies/obi -[UO]: https://terminology.nfdi4chem.de/ts/ontologies/uo -[QUDT]: http://www.qudt.org/pages/QUDToverviewPage.html -[PATO]: https://terminology.nfdi4chem.de/ts/ontologies/pato -[SIO]: https://terminology.nfdi4chem.de/ts/ontologies/sio -[EDAM]: https://terminology.nfdi4chem.de/ts/ontologies/edam +- their general research domain, +- their open access licence, +- the possibility of reusing them in a modular way (whereas a BFO alignment and OBO compatibility indicates an increased possibility), +- and, their use in known applications. + +| Ontology | Domain | Licence | Modularity | Used in | +| ---------- | ------------------------------- | ------------------------ | ---------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------- | +| [ChEBI] | chemistry | [CC-BY 4.0] | BFO & OBO based | YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB | +| [CHIRO] | chemistry | [CC0 1.0] | BFO & OBO based | unknown | +| [ChemOnt] | chemistry | custom OA licence | subsumable under BFO's _material entity_ | YMDB, HMDB, T3DB, ECMDB, DrugBank,PubChem, ChEBI, LIPID MAPS, MoNA | +| [CHEMINF] | chemistry | [CC-BY 3.0] | BFO & OBO based | PubChem, Open PHACTS | +| [CHMO] | chemistry | [CC-BY 4.0] | BFO & OBO based | Chemotion, Allotrope™ | +| [MOP] | chemistry | [CC-BY 4.0] | BFO & OBO based | RXNO | +| [RXNO] | chemistry | [CC-BY 4.0] | BFO & OBO based | NameRXN, Wikipedia, Chemotion | +| [OntoKin] | chemistry | [MIT] | OntoCAPE upper level & modules | J-Park Simulator | +| [AFO] | chemistry | [CC-BY 4.0] | BFO classes & relations, many AFO- some custom OBO-modules | Allotrope™ | +| [PROCO] | chemistry | [CC-BY 4.0] | BFO/AFO & OBO based | Allotrope™ | +| [MS] | chemistry | [CC-BY 4.0] | BFO & OBO mapping possible | mzML | +| [nmrCV] | chemistry | [Public Domain Mark 1.0] | BFO & OBO mapping possible | MetaboLights, HMDB | +| [BFO] | upper level (classes only) | [CC-BY 4.0] | OBO backbone | >300 ontologies & >50 organizations, PubChem | +| [RO] | upper level (relations) | [CC0 1.0] | BFO & OBO based | Monarch Initiative, OBO Foundry, Gene Ontology, PubChem | +| [IAO] | information artefacts | [CC-BY 4.0] | BFO & OBO based | OBO Foundry, Allotrope™, PubChem, ISA tools | +| [OBI] | biomedicine | [CC-BY 4.0] | BFO & OBO based | OBO Foundry, Allotrope™, PubChem | +| [UO] | scientific units | [CC-BY 4.0] | BFO & OBO based | OBO Foundry, UOM, PubChem | +| [QUDT] | scientific units | [CC-BY 4.0] | BFO & OBO based mapping possible | openPHACTS | +| [PATO] | phenotypic & physical qualities | [CC-BY 3.0] | BFO & OBO based | OBO Foundry, Allotrope™ | +| [SIO] | upper level | [CC-BY 4.0] | BFO alignment | PubChemRDF, Bio2RDF, SADI Semantic Web Services, DisGeNET, EBI's Gene Expression Atlas, Graph4Code project | +| [EDAM] | life-sciences & data management | [CC-BY 4.0] | BFO & OBO mapping possible | EMBOSS, Bio-jETI | +| [OntoCAPE] | upper level & engineering | [GNU GPLv2] | provides upper level concepts | J-Park Simulator | + +[ChEBI]: https://www.ebi.ac.uk/ols/ontologies/chebi +[CHIRO]: https://terminology.nfdi4chem.de/ts/ontologies/chiro +[ChemOnt]: http://classyfire.wishartlab.com/downloads +[CHEMINF]: https://terminology.nfdi4chem.de/ts/ontologies/cheminf +[CHMO]: https://terminology.nfdi4chem.de/ts/ontologies/chmo +[MOP]: https://terminology.nfdi4chem.de/ts/ontologies/mop +[RXNO]: https://terminology.nfdi4chem.de/ts/ontologies/rxno +[OntoKin]: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl +[AFO]: https://www.ebi.ac.uk/ols/ontologies/afo +[PROCO]: http://purl.obolibrary.org/obo/proco.owl +[MS]: https://terminology.nfdi4chem.de/ontologies/ms +[nmrCV]: https://terminology.nfdi4chem.de/ontologies/nmrcv +[BFO]: https://terminology.nfdi4chem.de/ontologies/bfo +[RO]: https://terminology.nfdi4chem.de/ts/ontologies/ro +[IAO]: https://terminology.nfdi4chem.de/ts/ontologies/iao +[OBI]: https://terminology.nfdi4chem.de/ts/ontologies/obi +[UO]: https://terminology.nfdi4chem.de/ts/ontologies/uo +[QUDT]: http://www.qudt.org/pages/QUDToverviewPage.html +[PATO]: https://terminology.nfdi4chem.de/ts/ontologies/pato +[SIO]: https://terminology.nfdi4chem.de/ts/ontologies/sio +[EDAM]: https://terminology.nfdi4chem.de/ts/ontologies/edam [OntoCAPE]: http://www.theworldavatar.com/ontology/ontocape/OntoCAPE.owl - -[CC-BY 3.0]: https://creativecommons.org/licenses/by/3.0/ -[CC-BY 4.0]: https://creativecommons.org/licenses/by/4.0/ -[CC0 1.0]: https://creativecommons.org/publicdomain/zero/1.0/ +[CC-BY 3.0]: https://creativecommons.org/licenses/by/3.0/ +[CC-BY 4.0]: https://creativecommons.org/licenses/by/4.0/ +[CC0 1.0]: https://creativecommons.org/publicdomain/zero/1.0/ [Public Domain Mark 1.0]: https://creativecommons.org/publicdomain/mark/1.0/deed -[GNU GPLv2]: https://www.gnu.org/licenses/old-licenses/gpl-2.0 -[MIT]: https://github.com/TheWorldAvatar/ontology/blob/main/LICENSE.txt +[GNU GPLv2]: https://www.gnu.org/licenses/old-licenses/gpl-2.0 +[MIT]: https://github.com/TheWorldAvatar/ontology/blob/main/LICENSE.txt ## General Scientific Ontologies @@ -209,20 +210,20 @@ Although the two chemistry related ontologies **Physico-chemical methods and pro In order to be able to speak about the existing ontologies in the domain of chemistry, we need to provide a very brief glossary of the most important technical terms that describe an ontology: -- **classes** represent those portions of reality that exist as generic entities, such as atoms and molecules, chemical reactions, lab equipment and experimental methods (e.g. the class _MassSpectrometer_) -- **instances**, **individuals** or **particulars** of a class are particular entities that exist in reality, (e.g. a particular mass spectrometer identified via a serial number) -- **relations** or **properties** are terms used to signify the interdependence between classes or individuals (e.g. a specific molecule _participates in_ a certain chemical reaction) -- **taxonomy** refers to a hierarchical structuring of classes into superclasses and subclasses (e.g _MassSpectrometer is_a Device_ or _HomoSapiens is_a Mamal_) -- **axioms** are the rules defined to express relations that always hold true between classes or instances of classes (e.g. _MolecularProcess_ is a _process_ that must have one or more _MolecularEntities_ as its participants) -- **upper ontologies** conceptualize the most general parts of reality (e.g. time, space, material matter, process, causality, parthood, etc) and thus can provide a semantic framework for domain or application ontologies - \*\* In a best case scenario there is only one upper ontology to be used by many domain ontologies to ensure their interoperability -- **domain ontologies** conceptualize specific aspects of a given domain (e.g. ChEBI conceptualizes only chemical entities like atoms and molecules as well as their roles in certain contexts) -- **application ontologies** are domain ontologies that are implemented in a concrete application and thus limited to the applications use cases +- **classes** represent those portions of reality that exist as generic entities, such as atoms and molecules, chemical reactions, lab equipment and experimental methods (e.g. the class _MassSpectrometer_) +- **instances**, **individuals** or **particulars** of a class are particular entities that exist in reality, (e.g. a particular mass spectrometer identified via a serial number) +- **relations** or **properties** are terms used to signify the interdependence between classes or individuals (e.g. a specific molecule _participates in_ a certain chemical reaction) +- **taxonomy** refers to a hierarchical structuring of classes into superclasses and subclasses (e.g _MassSpectrometer is_a Device_ or _HomoSapiens is_a Mamal_) +- **axioms** are the rules defined to express relations