Merge branch 'NFDI4Chem:localisation' into localisation

docs/50_data_publication/20_choose_repository/10_choose_repository.mdx

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+---
+title: "Choose a Repository"
+slug: "/choose_repository"
+---
+
+import useBaseUrl from "@docusaurus/useBaseUrl";
+
+# 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!
+
+![Choose a Repository - Decision Tree](/img/data_pub/Repo_decision_tree_v2.svg)
+
+:::danger Notice:
+Choosing the most appropriate repository can make data easier to find and cite. Field-specific repositories should be the first choice as these repositories enhance the FAIRness of specific types of chemistry data on behalf of the submitters. To retain the same level of FAIRness, data publishing in generic, multidisciplinary repositories requires manual, time-consuming and labour-intensive FAIRification.
+:::
+
+Based on the [criteria](https://doi.org/10.3897/rio.6.e55852) chosen by Task Area 3, NFDI4Chem also offers recommendations with essential information on chemistry-friendly repositories that are suitable and trustworthy, as outlined in the following lists.
+
+## Core Repositories
+
+-   [Chemotion Repository](https://www.chemotion-repository.net/)<br/>Field-specific sample and reaction-centric repository including analysis data such as NMR, UV-VIS, IR, and MS data.
+-   [MassBank EU](https://massbank.eu/MassBank/)\*<br/>Field-specific ecosystem of databases and tools for mass spectrometry reference spectra.
+-   [nmrXiv](https://docs.nmrxiv.org/)<br/>Field-specific repository for NMR data.
+-   [RADAR4Chem](https://radar4chem.radar-service.eu/)<br/>Generic, multidisciplinary repository that offers a free and reliable home for all chemical research data that do not fulfil the specifications of field-specific repositories.
+-   [STRENDA DB](https://www.beilstein-strenda-db.org/)<br/>Field-specific repository for enzymology data, which incorporates the STRENDA Guidelines for reporting enzymology data.
+-   [SUPRABANK](https://suprabank.org/)<br/>Field-specific repository for intermolecular interactions data.
+
+\*Resource which does not accept direct submission of MS data in vendor or mzML format, but data in MassBank format, see [RMassBank](https://bioconductor.org/packages/release/bioc/html/RMassBank.html).
+
+## Associated repositories
+
+-   [Cambridge Structural Database](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/)\*<br/>Field-specific repository for x-ray diffraction data of molecules generally containing at least carbon and hydrogen, operated by the Cambridge Crystallographic Data Centre (CCDC).
+-   [Inorganic Crystal Structure Database](https://icsd.fiz-karlsruhe.de/)\*<br/>Field-specific repository for x-ray diffraction data of inorganic compounds, elements, minerals, intermetallic phases and ionic solids, operated by FIZ Karlsruhe.
+-   [Joint CCDC/FIZ Access Structures Service](https://www.ccdc.cam.ac.uk/structures/)<br/>Service that provides open access to the CSD Structure Depot, but not to all CSD data.
+
+\*Resource for which a license agreement is required.
+
+## Further Repositories
+
+-   [NOMAD](https://nomad-lab.eu/)<br/>Field-specific repository for computational materials science data.
+-   [ioChem-BD](https://www.iochem-bd.org/)<br/>Field-specific repository for computational chemistry data.
+-   [RADAR](https://www.radar-service.eu/radar/en/home)\*<br/>Generic, multidisciplinary repository for all types of chemical research data that do not meet the specifications of any field-specific repository.
+-   [Zenodo](https://zenodo.org/)<br/>Generic repository developed under the European OpenAIRE program, operated by CERN.
+-   [EUDAT B2SHARE](https://sp.eudat.eu/catalog/resources/709c053d-3b3f-4c54-8ef4-6efeea387816)<br/>Generic repository operated by a pan-european network consisting of more than 25 research organisations, data and computing centers.
+
+\*Resource for which a license agreement is required.
+
+## Currently under Development within NFDI4Chem
+
+-   [VibSpecDB](https://vibspecdb.k8s.photonicdata.science/)<br/>Filed-specific repository for IR and Raman data.
+
+:::danger Notice:
+We published an [analysis of the landscape of repositories for chemistry research data in re3data](https://zenodo.org/doi/10.5281/zenodo.8347992) and [criteria for chemistry repositories](https://zenodo.org/doi/10.5281/zenodo.8199754) on Zenodo. These lists will be continuously updated with further recommendations on trusted and chemistry-friendly repositories.
+:::
+
+:::info Note:
+Further details of the repositories listed above can be found on the sub-pages of this page via the navigation pane on the left
+:::
+
+---
+
+Main authors: [ORCID:0000-0001-7696-7662](https://orcid.org/0000-0001-7696-7662), [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661) and [ORCID:0000-0002-5035-7978](https://orcid.org/0000-0002-5035-7978)
+
+_This page is licensed under a Creative Commons Universal ([CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/deed.en)) Public Domain Dedication International License to allow for reuse of these lists._
+
+![CC0 badge](/img/cc-zero.svg)

docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx

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+---
+title: "Data Types and Formats"
+slug: /pub_data_types_formats
+---
+
+# Common Data Types and Formats
+
+Based on the results generated by a [survey](https://doi.org/10.1002/zaac.202000339) carried out by the NFDI4Chem consortium in 2020 and the yearly interviews with the repository leaders performed by NFDI4Chem's Task Area 3 repository team, a list of the most common data types and formats within this community was collected and is reported in Table 1. This table displays which data types are most commonly collected within the chemistry community and suggests which repository is most suitable for storing your specific data type.
+
+The information provided in Table 1 will also guide you to efficiently and quickly select the best repository for the storage of your specific type of chemistry data.  
+
+| Data type | Data format | Suggested Repository | Criteria for selection |
+| :-------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | :----------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------- |
+| Nuclear Magnetic Resonance | Bruker format (as ZIP), JCAMP-DX | [Chemotion](https://www.chemotion-repository.net/) | Passing quality checks, curation/review prior publishing |
+| Nuclear Magnetic Resonance | Bruker format (as ZIP), JOEL format, JCAMP-DX, NMReData, nmrML | [nmrXiv](https://docs.nmrxiv.org/) | Validations / Minimum information reporting standards |
+| Mass Spectrometry | MassBank format see [RMassBank](https://bioconductor.org/packages/release/bioc/html/RMassBank.html) | [MassBank EU](https://massbank.eu/) | Passing validation, curation prior publishing |
+| Mass Spectrometry | mzML, JCAMP-DX; Vendor formats such as Thermo RAW are accepted and converted in Chemotion to mzML with Proteowizard's msconvert. | [Chemotion](https://www.chemotion-repository.net) | Passing quality checks, curation/review prior publishing |
+| Infrared and Raman | JCAMP-DX; certain vendor formats are accepted and converted to JCAMP-DX by ChemConverter. | [Chemotion](https://www.chemotion-repository.net) | Passing quality checks, curation/review prior publishing |
+| X-Ray Diffraction | JCAMP-DX; certain vendor formats are accepted and converted to JCAMP-DX by ChemConverter. | [Chemotion](https://www.chemotion-repository.net) | Passing quality checks, curation/review prior publishing |
+| Ultraviolet–Visible Spectroscopy | JCAMP-DX; certain vendor formats are accepted and converted to JCAMP-DX by ChemConverter. | [Chemotion](https://www.chemotion-repository.net) | Passing quality checks, curation/review prior publishing |
+| Cyclic Voltammetry | JCAMP-DX; certain vendor formats such as Gamry DTA, Metrohm CSV and TXT and PalmSens PSSESSION are accepted and converted to JCAMP-DX by ChemConverter. | [Chemotion](https://www.chemotion-repository.net) | Passing quality checks, curation/review prior publishing |
+| Circular Dichroism Spectroscopy | JCAMP-DX; certain vendor formats are accepted and converted to JCAMP-DX by ChemConverter. | [Chemotion](https://www.chemotion-repository.net) | Passing quality checks, curation/review prior publishing |
+| Dynamic Light Scattering | JJCAMP-DX; certain vendor formats are accepted and converted to JCAMP-DX by ChemConverter. | [Chemotion](https://www.chemotion-repository.net) | Passing quality checks, curation/review prior publishing |
+| HPLC-UV-VIS | JCAMP-DX; certain vendor formats are accepted and converted to JCAMP-DX by ChemConverter. | [Chemotion](https://www.chemotion-repository.net) | Passing quality checks, curation/review prior publishing |
+| Size Exclusion Chromatography | JCAMP-DX; certain vendor formats are accepted and converted to JCAMP-DX by ChemConverter. | [Chemotion](https://www.chemotion-repository.net) | Passing quality checks, curation/review prior publishing |
+| Thermogravimetric Analysis | JCAMP-DX; certain vendor formats are accepted and converted to JCAMP-DX by ChemConverter. | [Chemotion](https://www.chemotion-repository.net) | Passing quality checks, curation/review prior publishing |
+| Inorganic crystal structures | Crystallographic Information File (CIF) | [ICSD](https://icsd.fiz-karlsruhe.de/) | Crystal structure data available |
+| Crystal structures of organic and molecular inorganic compounds  | 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 molecular crystal structure data | primarily Crystallographic Information File (CIF, other file formats supported and accepted | [joint CCDC/FIZ Access Structures Service](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) |
+| Simulation | [50 supported codes](https://nomad-lab.eu/prod/v1/gui/about/information) | [NOMAD](https://nomad-lab.eu/) | Simulation data recognition during upload |
+| Multidisciplinary | format-independent | [RADAR4Chem](https://www.radar-service.eu/de) | Validation against metadata schema |
+| Enzyme kinetics data | currently none | [STRENDA DB](https://www.beilstein-strenda-db.org/strenda//) | None; STRENDA compliant, peer-reviewed data publishing |
+| Intermolecular and supramolecular interactions of molecular systems | JSON (DataCite), CDX\* (for 2D/3D molecule structure), PNG, proprietary formats | [Suprabank](https://suprabank.org/) | Non-judgmental plausibility |

docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx

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+---
+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
+
+-   **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.
+    -   NMR: Bruker format (as ZIP) and JCAMP-DX.
+    -   IR and Raman: JCAMP-DX
+    -   XRD: JCAMP-DX,
+    -   UV-VIS: JCAMP-DX,
+    -   Cyclic voltammetry: JCAMP-DX, vendor formats such as Gamry DTA, Metrohm CSV and TXT and PalmSens PSSESSION are accepted and converted by ChemConverter.
+-   **Used standards/ontologies:** [DataCite Metadata Schema](https://schema.datacite.org/), InChI and InChIKey, SMILES, Biovia Molfile V2000 and V3000, Chemical Methods/[CHMO Ontology](http://www.ontobee.org/ontology/CHMO), Name Reaction Ontology/[RXNO Ontology](http://www.ontobee.org/ontology/RXNO).
+-   **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.
+
+Please note: Chemotion Repository accepts all data types and some of them can be also processed and edited in spectral viewers.
+
+---
+
+Main authors: [ORCID:0000-0001-9513-2468](https://orcid.org/0000-0001-9513-2468), [ORCID:0000-0001-7696-7662](https://orcid.org/0000-0001-7696-7662), [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661) and [ORCID:0000-0002-5035-7978](https://orcid.org/0000-0002-5035-7978)

docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx

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+---
+title: "MassBank EU"
+slug: "/massbank_eu"
+---
+
+import useBaseUrl from "@docusaurus/useBaseUrl";
+
+# MassBank EU – 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).
+:::
+
+## 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).
+
+GitHub is used as their current **AAI environment** (open read access, limited write access), whereas [GitHub issues](https://github.com/MassBank/MassBank-web/issues) serves as their curation tracking system. The curation itself is performed by the [MassBank record validator](https://massbank.github.io/MassBank-documentation/contributor_documentation.html). The datasets can be **searched** for **compound** and mass spectrometry **information** and **peaks**. MassBank Record ID (Accession) and USI (Universal Spectrum Identifier) are used as **persistent identifier systems**. The MassBank EU spectrometric data is hosted in a revision control system with all spectrometric data and the corresponding metadata in a human-readable record format, and continuous integration (CI) checking record integrity for each change. Instances of the web interface are hosted at Helmholtz Centre for Environmental Research (UFZ) (Leipzig) and Leibniz Institute of Plant Biochemistry (IPB) (Halle) and can be installed locally as well. They offer interfaces for data import via Git (MassBank record format) and for data export (JSON-LD) and a REST API. On top of that [RMassBank](https://github.com/MassBank/RMassBank) is provided as a separated data processing/analysis tool.
+
+---
+
+Main authors: [ORCID:0000-0002-7899-7192](https://orcid.org/0000-0002-7899-7192), [ORCID:0000-0001-7696-7662](https://orcid.org/0000-0001-7696-7662), [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661) and [ORCID:0000-0002-5035-7978](https://orcid.org/0000-0002-5035-7978)