diff --git a/docs/10_domains/20_physical_chemistry.mdx b/docs/10_domains/20_physical_chemistry.mdx
index 09dce427..e7b80482 100644
--- a/docs/10_domains/20_physical_chemistry.mdx
+++ b/docs/10_domains/20_physical_chemistry.mdx
@@ -22,7 +22,7 @@ As mentioned, the data produced in physical chemistry and its diverse sub-discip
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. Many universities supply tools and templates for DMPs (see the [respective article](/docs/dmp) for more information).
-An [electronic lab notebooks (ELNs)](/docs/eln) helps in the day-to-day planning and structured documentation of experiments, while some also assist in data workflow management. For disciplines with diverse research, ELNs must be flexible and customizable. Certain universities may have a central option, while each research group may chose what best fits their needs and resources if they are able to host or procure their own solution. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) lists many options and the article on [choosing an ELN](/docs/chose_eln) provides further assistance:
+An [electronic lab notebooks (ELNs)](/docs/eln) helps in the day-to-day planning and structured documentation of experiments, while some also assist in data workflow management. For disciplines with diverse research, ELNs must be flexible and customizable. Certain universities may have a central option, while each research group may chose what best fits their needs and resources if they are able to host or procure their own solution. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) lists many options and the article on [choosing an ELN](/docs/choose_eln) provides further assistance:
diff --git a/docs/50_data_publication/00_data_publishing.mdx b/docs/50_data_publication/00_data_publishing.mdx
index 9890fc52..86f61e96 100644
--- a/docs/50_data_publication/00_data_publishing.mdx
+++ b/docs/50_data_publication/00_data_publishing.mdx
@@ -16,7 +16,7 @@ This page applies to all researchers who want to publish their data.
In chemical research, we strive to share results with others, commonly through articles in renowned scientific journals. To be able to actually work with and build upon these results, the scientific community also requires the data that the results were based on.
-Publishing and therefore sharing these chemistry research data in a [FAIR](/docs/fair) manner by considering aspects such as [persistent identifiers](/docs/pid/), rich [metadata](/docs/metadata), [provenance information](/docs/provenance/), [data formats standards](/docs/format_standards) for analytical data, information on the [license](/docs/licenses/) applied, and by providing [machine-readable chemical structures](/docs/machine-readable_chemical_structures) adds value to the research results and enables discovery and reuse.
+Publishing and therefore sharing these chemistry research data in a [FAIR](/docs/fair) manner by considering aspects such as [persistent identifiers](/docs/pid), rich [metadata](/docs/metadata), [provenance information](/docs/provenance), [data formats standards](/docs/format_standards) for analytical data, information on the [license](/docs/licences) applied, and by providing [machine-readable chemical structures](/docs/machine-readable_chemical_structures) adds value to the research results and enables discovery and reuse.
To publish data is essential to ensure that findings are transparent and reproducible. Moreover, it prevents duplicate efforts to generate data, hence, data publishing is also a measure of sustainability.
diff --git a/docs/50_data_publication/30_licences.mdx b/docs/50_data_publication/30_licences.mdx
index 6891c2f0..5353f3c8 100644
--- a/docs/50_data_publication/30_licences.mdx
+++ b/docs/50_data_publication/30_licences.mdx
@@ -7,14 +7,14 @@ import useBaseUrl from "@docusaurus/useBaseUrl";
# Licences
-Licences for research data often cause confusion among researchers. One of the main reasons for this is the interplay between **licences used for research data** and the requirements for referencing previous scientific work on which the current work is based, in accordance with the [Guidelines for Safeguarding Good Scientific Practice (DFG Code of Conduct)](https://wissenschaftliche-integritaet.de/en/code-of-conduct/).
+Licences for research data often cause confusion among researchers. One of the main reasons for this is the interplay between **licences used for research data** and the requirements for referencing previous scientific work on which the current work is based, in accordance with the [Guidelines for Safeguarding Good Scientific Practice (DFG Code of Conduct)](https://wissenschaftliche-integritaet.de/en/code-of-conduct/).