that always hold true between classes or instances of classes (e.g. _MolecularProcess_ is a _process_ that must have one or more _MolecularEntities_ as its participants) +- **upper ontologies** conceptualize the most general parts of reality (e.g. time, space, material matter, process, causality, parthood, etc) and thus can provide a semantic framework for domain or application ontologies + \*\* In a best case scenario there is only one upper ontology to be used by many domain ontologies to ensure their interoperability +- **domain ontologies** conceptualize specific aspects of a given domain (e.g. ChEBI conceptualizes only chemical entities like atoms and molecules as well as their roles in certain contexts) +- **application ontologies** are domain ontologies that are implemented in a concrete application and thus limited to the applications use cases ## Sources and further information -- [Ontologies4Chem Article](https://doi.org/10.1515/pac-2021-2007) -- [NFDI4Chem Terminology Service](https://terminology.nfdi4chem.de/ts/index) +- [Ontologies4Chem Article](https://doi.org/10.1515/pac-2021-2007) +- [NFDI4Chem Terminology Service](https://terminology.nfdi4chem.de/ts/index) --- diff --git a/docusaurus.config.js b/docusaurus.config.js index ceb2f6dc..34d80d4a 100644 --- a/docusaurus.config.js +++ b/docusaurus.config.js @@ -1,91 +1,95 @@ /** @type {import('@docusaurus/types').Config} */ -import { themes as prismThemes } from "prism-react-renderer"; +import {themes as prismThemes} from "prism-react-renderer"; const announcementBarActive = false; // set to true to activate the announcement bar const announcementBar = announcementBarActive - ? require("./announcementBar.json") - : {}; + ? require("./announcementBar.json") + : {}; + +let title = "NFDI4Chem Knowledge Base"; + +// Uncomment for staging: +// title += " (STAGING)"; -const title = "NFDI4Chem Knowledge Base"; const description = - "Supporting scientists to digitalise all steps of chemical research: to collect, store, process, analyse, publish, and reuse research data"; + "Supporting scientists to digitalise all steps of chemical research: to collect, store, process, analyse, publish, and reuse research data"; const url = "https://knowledgebase.nfdi4chem.de/"; -const baseUrl = "/knowledge_base/"; + +let baseUrl = "/knowledge_base/"; + +// Uncomment for stagging: +// baseUrl = "/staging" + baseUrl; const navbar = require("./navbar.json"); const footerLinks = require("./footer.json"); -// Use for stagging: -// const baseUrl = '/staging/knowledge_base_matomo/'; -// const baseUrl = "/staging/knowledge_base/"; - const config = { - title: title, - url: url, - baseUrl: baseUrl, - customFields: { - description: description, - }, - onBrokenLinks: "warn", - markdown: { - hooks: { - onBrokenMarkdownLinks: "warn", - onBrokenMarkdownImages: "warn", - }, - }, - favicon: "img/favicon.png", - organizationName: "NFDI4Chem", // Usually your GitHub org/user name. - projectName: "knowledge_base", // Usually your repo name. - trailingSlash: "true", - i18n: { - defaultLocale: "en", - locales: ["en", "de"], - localeConfigs: { - en: { - htmlLang: "en-GB", - }, - }, - }, - plugins: ["docusaurus-plugin-matomo"], - themeConfig: { - ...(Object.keys(announcementBar).length > 0 && { - announcementBar: announcementBar, - }), - metadata: [ - { - name: "google-site-verification", - content: "wgYVjYSe_T6v6BPPM6fPo1ffl7MYYnuVw-h9RoAYfM0", - }, - ], - matomo: { - matomoUrl: "https://knowledgebase.nfdi4chem.de/matomo/", - siteId: "1", - phpLoader: "matomo.php", - jsLoader: "matomo.js", - }, - navbar: navbar, - footer: { - style: "dark", - links: [ - { - items: [ - { - html: - ` + title: title, + url: url, + baseUrl: baseUrl, + customFields: { + description: description, + }, + onBrokenLinks: "warn", + markdown: { + hooks: { + onBrokenMarkdownLinks: "warn", + onBrokenMarkdownImages: "warn", + }, + }, + favicon: "img/favicon.png", + organizationName: "NFDI4Chem", // Usually your GitHub org/user name. + projectName: "knowledge_base", // Usually your repo name. + trailingSlash: "true", + i18n: { + defaultLocale: "en", + locales: ["en", "de"], + localeConfigs: { + en: { + htmlLang: "en-GB", + }, + }, + }, + plugins: ["docusaurus-plugin-matomo"], + themeConfig: { + ...