Merge pull request #358 from NFDI4Chem/merge-357

Merge 357
NFDI4Chem · May 7, 2024 · bba21d5 · bba21d5
2 parents f80ad29 + 429f6fc
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diff --git a/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx b/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx
@@ -4,13 +4,13 @@ slug: "/choose_repository"
 ---
 
 import useBaseUrl from "@docusaurus/useBaseUrl";
-import DecisionTree from "@site/src/components/DecisionTree";
+import DecisionTree from "@site/src/components/repos/DecisionTree";
 
 # Choose a Repository
 
 The NFDI4Chem aims to support researchers in collecting, storing, processing, analysing, publishing, and reusing research data. Based on the [NFDI4Chem Community Survey](https://doi.org/10.1002/zaac.202000339), a list of the most [common data types and formats](/docs/pub_data_types_formats) of the community has been compiled to suggests suitable trusted chemistry-friendly repositories.
 
-This decision tree will guide users to quickly select a suitable repository for publishing their research data!
+This decision tree will guide users to quickly select a suitable repository for publishing their research data. Click on the repositories to learn more!
 
 <DecisionTree />
 

diff --git a/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx b/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx
@@ -3,13 +3,27 @@ title: "Chemotion Repository"
 slug: /chemotion_repository
 ---
 
-# Chemotion Repository – Repository for Samples, Reactions and Research data
-
-:::info Note:
-Link to [Chemotion Repository](https://www.chemotion-repository.net/), Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.iagXcR), Link to [re3data](http://doi.org/10.17616/R34P5T).
-:::
-
-## Quick facts
+import RepoButton from "@site/src/components/repos/RepoButton";
+
+_Repository for Samples, Reactions and Research data_
+
+<RepoButton
+    url="https://www.chemotion-repository.net/"
+    intro="Link to"
+    name="Chemotion Repository"
+/>
+<RepoButton
+    url="https://doi.org/10.25504/FAIRsharing.iagXcR"
+    intro="Entry on"
+    name="FAIRsharing"
+/>
+<RepoButton
+    url="http://doi.org/10.17616/R34P5T"
+    intro="Entry on"
+    name="re3data"
+/>
+
+:::info Quick facts
 
 -   **Accepted data types:**
     -   Mass spectrometry: mzML, mzXML, JCAMP-DX, vendor formats such as Thermo RAW are accepted and converted to mzML with Proteowizard's msconvert.
@@ -22,7 +36,7 @@ Link to [Chemotion Repository](https://www.chemotion-repository.net/), Link to [
 -   **Data deposition condition:** open
 -   **Recommended by Journals/Societies:** Recommended by [Angewandte Chemie](https://onlinelibrary.wiley.com/page/journal/15213773/homepage/notice-to-authors#sectFDataDeposition) and further Wiley journals.
 
-## Details
+:::
 
 Chemotion Repository is a **field-specific** repository and covers research data that is assigned to molecules, their properties and characterisation as well as reactions and experimental investigations. It is hosted at Karlsruhe Institute for Technology (KIT). Scientists in the domains of **molecular** and **synthetic chemistry** are supported in their efforts to handle data in a **FAIR** manner: the data is stored according to the common practices of scientists assigned to molecules and reactions and the system provides the required [Digital Object Identifiers](https://www.doi.org/) (DOIs) without additional effort for the scientist. The given metadata is supported by the implementation of ontology terms. The **findability** of the data is achieved by text, structure, and identifier search options and the submitted samples and their structure are referenced in PubChem to gain higher visibility of the work for the scientists. The repository is interoperable with the **Chemotion ELN** which means that data can be transferred from ELN to the repository. Data is curated by [automatic checks](https://www.chemotion-repository.net/home/howto/c40fdb44-8854-46bf-88b3-cc9d6adc3543) and a peer review process. The integration of data stored in the repository in publications was shown with several examples and its usage is currently recommended by [Chemistry—Methods](https://chemistry-europe.onlinelibrary.wiley.com/journal/26289725). Authors can be referenced by their [ORCID iDs](https://orcid.org/). Chemists and materials scientists can publish data for open access (data view) and registered access (dataset contribution and download). Stored data can be searched by chemical structure, author, dataset type, status, identifier, and DOI. The **current AAI solution** is based on an internal user administration (administrator, anonymous and registered user, curator). **Metadata** according to **DataCite** is compliant with the [Open Archives Initiative Protocol for Metadata Harvesting](http://www.openarchives.org/pmh/) **(OAI-PMH)** scheme. The Chemotion Repository offers an internal substance register, spectra viewers (ChemSpectra and NMRium), a structure editor (Ketcher), and their own data converter.
 

