From ca4b4953cdbfc02f19fcd1700d7a7be6b7f1b257 Mon Sep 17 00:00:00 2001 From: Johannes Liermann Date: Tue, 26 Mar 2024 11:00:46 +0100 Subject: [PATCH 01/14] chore: template for new "choose repo" structure --- .../10_choose_repository.mdx} | 0 .../20_chemotion_repo.mdx | 21 +++++++++++++++++++ .../20_choose_repository/_category_.json | 7 +++++++ 3 files changed, 28 insertions(+) rename docs/50_data_publication/{20_choose_repository.mdx => 20_choose_repository/10_choose_repository.mdx} (100%) create mode 100644 docs/50_data_publication/20_choose_repository/20_chemotion_repo.mdx create mode 100644 docs/50_data_publication/20_choose_repository/_category_.json diff --git a/docs/50_data_publication/20_choose_repository.mdx b/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx similarity index 100% rename from docs/50_data_publication/20_choose_repository.mdx rename to docs/50_data_publication/20_choose_repository/10_choose_repository.mdx diff --git a/docs/50_data_publication/20_choose_repository/20_chemotion_repo.mdx b/docs/50_data_publication/20_choose_repository/20_chemotion_repo.mdx new file mode 100644 index 00000000..9923f129 --- /dev/null +++ b/docs/50_data_publication/20_choose_repository/20_chemotion_repo.mdx @@ -0,0 +1,21 @@ +--- +slug: /chemotion_repo +--- + +# Chemotion Repository + +:::info Quick stats + +- **Accepted data types:** mass spectrometry: JCAMP-DX, mzMl, mzXML (open, visualisable and processable), RAW for selected mass data types (processed and converted in JCAMP-DX), NMR: Bruker XWIN-NMR format (zip) and 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. +- **Used standards/ontologies:** [DataCite Metadata Schema](https://schema.datacite.org/), InChI, SMILES, molfile V2000 and V3000 [CHMO Ontology](http://www.ontobee.org/ontology/CHMO), [RXNO Ontology](http://www.ontobee.org/ontology/RXNO) +- **Access rights/licence information/embargo:** CC0, CCBY, CCBY-SA, public domain; embargo period possible (unlimited) +- **Recommended by Journals/Societies:** Recommended by [Angewandte Chemie](https://onlinelibrary.wiley.com/page/journal/15213773/homepage/notice-to-authors#sectFDataDeposition) and further Wiley journals. + +::: + +## Chemotion - Repository for molecules and research data + +The Chemotion Repository is a field-specific repository and covers research data that is assigned to molecules, their properties and characterization as well as reactions and experimental investigations. It is hosted at Karlsruhe Institute for Technology (KIT) and is used by several groups in Germany and beyond. 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 but only few of them can be processed and edited in viewers. diff --git a/docs/50_data_publication/20_choose_repository/_category_.json b/docs/50_data_publication/20_choose_repository/_category_.json new file mode 100644 index 00000000..d44a2972 --- /dev/null +++ b/docs/50_data_publication/20_choose_repository/_category_.json @@ -0,0 +1,7 @@ +{ + "label": "How to Choose the Right Repository", + "link": { + "type": "doc", + "id": "choose_repository" + } +} From 7f22a9b045226c254683c3514b3c12b23d44f4cf Mon Sep 17 00:00:00 2001 From: Johannes Liermann Date: Tue, 26 Mar 2024 11:12:08 +0100 Subject: [PATCH 02/14] chore: move selection criteria --- .../10_choose_repository.mdx | 18 +----------------- .../999_selection_criteria.mdx | 19 +++++++++++++++++++ 2 files changed, 20 insertions(+), 17 deletions(-) create mode 100644 docs/50_data_publication/20_choose_repository/999_selection_criteria.mdx 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 index 35959b83..ca552805 100644 --- a/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx +++ b/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx @@ -7,22 +7,6 @@ import useBaseUrl from "@docusaurus/useBaseUrl"; # How to Choose the Right Repository -## Introduction to our recommendations - -The consortium for chemistry (NFDI4Chem) within the NFDI aims to support researchers in collecting, storing, processing, analysing, publishing, and reusing research data by establishing a federation of repositories. To identify the **core repositories** that are part of the federation and have potential for development, the TA3 repository