(Object.keys(announcementBar).length > 0 && { + announcementBar: announcementBar, + }), + metadata: [ + { + name: "google-site-verification", + content: "wgYVjYSe_T6v6BPPM6fPo1ffl7MYYnuVw-h9RoAYfM0", + }, + ], + matomo: { + matomoUrl: "https://knowledgebase.nfdi4chem.de/matomo/", + siteId: "1", + phpLoader: "matomo.php", + jsLoader: "matomo.js", + }, + navbar: navbar, + footer: { + style: "dark", + links: [ + { + items: [ + { + html: + ` + baseUrl + + `img/dfg_logo_schriftzug_weiss_foerderung_en.png" />

NFDI4Chem is funded by DFG
Project Number 441958208

`, - }, - ], - }, - ...footerLinks, - ], - copyright: ` + }, + ], + }, + ...footerLinks, + ], + copyright: `
Creative Commons License @@ -96,67 +100,67 @@ const config = {
`, - }, - algolia: { - appId: "K32QMEOD1G", - apiKey: "6ba494183b866a52e3dfd54388379f77", - indexName: "nfdi4chem_knowledge_base", - contextualSearch: true, - // replaceSearchResultPathname: { - // from: "/knowledge_base/", - // to: "/", - // }, - // Optional: whether you want to use the new Ask AI feature (undefined by default) - // askAi: "YOUR_ALGOLIA_ASK_AI_ASSISTANT_ID", - }, - colorMode: { disableSwitch: true }, - prism: { - theme: prismThemes.github, - darkTheme: prismThemes.dracula, - }, - }, - presets: [ - [ - "classic", - /** @type {import('@docusaurus/preset-classic').Options} */ - { - docs: { - sidebarPath: "./sidebars.js", - editUrl: - "https://github.com/NFDI4Chem/knowledge_base/tree/main/", - }, - theme: { - customCss: "./src/css/custom.css", - }, - sitemap: { - lastmod: "datetime", - ignorePatterns: ["/tags/**"], - createSitemapItems: async (params) => { - const { defaultCreateSitemapItems, ...rest } = params; - const items = await defaultCreateSitemapItems(rest); - return items.filter( - (item) => !item.url.includes("/page/") - ); - }, - }, - }, - ], - ], - // themes: [ - // [ - // require.resolve("@easyops-cn/docusaurus-search-local"), - // { - // hashed: true, - // highlightSearchTermsOnTargetPage: true, - // }, - // ], - // ], - future: { - experimental_faster: { - rspackBundler: true, - rspackPersistentCache: true, - }, - }, + }, + algolia: { + appId: "K32QMEOD1G", + apiKey: "6ba494183b866a52e3dfd54388379f77", + indexName: "nfdi4chem_knowledge_base", + contextualSearch: true, + // replaceSearchResultPathname: { + // from: "/knowledge_base/", + // to: "/", + // }, + // Optional: whether you want to use the new Ask AI feature (undefined by default) + // askAi: "YOUR_ALGOLIA_ASK_AI_ASSISTANT_ID", + }, + colorMode: {disableSwitch: true}, + prism: { + theme: prismThemes.github, + darkTheme: prismThemes.dracula, + }, + }, + presets: [ + [ + "classic", + /** @type {import('@docusaurus/preset-classic').Options} */ + { + docs: { + sidebarPath: "./sidebars.js", + editUrl: + "https://github.com/NFDI4Chem/knowledge_base/tree/main/", + }, + theme: { + customCss: "./src/css/custom.css", + }, + sitemap: { + lastmod: "datetime", + ignorePatterns: ["/tags/**"], + createSitemapItems: async (params) => { + const {defaultCreateSitemapItems, ...rest} = params; + const items = await defaultCreateSitemapItems(rest); + return items.filter( + (item) => !item.url.includes("/page/"), + ); + }, + }, + }, + ], + ], + // themes: [ + // [ + // require.resolve("@easyops-cn/docusaurus-search-local"), + // { + // hashed: true, + // highlightSearchTermsOnTargetPage: true, + // }, + // ], + // ], + future: { + experimental_faster: { + rspackBundler: true, + rspackPersistentCache: true, + }, + }, }; export default config; diff --git a/package-lock.json b/package-lock.json index dd3571af..6e2bc2e1 100644 --- a/package-lock.json +++ b/package-lock.json @@ -24,7 +24,7 @@ "react-dom": "^19", "react-tagcloud": "^2.3.3", "use-immer": "^0.11.0", - "video-privacy": "^1.1.2" + "video-privacy": "^1.2.0" }, "devDependencies": { "@docusaurus/module-type-aliases": "^3.9.2", @@ -18711,16 +18711,16 @@ } }, "node_modules/video-privacy": { - "version": "1.1.2", - "resolved": "https://registry.npmjs.org/video-privacy/-/video-privacy-1.1.2.tgz", - "integrity": "sha512-yPiGAZrDzJ9WffoIKXyYtnlPBOrNulJzwXKF1XKVr78xUnTyl6LuWd+t+pCs7Mm+QOlbkCNBsjFTiDPOxMvRPA==", + "version": "1.2.0", + "resolved": "https://registry.npmjs.org/video-privacy/-/video-privacy-1.2.0.tgz", + "integrity": "sha512-mQytGyHQtnV3JXnfUO/8IfxzquTVnn6tog+1JEEmpby/HyhNBbHnwgD50U9yuT0dJ/9frs2JgdJ8Wy3BrXcLqQ==", "license": "CC-BY-SA-4.0", "dependencies": { "js-cookie": "^3.0.5" }, "peerDependencies": { - "react": "^18 || ^19", - "react-dom": "^18 || ^19" + "react": "^19 || ^18", + "react-dom": "^19 || ^18" } }, "node_modules/watchpack": { diff --git a/package.json b/package.json index a6282090..dfbbcdc5 100644 --- a/package.json +++ b/package.json @@ -1,54 +1,55 @@ { - "name": "nfdi-4-chem-knowledge-base", - "version": "0.0.0", - "private": true, - "scripts": { - "docusaurus": "docusaurus", - "start": "docusaurus start", - "build": "docusaurus build", - "swizzle": "docusaurus swizzle", - "deploy": "docusaurus deploy", - "clear": "docusaurus clear", - "serve": "docusaurus serve", - "write-translations": "docusaurus write-translations", - "write-heading-ids": "docusaurus write-heading-ids", - "crowdin": "crowdin" - }, - "dependencies": { - "@crowdin/cli": "^4.12.0", - "@docusaurus/core": "^3.9.2", - "@docusaurus/faster": "^3.9.2", - "@docusaurus/plugin-sitemap": "^3.9.2", - "@docusaurus/preset-classic": "^3.9.2", - "@fontsource/ibm-plex-sans": "^5.2.8", - "@mdx-js/react": "^3.1.1", - "clsx": "^2.1.1", - "docusaurus-plugin-matomo": "^0.0.8", - "moment": "^2.30.1", - "prism-react-renderer": "^2.4.1", - "react": "^19", - "react-dom": "^19", - "react-tagcloud": "^2.3.3", - "use-immer": "^0.11.0", - "video-privacy": "^1.1.2" - }, - "devDependencies": { - "@docusaurus/module-type-aliases": "^3.9.2", - "@docusaurus/types": "^3.9.2" - }, - "browserslist": { - "production": [ - ">0.5%", - "not dead", - "not op_mini all" - ], - "development": [ - "last 3 chrome version", - "last 3 firefox version", - "last 5 safari version" - ] - }, - "engines": { - "node": ">=18.0" - } + "name": "nfdi-4-chem-knowledge-base", + "version": "0.0.0", + "private": true, + "scripts": { + "docusaurus": "docusaurus", + "start": "docusaurus start", + "build": "docusaurus build", + "swizzle": "docusaurus swizzle", + "deploy": "docusaurus deploy", + "clear": "docusaurus clear", + "serve": "docusaurus serve", + "write-translations": "docusaurus write-translations", + "write-heading-ids": "docusaurus write-heading-ids", + "crowdin": "crowdin" + }, + "dependencies": { + "@crowdin/cli": "^4.12.0", + "@docusaurus/core": "^3.9.2", + "@docusaurus/faster": "^3.9.2", + "@docusaurus/plugin-sitemap": "^3.9.2", + "@docusaurus/preset-classic": "^3.9.2", + "@fontsource/ibm-plex-sans": "^5.2.8", + "@mdx-js/react": "^3.1.1", + "clsx": "^2.1.1", + "docusaurus-plugin-matomo": "^0.0.8", + "moment": "^2.30.1", + "nuka-carousel": "^8.2.0", + "prism-react-renderer": "^2.4.1", + "react": "^19", + "react-dom": "^19", + "react-tagcloud": "^2.3.3", + "use-immer": "^0.11.0", + "video-privacy": "^1.2.0" + }, + "devDependencies": { + "@docusaurus/module-type-aliases": "^3.9.2", + "@docusaurus/types": "^3.9.2" + }, + "browserslist": { + "production": [ + ">0.5%", + "not dead", + "not op_mini all" + ], + "development": [ + "last 3 chrome version", + "last 3 firefox version", + "last 5 safari version" + ] + }, + "engines": { + "node": ">=18.0" + } } diff --git a/src/components/chemotion/ChemotionCarousel.js b/src/components/chemotion/ChemotionCarousel.js new file mode 100644 index 00000000..cfe5a4fb --- /dev/null +++ b/src/components/chemotion/ChemotionCarousel.js @@ -0,0 +1,61 @@ +import {Carousel} from "nuka-carousel"; +import style from "./ChemotionCarousel.module.css"; +import {useCarousel} from "nuka-carousel"; + +function CustomDots() { + const {totalPages, currentPage, goToPage} = useCarousel(); + + const className = (index) => { + let value = style.chemotionCarouselDot; + if (currentPage === index) { + value += " " + style.chemotionCarouselDotActive; + } + return value; + }; + + return ( +
+ {[...Array(totalPages)].map((_, index) => ( + goToPage(index)} + className={className(index)} + > + • + + ))} +
+ ); +} + +function ChemotionCarousel({icon, images}) { + return ( +
+ {icon.alt} +
+ } + > + {images.map((image, index) => ( + {image.alt} + ))} + +
+
+ ); +} + +export default ChemotionCarousel; diff --git a/src/components/chemotion/ChemotionCarousel.module.css b/src/components/chemotion/ChemotionCarousel.module.css new file mode 100644 index 00000000..f4001134 --- /dev/null +++ b/src/components/chemotion/ChemotionCarousel.module.css @@ -0,0 +1,56 @@ +.chemotionCarousel { + display: flex; + flex-direction: row; +} + +.chemotionCarouselIcon { + margin-inline: 1em; + width: 180px; +} + +.chemotionCarouselContainer { + display: flex; + flex-direction: column; + align-items: center; + margin: 2em; + position: relative; + box-shadow: 0.6em 0.6em 0.5em -0.75em; +} + +.chemotionCarouselImage { + align-self: center; +} + +.chemotionCarouselDots { + position: absolute; + bottom: 0.1em; +} + +.chemotionCarouselDot { + font-size: 1.5em; + color: rgba(146, 148, 151); + border: none; + cursor: pointer; + opacity: 0.5; +} + +.chemotionCarouselDotActive { + color: var(--ifm-color-primary); +} + +.chemotionCarouselDot:hover { + opacity: 0.65; +} + +@media screen and (max-width: 968px) { + .chemotionCarousel { + display: flex; + flex-direction: column; + align-items: center; + } + + .chemotionCarouselIcon { + margin: 0.5em; + width: 25%; + } +} diff --git a/src/components/chemotion/ChemotionLifecycle.js b/src/components/chemotion/ChemotionLifecycle.js new file mode 100644 index 00000000..c823d80f --- /dev/null +++ b/src/components/chemotion/ChemotionLifecycle.js @@ -0,0 +1,197 @@ +import Link from "@docusaurus/Link"; +import Translate from "@docusaurus/Translate"; + +import styles from "./ChemotionLifecycle.module.css"; + +const ChemotionLifecycle = () => { + return ( +
+ + + + + + Experiment + + + Design + + + + + + + + + + + Experiment + + + + + + + + + Analysis + + + + + + + + + Data Collection & + + + Processing + + + + + + + + + Data + + + Publication + + + + + + + + + Re-use + + + + + + + + + + +
+ ); +}; + +export default ChemotionLifecycle; diff --git a/src/components/chemotion/ChemotionLifecycle.module.css b/src/components/chemotion/ChemotionLifecycle.module.css new file mode 100644 index 00000000..bb51c590 --- /dev/null +++ b/src/components/chemotion/ChemotionLifecycle.module.css @@ -0,0 +1,56 @@ +:root { + --svgLifecycle-duration: 0.2s; + --svgGrayedOut: #c0c0c0; +} + +.svgLifecycleContainer { + display: flex; + max-height: 560px; +} + +.svgIcons { + fill: var(--ifm-color-primary); +} + +.svgIconText { + font-size: 15px; + fill: var(--ifm-color-primary); + font-weight: 300; +} + +g.svgLifecycle { + scale: 0.9; + transform-origin: 50% 50%; + max-height: 100%; +} + +g.svgLifecycle * { + stroke-width: 30px; + stroke: black; + stroke-opacity: 0; + transform: scale(1); + transform-origin: 50% 50%; + transition-duration: var(--svgLifecycle-duration); +} + +g.svgLifecycle:hover *, +g.svgLifecycle:hover + * { + fill: var(--svgGrayedOut); + text-decoration: none; +} + +g.hoverGroup:hover * { + fill: var(--ifm-color-secondary); + transform: scale(1.02); + transform-origin: 