diff --git a/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx b/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx
@@ -3,22 +3,30 @@ title: "MassBank EU"
 slug: "/massbank_eu"
 ---
 
-import useBaseUrl from "@docusaurus/useBaseUrl";
+import RepoButton from "@site/src/components/repos/RepoButton";
 
-# MassBank EU – High Quality Mass Spectrometry Reference Database
+_High Quality Mass Spectrometry Reference Database_
 
-:::info Note:
-Link to [MassBank EU](https://massbank.eu/) and [RMassBank](https://bioconductor.org/packages/release/bioc/html/RMassBank.html), Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.dk451a), Link to [re3data](http://doi.org/10.17616/R3K05Z).
-:::
+<RepoButton url="https://massbank.eu/" intro="Link to" name="MassBank EU" />
+<RepoButton
+    url="https://doi.org/10.25504/FAIRsharing.dk451a"
+    intro="Entry on"
+    name="FAIRsharing"
+/>
+<RepoButton
+    url="http://doi.org/10.17616/R3K05Z"
+    intro="Entry on"
+    name="re3data"
+/>
 
-## Quick facts
+:::info Quick facts
 
 -   **Accepted data types:** MassBank format, see [RMassBank](https://bioconductor.org/packages/release/bioc/html/RMassBank.html).
 -   **Used standards/ontologies:** [MassBank Record Format](https://github.com/MassBank/MassBank-web/blob/main/Documentation/MassBankRecordFormat.md)
 -   **Data deposition condition:** open
 -   **Recommended by Journals/Societies:** Official database of the [Mass Spectrometry Society of Japan](https://www.mssj.jp/index_en.html)
 
-## Details
+:::
 
 MassBank EU is a **field-specific** and the first public repository of **mass spectrometry reference spectra**. Their target user groups in the domains of **chemistry** and **life sciences** are analytical chemists, metabolomics, biochemists, and bioinformaticians. Datasets from community users and projects are **openly accessible** and represent the official database of the [Mass Spectroscopy Society of Japan](https://www.mssj.jp/index_en.html).
 

diff --git a/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx b/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx
@@ -1,40 +1,53 @@
 ---
+title: "nmrXiv"
 slug: "/nmrxiv"
 ---
 
-import useBaseUrl from "@docusaurus/useBaseUrl";
+_Open, FAIR and Consensus-Driven NMR spectroscopy data repository and analysis platform_
 
-# nmrXiv
+import RepoButton from "@site/src/components/repos/RepoButton";
 
-:::info Note:
-Link to [nmrXiv](https://nmrxiv.org/), Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.052828), Link to [re3data](http://doi.org/10.17616/R31NJNGJ).
-:::
+<RepoButton url="https://nmrxiv.org/" intro="Link to" name="nmrXiv" />
+<RepoButton
+    url="https://doi.org/10.25504/FAIRsharing.052828"
+    intro="Entry on"
+    name="FAIRsharing"
+/>
+<RepoButton
+    url="http://doi.org/10.17616/R31NJNGJ"
+    intro="Entry on"
+    name="re3data"
+/>
 
-## Quick facts
+:::info Quick facts
 
 -   **Accepted data types:** all major NMR data formats – NMReData, Bruker
 -   **Used standards/ontologies:** [ontologies used](https://docs.nmrxiv.org/introduction/data/ontologies.html)
 -   **Data deposition condition:** open
 -   **Recommended by Journals/Societies:** The repository is recommended by [The Journal of Natural Products](https://pubs.acs.org/doi/10.1021/acs.jnatprod.3c00281) and by [Angewandte Chemie](https://onlinelibrary.wiley.com/page/journal/15213773/homepage/notice-to-authors)
 
-## Details
+:::
+
+### General Information
 
-**General Information**
 nmrXiv (pronounced nm-archive) is a FAIR and Open, Consensus-Driven Nuclear Magnetic Resonance (NMR) Data Repository and Computational platform. It is currently being developed with the ultimate goal of accelerating broader coordination and data sharing among researchers by creating a platform for managing, sharing, and analyzing raw and processed NMR spectral data.
 
 The immediate goal of nmrXiv is to integrate and execute the following objectives by establishing nmrXiv as a consensus-driven resource designed to serve global chemistry research and adjacent natural products / metabolomics communities.
 