The DFG Code of Conduct requires researchers to cite original sources, i.e. to include original sources in reference sections. Providing a licence for research data is a way to provide permission to share and reuse the data.
-Work on dedicated licences for research data is ongoing. Until these licences are available, we recommend switching to [Creative Commons]((https://creativecommons.org/)) licences, which were developed to license creative works.
+Work on dedicated licences for research data is ongoing. Until these licences are available, we recommend switching to [Creative Commons](https://creativecommons.org/) licences, which were developed to license creative works.
:::info Recommendation:
-NFDI4Chem recommends the use the least restrictive [Creative Commons](https://creativecommons.org/) licences such as [CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/deed.en)
+NFDI4Chem recommends the use the least restrictive [Creative Commons](https://creativecommons.org/) licences such as [CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/deed.en)
:::
:::danger Notice:
@@ -27,10 +27,10 @@ Disclaimer: It should be checked on a case-by-case basis whether research data i
In order to provide you with further helpful information, we have compiled a list of links:
-- [Heidi Seibold - Choosing an open license](https://heidiseibold.ck.page/posts/choosing-an-open-license)
-- [Forschungsdaten.info - Forschungsdaten Veröffentlichen](https://forschungsdaten.info/themen/rechte-und-pflichten/forschungsdaten-veroeffentlichen/) (in German)
-- [Forschungsdaten.info - Urheberrecht](https://forschungsdaten.info/themen/rechte-und-pflichten/urheberrecht/) (in German)
-- [Creative Commons - About CC Licenses](https://creativecommons.org/share-your-work/cclicenses/)
-- [Creative Commons - License Chooser](https://creativecommons.org/choose/)
-- [Forschungsdaten in den Naturwissenschaften: Eine urheberrechtliche Bestandsaufnahme mit ihren Implikationen für universitäres FDM](https://doi.org/10.11588/heibooks.979.c13728) (in German)
-- [Open Knowledge Foundation - Open Data Commons](https://opendatacommons.org/licenses/odbl/)
+- [Heidi Seibold - Choosing an open license](https://heidiseibold.ck.page/posts/choosing-an-open-license)
+- [Forschungsdaten.info - Forschungsdaten Veröffentlichen](https://forschungsdaten.info/themen/rechte-und-pflichten/forschungsdaten-veroeffentlichen/) (in German)
+- [Forschungsdaten.info - Urheberrecht](https://forschungsdaten.info/themen/rechte-und-pflichten/urheberrecht/) (in German)
+- [Creative Commons - About CC Licenses](https://creativecommons.org/share-your-work/cclicenses/)
+- [Creative Commons - License Chooser](https://creativecommons.org/choose/)
+- [Forschungsdaten in den Naturwissenschaften: Eine urheberrechtliche Bestandsaufnahme mit ihren Implikationen für universitäres FDM](https://doi.org/10.11588/heibooks.979.c13728) (in German)
+- [Open Knowledge Foundation - Open Data Commons](https://opendatacommons.org/licenses/odbl/)
diff --git a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
index c34472d5..de11fda4 100644
--- a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
+++ b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx
@@ -6,7 +6,7 @@ slug: "/publishing_standards_publishers"
### Recommendations for trusted, chemistry-friendly repositories
:::tip Standard
-*Journals should recommend trusted, chemistry-friendly research data repositories.*
+_Journals should recommend trusted, chemistry-friendly research data repositories._
:::
To assist authors in selecting **well-established and community-specific [repositories](/docs/repositories/)** for their research data, [trusted chemistry friendly repositories](/docs/choose_repository/) should be recommended by journals. These should be included within the author guidelines or the data policies.