50% 50%; + transition-duration: var(--svgLifecycle-duration); +} + +g.hoverGroup:hover .svgIconText { + font-weight: 700; +} + +.chemotionLogo { + scale: 0.75; + transform-origin: 50% 50%; +} diff --git a/src/components/commons/FloatImage.js b/src/components/commons/FloatImage.js new file mode 100644 index 00000000..58d6d616 --- /dev/null +++ b/src/components/commons/FloatImage.js @@ -0,0 +1,44 @@ +import useBaseUrl from "@docusaurus/useBaseUrl"; +import Link from "@docusaurus/Link"; + +import styles from "./FloatImage.module.css"; + +function FloatImage({ url, alt, ...props }) { + // Object for custom styles + + let style = {}; + + // Populate style object with all props except 'link' + + Object.keys(props).forEach((key) => { + if (key !== "link") { + style[key] = props[key]; + } + }); + + // Component for image + + const ThisImg = () => { + return ( + {alt} + ); + }; + + // If link prop is given, wrap image in link + + if (props.link && props.link.length > 0) { + return ( + + + + ); + } + + return ; +} +export default FloatImage; diff --git a/src/components/commons/FloatImage.module.css b/src/components/commons/FloatImage.module.css new file mode 100644 index 00000000..ad4090e5 --- /dev/null +++ b/src/components/commons/FloatImage.module.css @@ -0,0 +1,10 @@ +.FloatImage { + width: min(120px, 50%); + float: right; + margin: 0px 20px 0px 20px; +} + +a > .FloatImage:hover { + transform: scale(var(--n4c-hover-scale)); + transition: transform var(--n4c-transform-time) ease-in-out; +} diff --git a/src/css/video.module.css b/src/css/video.module.css new file mode 100644 index 00000000..e4a5afb7 --- /dev/null +++ b/src/css/video.module.css @@ -0,0 +1,18 @@ +.videoInfo { + color: white; + font: bold var(--ifm-h3-font-size) / var(--ifm-heading-line-height) + var(--ifm-font-family-base); + margin-bottom: var(--ifm-heading-margin-bottom); + text-align: center; +} + +@media screen and (max-width: 1350px) { + .videoInfo { + color: white; + + font: bold var(--ifm-h5-font-size) / var(--ifm-heading-line-height) + var(--ifm-font-family-base); + margin-bottom: var(--ifm-heading-margin-bottom); + text-align: center; + } +} diff --git a/static/img/ChemotionELN_Logo.png b/static/img/ChemotionELN_Logo.png new file mode 100644 index 00000000..2b15b5dc Binary files /dev/null and b/static/img/ChemotionELN_Logo.png differ diff --git a/static/img/ChemotionRepo_Logo.svg b/static/img/ChemotionRepo_Logo.svg new file mode 100644 index 00000000..3ba5ba4f --- /dev/null +++ b/static/img/ChemotionRepo_Logo.svg @@ -0,0 +1,148 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/static/img/LabIMotion_logo.png b/static/img/LabIMotion_logo.png new file mode 100644 index 00000000..53180b09 Binary files /dev/null and b/static/img/LabIMotion_logo.png differ diff --git a/static/img/nmrXiv.svg b/static/img/nmrXiv.svg new file mode 100644 index 00000000..b3f206c4 --- /dev/null +++ b/static/img/nmrXiv.svg @@ -0,0 +1,6 @@ + + + + + + diff --git a/static/img/nmrium-logo.svg b/static/img/nmrium-logo.svg new file mode 100644 index 00000000..417ee4b5 --- /dev/null +++ b/static/img/nmrium-logo.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/static/img/radar4chem_Logo.svg b/static/img/radar4chem_Logo.svg new file mode 100644 index 00000000..e1c4cb45 --- /dev/null +++ b/static/img/radar4chem_Logo.