-**Software Development**
+### Software Development
+
 To develop nmrXiv based on a voluntarily FAIR, cloud-based infrastructure that uses freely shared source code and deployment methods. Apply industry-grade development practices to ensure platform reliability, safety, and efficacy. Use Continuous Improvement principles will ensure an always-on user experience and high reliability. Release the codebase and infrastructure details (including the development, documentation, and usage practices) through MIT Open Source License for openness.
 
 More details about the platform architecture and related topics – [here](https://docs.nmrxiv.org/developer-guides/architecture.html)
 
-**Submission, Curation, and Analysis**
+### Submission, Curation, and Analysis
+
 Enable the FAIR sharing of raw NMR data to enhance the quality of chemical research and dissemination. Also, to develop non-prescriptivist curation and analysis standards for data and metadata. Build standards with input and contributions from the community and make them compatible with existing and potential newly developed formats and approaches.
 
 More details about the data standards and related topics – [here](https://docs.nmrxiv.org/category/data.html)
 
-**Workshops and Training**
+### Workshops and Training
+
 To engage analytical chemistry researchers and adjacent communities through webinars, workshops, tutorials, and community calls to ensure that nmrXiv meets the researchers’ needs and implements adequate incentive mechanisms for data contributions and curation.
 
 This documentation site comprises detailed walk-through explanations from basic to more complex functionalities for developers (Developer Guides), submitters (Submission Guides) and users (Search and API) of nmrXiv. All the adopted core concepts, such as Data Schemas, NMR File Formats, tools & Converters, Ontologies, FAIR best practices, etc., are documented to ensure a clear scaffolding for developers to revisit previously developed parts and continue building upon them. This documentation-first approach allows developers and users to discuss proposed features and ensure that the implementations reflect the actual use cases.

diff --git a/docs/50_data_publication/20_choose_repository/60_nomad.mdx b/docs/50_data_publication/20_choose_repository/60_nomad.mdx
@@ -3,22 +3,30 @@ title: "NOMAD"
 slug: "/nomad"
 ---
 
-import useBaseUrl from "@docusaurus/useBaseUrl";
+import RepoButton from "@site/src/components/repos/RepoButton";
 
-# NOMAD – NOvel MAterials Discovery
+_NOvel MAterials Discovery_
 
-:::info Note:
-Link to [NOMAD](https://nomad-lab.eu/), Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.aq20qn), Link to [re3data](http://doi.org/10.17616/R32K89).
-:::
+<RepoButton url="https://nomad-lab.eu/" intro="Link to" name="NOMAD" />
+<RepoButton
+    url="https://doi.org/10.25504/FAIRsharing.aq20qn"
+    intro="Entry on"
+    name="FAIRsharing"
+/>
+<RepoButton
+    url="http://doi.org/10.17616/R32K89"
+    intro="Entry on"
+    name="re3data"
+/>
 
-## Quick facts
+:::info Quick facts
 
 -   **Accepted data types:** [50 supported codes](https://nomad-lab.eu/prod/v1/gui/about/information)
 -   **Used standards/ontologies:** DataCite; no ontology at the moment (planned to create ontologies for specific parts of the data)
 -   **Data deposition condition:** open
 -   **Recommended by Journals/Societies:** The repository is recommended by [Scientific Data](https://www.nature.com/sdata/policies/repositories#materials), recommended by [Angewandte Chemie](https://onlinelibrary.wiley.com/page/journal/15213773/homepage/notice-to-authors#sectFDataDeposition) and further Wiley journals.
 
-## Details
+:::
 
 Nomad is a public repository operating since 2015 that is hosted at the MPCDF (Max Planck Computing and Data Facility) in Garching, Munich. It contains over 12 million datasets **(simulations)** generated from over 500 users, 98% of which is published. DOIs are attributed to almost half of them. Their target audience are solid state physicists and theoretical chemists. Data on **computational** materials science, computational **chemistry**, and molecular physics are those typically contained in the repository. There is a simulation data recognition process during upload and the repository supports the input/output formats of 50 different codes. NOMAD offers an API for data import and export. The repository is recommended by [Scientific Data](https://www.nature.com/sdata/policies/repositories#materials) of the Nature publishing group.
 

diff --git a/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx b/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx
@@ -3,22 +3,34 @@ title: "RADAR4Chem"
 slug: "/radar4chem"
 ---
 