@@ -14,15 +14,15 @@ To assist authors in selecting **well-established and community-specific [reposi
### Recommendations to include data availability statements
:::tip Standard
-*Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.*
+_Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration._
:::
-[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should be made available to authors in the journal's author guidelines. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned whether the templates are selectable and the information should be provided via the manuscript submission system or whether this information should be manually inserted into the initially submitted manuscript by the authors.
+[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should be made available to authors in the journal's author guidelines. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](/docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned whether the templates are selectable and the information should be provided via the manuscript submission system or whether this information should be manually inserted into the initially submitted manuscript by the authors.
-### Data availability statements and manuscript submission systems
+### Data availability statements and manuscript submission systems
:::tip Standard
-*Journals should add a data availability statement to published articles and collect the necessary information through their submission systems.*
+_Journals should add a data availability statement to published articles and collect the necessary information through their submission systems._
:::
[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g. `https://doi.org/10.1000/182` ), repository name, third party name and contact information (in case of third-party data ownership), or reasons for restricted access and information on how to access a dataset, depending on the template used.
@@ -30,23 +30,22 @@ To assist authors in selecting **well-established and community-specific [reposi
### Link datasets to articles in Crossref DOI metadata
:::tip Standard
-*Journals should use the information available in data availability statements to enhance Crossref DOI metadata by linking articles to datasets.*
+_Journals should use the information available in data availability statements to enhance Crossref DOI metadata by linking articles to datasets._
:::
-With the DOI and repository name in hand, journals should enrich Crossref DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. Without defining a relation in the Crossref metadata, only humans can effectively interpret this connection through the data availability statement, effectively resulting in a missing link between the the reported results in the article and the underlying research data. For Crossref metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata).
-
-
+With the DOI and repository name in hand, journals should enrich Crossref DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. Without defining a relation in the Crossref metadata, only humans can effectively interpret this connection through the data availability statement, effectively resulting in a missing link between the the reported results in the article and the underlying research data. For Crossref metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata).
In agreement with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/), the relationship type `isSupplementedBy` should be used.
In XML:
+
```xml
- Dataset in <<>>.
+ Dataset in <<>>.
- 10.prefix/suffix
@@ -56,38 +55,39 @@ identifier-type="doi">10.prefix/suffix
### Add data publications to prior publication policy
:::tip Standard
-*Journal author guidelines should explicitly encourage pre-submission of datasets.*
+_Journal author guidelines should explicitly encourage pre-submission of datasets._
:::
Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is also already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of datasets are registered. DOIs can therefore be validated and datasets can be included in the review process.
:::danger Danger
-A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset must then be manually updated by the authors after the article has been published. Datasets with status *under review* are one way to overcome this disadvantage (see below).
+A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset must then be manually updated by the authors after the article has been published. Datasets with status _under review_ are one way to overcome this disadvantage (see below).
:::
### Recommendations to include research data in the review process
:::tip Standard
-*Journal author guidelines should explicitly encourage research data to be included in the review process.*
+_Journal author guidelines should explicitly encourage research data to be included in the review process._
:::
-Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not yet published, i.e. it does not have a DOI registered. Therefore, the DOI cannot be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers.
+Some repositories have an _under review_ status alongside the _draft_ and _published_ statuses. A dataset _under review_ is not editable and not yet published, i.e. it does not have a DOI registered. Therefore, the DOI cannot be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers.
-### Encourage authors to publish datasets *under review* prior to article publication
+### Encourage authors to publish datasets _under review_ prior to article publication
:::tip Standard
-*Journal author guidelines should require that datasets with status under review to be published prior to the publication of the associated article.*
+_Journal author guidelines should require that datasets with status under review to be published prior to the publication of the associated article._
:::
-To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published before the article is published**. Once a manuscript has been accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journals can run quality control checks on the provided DOI such as validation. Publishers must explicitly communicate this process with authors through the author guidelines. In addition, other communication upon acceptance may also include this informaton. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article is published, and its DOI is registered.