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/static/img/smartlab/chemotion/analysis1.png b/static/img/smartlab/chemotion/analysis1.png new file mode 100644 index 00000000..efc52e03 Binary files /dev/null and b/static/img/smartlab/chemotion/analysis1.png differ diff --git a/static/img/smartlab/chemotion/analysis2.png b/static/img/smartlab/chemotion/analysis2.png new file mode 100644 index 00000000..b37c386e Binary files /dev/null and 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00000000..4c49ff7c Binary files /dev/null and b/static/img/smartlab/chemotion/chemotion_dataCollection_banner.png differ diff --git a/static/img/smartlab/chemotion/chemotion_dataLifecycle_banner.png b/static/img/smartlab/chemotion/chemotion_dataLifecycle_banner.png new file mode 100644 index 00000000..769f8ea1 Binary files /dev/null and b/static/img/smartlab/chemotion/chemotion_dataLifecycle_banner.png differ diff --git a/static/img/smartlab/chemotion/chemotion_experiment_banner.png b/static/img/smartlab/chemotion/chemotion_experiment_banner.png new file mode 100644 index 00000000..dea8dcf1 Binary files /dev/null and b/static/img/smartlab/chemotion/chemotion_experiment_banner.png differ diff --git a/static/img/smartlab/chemotion/chemotion_icons/chemotion_DoE.svg b/static/img/smartlab/chemotion/chemotion_icons/chemotion_DoE.svg new file mode 100644 index 00000000..a0a62688 --- /dev/null +++ b/static/img/smartlab/chemotion/chemotion_icons/chemotion_DoE.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/static/img/smartlab/chemotion/chemotion_icons/chemotion_analysis.svg b/static/img/smartlab/chemotion/chemotion_icons/chemotion_analysis.svg new file mode 100644 index 00000000..3de2c32a --- /dev/null +++ b/static/img/smartlab/chemotion/chemotion_icons/chemotion_analysis.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/static/img/smartlab/chemotion/chemotion_icons/chemotion_dataCollection_Processing.svg b/static/img/smartlab/chemotion/chemotion_icons/chemotion_dataCollection_Processing.svg new file mode 100644 index 00000000..cd1a8df0 --- /dev/null +++ b/static/img/smartlab/chemotion/chemotion_icons/chemotion_dataCollection_Processing.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/static/img/smartlab/chemotion/chemotion_icons/chemotion_dataPublication.svg b/static/img/smartlab/chemotion/chemotion_icons/chemotion_dataPublication.svg new file mode 100644 index 00000000..912ceabc --- /dev/null +++ b/static/img/smartlab/chemotion/chemotion_icons/chemotion_dataPublication.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/static/img/smartlab/chemotion/chemotion_icons/chemotion_experiment.svg b/static/img/smartlab/chemotion/chemotion_icons/chemotion_experiment.svg new file mode 100644 index 00000000..876ca9b5 --- /dev/null +++ b/static/img/smartlab/chemotion/chemotion_icons/chemotion_experiment.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/static/img/smartlab/chemotion/chemotion_icons/chemotion_reuse.svg b/static/img/smartlab/chemotion/chemotion_icons/chemotion_reuse.svg new file mode 100644 index 00000000..a9424482 --- /dev/null +++ b/static/img/smartlab/chemotion/chemotion_icons/chemotion_reuse.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/static/img/smartlab/chemotion/chemotion_lifecycle.svg b/static/img/smartlab/chemotion/chemotion_lifecycle.svg new file mode 100644 index 00000000..156017b7 --- /dev/null +++ b/static/img/smartlab/chemotion/chemotion_lifecycle.svg @@ -0,0 +1,112 @@ + + + + + + Experiment + Design + + + + Experiment + + + + Analysis + + + + + Data + Collection & + Processing + + + + + + Data + Publication + + + + Re-use + + + + + + + + \ No newline at end of file diff --git a/static/img/smartlab/chemotion/chemotion_publish_banner.png b/static/img/smartlab/chemotion/chemotion_publish_banner.png new file mode 100644 index 00000000..87a502c8 Binary files /dev/null and b/static/img/smartlab/chemotion/chemotion_publish_banner.png differ diff --git a/static/img/smartlab/chemotion/dataCollection1.png b/static/img/smartlab/chemotion/dataCollection1.png new file mode 100644 index 00000000..d1576f93 Binary files /dev/null and b/static/img/smartlab/chemotion/dataCollection1.png differ diff --git a/static/img/smartlab/chemotion/dataCollection2.png b/static/img/smartlab/chemotion/dataCollection2.png new file mode 100644 index 00000000..38b174f9 Binary files /dev/null and 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