team has selected the following criteria: - -- The repository is suitable for the deposition of molecule-related data -- The repository contains reusable data or functionality such as viewers, editors, or analysis tools that fulfil the needs of the NFDI4Chem community -- The repository software is open source -- The operators of the repositories have declared their willingness to adapt their services to the standards developed by NFDI4Chem as well as the [FAIR data principles](/docs/fair/) -- The repository operators can be funded in accordance with the funding guidelines of the NFDI, i.e. the main operator is based in Germany and is a non-profit organisation - -The repositories that fulfil the above-mentioned criteria are reported in the following list as **core repositories**. Cases that do not meet all criteria are included as associated or relevant repositories, supplementing the following list of recommended and trusted, chemistry-friendly repositories. - -:::danger Notice: -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. -::: - ## Core repositories - [Chemotion Repository](https://www.chemotion-repository.net/welcome)
Field-specific sample and reaction-centric repository including analysis data such as NMR, IR, and mass data. @@ -83,7 +67,7 @@ The recommendations provided in Table 1 will guide you to efficiently and quickl | 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) | | Simulation | [50 supported codes](https://nomad-lab.eu/prod/v1/gui/about/information) | [NOMAD](https://nomad-lab.eu/) | Simulation data Recognition during upload | | 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 | -| Enzyme kinetics data | currently none | [STRENDA DB](https://www.beilstein-strenda-db.org/strenda//) | None; STRENDA compliant, peer-reviewed data publishing | +| 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 | ## Brief description of repositories diff --git a/docs/50_data_publication/20_choose_repository/999_selection_criteria.mdx b/docs/50_data_publication/20_choose_repository/999_selection_criteria.mdx new file mode 100644 index 00000000..975d6b2d --- /dev/null +++ b/docs/50_data_publication/20_choose_repository/999_selection_criteria.mdx @@ -0,0 +1,19 @@ +--- +slug: /selection_criteria +--- + +# Selection Criteria + +The consortium for chemistry (NFDI4Chem) within the NFDI aims to support researchers in collecting, storing, processing, analysing, publishing, and reusing research data by establishing a federation of repositories. To identify the **core repositories** that are part of the federation and have potential for development, the TA3 repository team has selected the following criteria: + +- The repository is suitable for the deposition of molecule-related data +- The repository contains reusable data or functionality such as viewers, editors, or analysis tools that fulfil the needs of the NFDI4Chem community +- The repository software is open source +- The operators of the repositories have declared their willingness to adapt their services to the standards developed by NFDI4Chem as well as the [FAIR data principles](/docs/fair/) +- The repository operators can be funded in accordance with the funding guidelines of the NFDI, i.e. the main operator is based in Germany and is a non-profit organisation + +The repositories that fulfil the above-mentioned criteria are reported in the following list as **core repositories**. Cases that do not meet all criteria are included as associated or relevant repositories, supplementing the following list of recommended and trusted, chemistry-friendly repositories. + +:::danger Notice: +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. +::: From be05d78f843ff62e41ebe26d9605fe9049711bdc Mon Sep 17 00:00:00 2001 From: tilfischer Date: Thu, 25 Apr 2024 10:04:36 +0200 Subject: [PATCH 03/14] feat: added structure for choose repo pages --- .../20_choose_repository/100_nmrxiv.mdx | 8 ++++++++ ...ection_criteria.mdx => 20_common_data_and_formats.mdx} | 0 .../{20_chemotion_repo.mdx => 30_chemotion_repo.mdx} | 0 .../20_choose_repository/40_massbank_eu.mdx | 8 ++++++++ .../20_choose_repository/50_radar4chem.mdx | 8 ++++++++ .../20_choose_repository/60_strenda_db.mdx | 8 ++++++++ .../20_choose_repository/70_suprabank.mdx | 8 ++++++++ .../20_choose_repository/80_csd_icsd.mdx | 8 ++++++++ .../50_data_publication/20_choose_repository/90_nomad.mdx | 8 ++++++++ 9 files changed, 56 insertions(+) create mode 100644 docs/50_data_publication/20_choose_repository/100_nmrxiv.mdx rename docs/50_data_publication/20_choose_repository/{999_selection_criteria.mdx => 20_common_data_and_formats.mdx} (100%) rename docs/50_data_publication/20_choose_repository/{20_chemotion_repo.mdx => 30_chemotion_repo.mdx} (100%) create mode 100644 docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx create mode 100644 docs/50_data_publication/20_choose_repository/50_radar4chem.mdx create mode 100644 docs/50_data_publication/20_choose_repository/60_strenda_db.mdx create mode 100644 docs/50_data_publication/20_choose_repository/70_suprabank.mdx create mode 100644 docs/50_data_publication/20_choose_repository/80_csd_icsd.mdx create mode 100644 docs/50_data_publication/20_choose_repository/90_nomad.mdx diff --git a/docs/50_data_publication/20_choose_repository/100_nmrxiv.mdx b/docs/50_data_publication/20_choose_repository/100_nmrxiv.mdx new file mode 100644 index 00000000..b60b62c4 --- /dev/null +++ b/docs/50_data_publication/20_choose_repository/100_nmrxiv.mdx @@ -0,0 +1,8 @@ +--- +title: "nmrXiv" +slug: "/nmrxiv" +--- + +import useBaseUrl from "@docusaurus/useBaseUrl"; + +# Heading 1 \ No newline at end of file diff --git a/docs/50_data_publication/20_choose_repository/999_selection_criteria.mdx b/docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx similarity index 100% rename from docs/50_data_publication/20_choose_repository/999_selection_criteria.mdx rename to docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx diff --git a/docs/50_data_publication/20_choose_repository/20_chemotion_repo.mdx b/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx similarity index 100% rename from docs/50_data_publication/20_choose_repository/20_chemotion_repo.mdx rename to docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx 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 new file mode 100644 index 00000000..93d25953 --- /dev/null +++ b/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx @@ -0,0 +1,8 @@ +--- +title: "MassBank EU" +slug: "/massbank_eu" +--- + +import useBaseUrl from "@docusaurus/useBaseUrl"; + +# Heading 1 \ No newline at end of file diff --git a/docs/50_data_publication/20_choose_repository/50_radar4chem.mdx b/docs/50_data_publication/20_choose_repository/50_radar4chem.mdx new file mode 100644 index 00000000..8e4e4303 --- /dev/null +++ b/docs/50_data_publication/20_choose_repository/50_radar4chem.mdx @@ -0,0 +1,8 @@ +--- +title: "RADAR4Chem" +slug: "/radar4chem" +--- + +import useBaseUrl from "@docusaurus/useBaseUrl"; + +# Heading 1 \ No newline at end of file diff --git a/docs/50_data_publication/20_choose_repository/60_strenda_db.mdx b/docs/50_data_publication/20_choose_repository/60_strenda_db.mdx new file mode 100644 index 00000000..defdfb5a --- /dev/null +++ b/docs/50_data_publication/20_choose_repository/60_strenda_db.mdx @@ -0,0 +1,8 @@ +--- +title: "Strenda DB" +slug: "/strenda_db" +--- + +import useBaseUrl from "@docusaurus/useBaseUrl"; + +# Heading 1 \ No newline at end of file diff --git a/docs/50_data_publication/20_choose_repository/70_suprabank.mdx b/docs/50_data_publication/20_choose_repository/70_suprabank.mdx new file mode 100644 index 00000000..3dda8b09 --- /dev/null +++ b/docs/50_data_publication/20_choose_repository/70_suprabank.mdx @@ -0,0 +1,8 @@ +--- +title: "SupraBank" +slug: "/suprabank" +--- + +import useBaseUrl from "@docusaurus/useBaseUrl"; + +# Heading 1 \ No newline at end of file diff --git a/docs/50_data_publication/20_choose_repository/80_csd_icsd.mdx b/docs/50_data_publication/20_choose_repository/80_csd_icsd.mdx new file mode 100644 index 00000000..d3ef0af4 --- /dev/null +++ b/docs/50_data_publication/20_choose_repository/80_csd_icsd.mdx @@ -0,0 +1,8 @@ +--- +title: "CSD, ICSD - Joint CCDC/FIZ Access Structure Service" +slug: "/csd_icsd" +--- + +import useBaseUrl from "@docusaurus/useBaseUrl"; + +# Heading 1 \ No newline at end of file diff --git