-import useBaseUrl from "@docusaurus/useBaseUrl";
-
-# RADAR4Chem – Research Data Repository for Chemistry
-
-:::info Note:
-Link to [RADAR4Chem](https://radar4chem.radar-service.eu/), Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.3b3157), Link to [re3data](http://doi.org/10.17616/R31NJNAY).
-:::
-
-## Quick facts
+import RepoButton from "@site/src/components/repos/RepoButton";
+
+_Research Data Repository for Chemistry_
+
+<RepoButton
+    url="https://radar4chem.radar-service.eu/"
+    intro="Link to"
+    name="RADAR4Chem"
+/>
+<RepoButton
+    url="https://doi.org/10.25504/FAIRsharing.3b3157"
+    intro="Entry on"
+    name="FAIRsharing"
+/>
+<RepoButton
+    url="http://doi.org/10.17616/R31NJNAY"
+    intro="Entry on"
+    name="re3data"
+/>
+
+:::info Quick facts
 
 -   **Accepted data types:** All data types/formats ([format recommendations](https://radar.products.fiz-karlsruhe.de/en/radarabout/dateiformate) exist)
 -   **Used standards/ontologies:** [RADAR Metadata Schema](https://radar.products.fiz-karlsruhe.de/en/radarfeatures/radar-metadatenschema) (based on DataCite Metadata Schema 4.0), Dublin Core, schema.org
 -   **Data deposition condition:** controlled
 -   **Recommended by Journals/Societies:** Recommended by [Angewandte Chemie](https://onlinelibrary.wiley.com/page/journal/15213773/homepage/notice-to-authors#sectFDataDeposition) and further Wiley journals.
 
-## Details
+:::
 
 RADAR4Chem is a **multidisciplinary** repository for the publication of research data from **all disciplines** of **chemistry**. It was created in 2022 and is hosted at FIZ Karlsruhe (Leibniz Institute for Information Infrastructure). RADAR4Chem is based on the established research data repository **RADAR Cloud**. RADAR Cloud is primarily used by academic institutions for institutional research data management (data archiving and publication). The use of **RADAR Cloud** is subject to a **fee** and requires the stipulation of a **contract**. **RADAR4Chem**, on the other hand, is exclusively directed to researchers in the field of chemistry at publicly funded research institutions and universities in Germany. **No contract** is required and **no fees** are charged. RADAR4Chem allows discipline- and format-independent publication and storage (**at least 25 years**) of **research data** from all disciplines of chemistry. It complements the already existing portfolio of discipline specific repositories and is e.g. ideally suited for cross-disciplinary data or datasets with a multitude of different data formats. RADAR4Chem is easy and low-threshold to use. The researchers are responsible for the upload, organisation, annotation, and curation of research data as well as the peer-review process (as an optional step) and finally their publication. Using the service requires [advising from FIZ Karlsruhe](https://www.nfdi4chem.de/index.php/2650-2/), registration to RADAR4Chem, and consent to the [RADAR4Chem license and usage instructions](https://radar.products.fiz-karlsruhe.de/sites/default/files/radar/docs/terms/License_and_User_Instructions_for_Data_Providers_RADAR4Chem.pdf). Authentication is supported after self-registration and via [DFN-AAI](https://doku.tid.dfn.de/en:dfnaai:start) ([Shibboleth](https://www.incommon.org/software/shibboleth/). **Metadata** are recorded using the internal [RADAR Metadata Schema](https://radar.products.fiz-karlsruhe.de/en/radarfeatures/radar-metadatenschema) (based on [DataCite Metadata Schema 4.0](https://schema.datacite.org/)), which supports 10 **mandatory** and 13 **optional metadata fields**. Annotation can be made on the dataset level and on the individual files and folders level. A [user license](https://radar.products.fiz-karlsruhe.de/en/radarfeatures/lizenzen-fuer-forschungsdaten) which indicates re-use rules for the data, must be defined for each dataset. Each published dataset receives a **DOI** which is registered with [DataCite](https://datacite.org/). RADAR Metadata uses a combination of controlled lists and free text entries. Author identification is ensured by ORCID iD and funder identification by [CrossRef Open Funder Registry](https://www.crossref.org/pdfs/about-funder-registry.pdf) (more interfacing options will be implemented in the future). Datasets can be easily linked with other digital resources (e.g. text publications) via a **“related identifier”**. To maximise data dissemination and discoverability, the metadata of published datasets are indexed in various formats (e.g. RADAR and DataCite) and offered for public metadata harvesting e.g. via an [OAI-provider](https://radar.products.fiz-karlsruhe.de/en/radarfeatures/radar-oai-provider). The **research data** is **stored permanently** on magnetic tapes redundantly in three copies at different locations at the Steinbuch Centre for Computing (SCC) of the Karlsruhe Institute of Technology (KIT, 2 copies) and at the Centre for Information Services and High Performance Computing (ZIH) of the TU Dresden (1 copy).