+To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets _under review_ should be published before the article is published**. Once a manuscript has been accepted, the authors should be informed to publish their dataset _under review_. This ensures that the data has a registered DOI when the article gets published. Consequently, journals can run quality control checks on the provided DOI such as validation. Publishers must explicitly communicate this process with authors through the author guidelines. In addition, other communication upon acceptance may also include this informaton. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article is published, and its DOI is registered.
### Scholix.org
:::tip Standard
-*Journals and publishers should use Scholix.org.*
+_Journals and publishers should use Scholix.org._
:::
[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above).
-----
+---
+
Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840)
diff --git a/docs/60_topics/00_topics_guide.mdx b/docs/60_topics/00_topics_guide.mdx
index c95d1529..8daefcc6 100644
--- a/docs/60_topics/00_topics_guide.mdx
+++ b/docs/60_topics/00_topics_guide.mdx
@@ -4,9 +4,8 @@ slug: "/topics_guide"
id: "topics_guide"
---
-
:::info Info:
-The topics and concepts section offers topic-specific articles on very specific subjects in research data management and digitalization in chemistry This section is sub-divided into further categories for easy reference.
+The topics and concepts section offers topic-specific articles on very specific subjects in research data management and digitalization in chemistry This section is sub-divided into further categories for easy reference.
:::
For data to be interoperable and reusable, [data formats standards](62_data_formats/00_format_standards.mdx) are of utmost importance. Development here is ongoing and we will continue to add information on formats.
@@ -15,15 +14,8 @@ In order to ensure that data are permanently referenced and cited, repositories
Annotating data with machine-readable [metadata](63_data_description_annotation/10_metadata.mdx) plays into nearly all aspects of FAIR and ensures data are understood by machines and humans alike. Here, the core concepts of [ontologies](/docs/ontology) in one's research domain proves helpful.
+## Topics in this Section
-
- Click to expand for all the Categories
-
- Topics & Concepts
-
-Identifiers
-Data Formats
-Data Description and Annotation
-
-
-
+- [Identifiers](/docs/identifiers)
+- [Data Formats](/docs/format_standards)
+- [Data Description and Annotation](/docs/data_description_annotation)
diff --git a/docusaurus.config.js b/docusaurus.config.js
index 0902e44e..e775ebcc 100644
--- a/docusaurus.config.js
+++ b/docusaurus.config.js
@@ -123,6 +123,9 @@ const config = {
},
],
],
+ future: {
+ experimental_faster: true,
+ },
};
export default config;
diff --git a/package.json b/package.json
index b07b125d..aad33d0f 100644
--- a/package.json
+++ b/package.json
@@ -15,12 +15,13 @@
"crowdin": "crowdin"
},
"dependencies": {
- "@crowdin/cli": "^4.1.2",
- "@docusaurus/core": "^3.5.2",
- "@docusaurus/preset-classic": "^3.5.2",
- "@easyops-cn/docusaurus-search-local": "^0.44.5",
+ "@crowdin/cli": "^4.3.0",
+ "@docusaurus/core": "^3.6.1",
+ "@docusaurus/faster": "^3.6.1",
+ "@docusaurus/preset-classic": "^3.6.1",
+ "@easyops-cn/docusaurus-search-local": "^0.45.0",
"@fontsource/ibm-plex-sans": "^5.1.0",
- "@mdx-js/react": "^3.0.1",
+ "@mdx-js/react": "^3.1.0",
"clsx": "^2.1.1",
"docusaurus-plugin-matomo": "^0.0.8",
"i": "^0.3.7",
@@ -33,8 +34,8 @@
"video-privacy": "^1.1.0"
},
"devDependencies": {
- "@docusaurus/module-type-aliases": "^3.5.2",
- "@docusaurus/types": "3.5.2"
+ "@docusaurus/module-type-aliases": "^3.6.1",
+ "@docusaurus/types": "3.6.1"
},
"browserslist": {
"production": [