a/docs/50_data_publication/20_choose_repository/90_nomad.mdx b/docs/50_data_publication/20_choose_repository/90_nomad.mdx new file mode 100644 index 00000000..b67b8282 --- /dev/null +++ b/docs/50_data_publication/20_choose_repository/90_nomad.mdx @@ -0,0 +1,8 @@ +--- +title: "NOMAD - NOvel MAterials Discovery" +slug: "/nomad" +--- + +import useBaseUrl from "@docusaurus/useBaseUrl"; + +# Heading 1 \ No newline at end of file From 1d56effddd00d212277709a1c7098ecfeddf9405 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Thu, 25 Apr 2024 10:05:27 +0200 Subject: [PATCH 04/14] feat: updated category.json choose repo --- docs/50_data_publication/20_choose_repository/_category_.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/50_data_publication/20_choose_repository/_category_.json b/docs/50_data_publication/20_choose_repository/_category_.json index d44a2972..1ee639fd 100644 --- a/docs/50_data_publication/20_choose_repository/_category_.json +++ b/docs/50_data_publication/20_choose_repository/_category_.json @@ -1,5 +1,5 @@ { - "label": "How to Choose the Right Repository", + "label": "Choose a Repository", "link": { "type": "doc", "id": "choose_repository" From ea649849f208a7031629698b47a0a04cff0f4413 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Thu, 25 Apr 2024 10:14:42 +0200 Subject: [PATCH 05/14] feat: added content to choose a repo and figure --- .../10_choose_repository.mdx | 290 +- static/img/data_pub/Repo_decision_tree.svg | 3998 ----------------- static/img/data_pub/Repo_decision_tree_v2.svg | 917 ++++ 3 files changed, 954 insertions(+), 4251 deletions(-) delete mode 100644 static/img/data_pub/Repo_decision_tree.svg create mode 100644 static/img/data_pub/Repo_decision_tree_v2.svg 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 index ca552805..5f44a91c 100644 --- a/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx +++ b/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx @@ -5,283 +5,67 @@ slug: "/choose_repository" import useBaseUrl from "@docusaurus/useBaseUrl"; -# How to Choose the Right Repository +# Choose a Repository -## Core repositories +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](LINK_TO_TABLE_PAGE) of the community has been compiled to suggests suitable trusted chemistry-friendly repositories. -- [Chemotion Repository](https://www.chemotion-repository.net/welcome)
Field-specific sample and reaction-centric repository including analysis data such as NMR, IR, and mass data. -- [MassBank EU](https://massbank.eu/MassBank/)
Field-specific ecosystem of databases and tools for mass spectrometry reference spectra. -- [nmrXiv](https://docs.nmrxiv.org/)
A field-specific repository for NMR data. -- [RADAR4Chem](https://www.nfdi4chem.de/index.php/2650-2/)
Generic, multi-domain 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/)
Field-specific repository for enzymology data, which incorporates the STRENDA Guidelines for reporting enzymology data. -- [SUPRABANK](https://suprabank.org/)
Field-specific repository for intermolecular interactions data. - -## Associated repositories +This decision tree will guide users to quickly select a suitable repository for publishing their research data! -- [Cambridge Structural Database](https://www.ccdc.cam.ac.uk/structures/)
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/)
Field-specific repository for x-ray diffraction data of inorganic compounds, elements, minerals, and intermetallic compounds, operated by FIZ Karlsruhe. -- [Joint CCDC/FIZ Access Structures Service](https://www.ccdc.cam.ac.uk/structures/) - -## Other relevant repositories - -- [NOMAD](https://nomad-lab.eu/)
Field-specific repository for materials science data. -- [ioChem-BD](https://www.iochem-bd.org/)
Field-specific repository for computational chemistry. -- [RADAR](https://www.radar-service.eu/radar/en/home)
Generic, multi-disciplinary research data repository. -- [Zenodo](https://zenodo.org/)
Generic repository developed under the European OpenAIRE program, operated by CERN. -- [EUDAT B2SHARE](https://sp.eudat.eu/catalog/resources/709c053d-3b3f-4c54-8ef4-6efeea387816)
Generic repository operated by a pan-european network consisting of more than 25 research organisations, data and computing centers. - -## Further repositories (currently in development): - -- VibSpecDB (IR, Raman, UV/VIS, and luminescence data) - -Moreover, the consortium supports further databases and data repositories on interoperability issues and encourages them to participate in the development of NFDI4Chem standards and interfaces. +![Choose a Repository - Decision Tree](/img/data_pub/Repo_decision_tree_v2.svg) :::danger Notice: -These lists will be continuously updated with further recommendations on trusted and chemistry-friendly repositories. We recently published an [analysis of the landscape of repositories for Chemistry in re3data](https://zenodo.org/doi/10.5281/zenodo.8347992) and [criteria for chemistry repositories](https://zenodo.org/doi/10.5281/zenodo.8199754). We will continue to update the list of repositories in the first and will update this page as we go. +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. ::: -Further details of the repositories listed above is provided in the following sections. - -## Mapping matrix data-repository - -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 TA3 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. Table 1 is also visualised in the following figure: - - - -The recommendations provided in Table 1 will guide you to efficiently and quickly select the best repository for the storage of your data. Selection of the most appropriate database can have a significant impact on the findability and citability of the data as well as the visibility of the scientist. - -**Table 1: Data types and data formats in the NFDI4Chem community.** - -| Data type | Data format | Suggested Repository | Criteria for selection | -| :-------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | :----------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------- | -| Nuclear Magnetic Resonance | Bruker XWIN-NMR format (zip), 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, 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) | -| Simulation | [50 supported codes](https://nomad-lab.eu/prod/v1/gui/about/information) | [NOMAD](https://nomad-lab.eu/) | Simulation data Recognition during upload | -| 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 | -| 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 | - -## Brief description of repositories - -A summary from our survey and interviews with repository operators, including the most relevant information for each repository, is reported in the following section. - -### Chemotion Repository - repository for molecules and research data - -Quick stats: - -- **Accepted data types:** mass spectrometry: JCAMP-DX, mzMl, mzXML (open, visualisable and processable), RAW for selected mass data types (processed and converted in JCAMP-DX), NMR: Bruker XWIN-NMR format (zip) and 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. -- **Used standards/ontologies:** [DataCite Metadata Schema](https://schema.datacite.org/), InChI, SMILES, molfile V2000 and V3000 [CHMO Ontology](http://www.ontobee.org/ontology/CHMO), [RXNO Ontology](http://www.ontobee.org/ontology/RXNO) -- **Access rights/licence information/embargo:** CC0, CCBY, CCBY-SA, public domain; embargo period possible (unlimited) -- **Recommended by Journals/Societies:** Recommended by [Angewandte Chemie](https://onlinelibrary.wiley.com/page/journal/15213773/homepage/notice-to-authors#sectFDataDeposition) and further Wiley journals. - -
- Click to expand for more details about Chemotion! - -

Chemotion - Repository for molecules and research data

- - The Chemotion Repository is a field-specific repository and covers research data that is assigned to molecules, their properties and characterization as well as reactions and experimental investigations. It is hosted at Karlsruhe Institute for Technology (KIT) and is used by several groups in Germany and beyond. 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 (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 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. Authors can be referenced by their ORCID iDs. 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 (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 but only few of them can be processed and edited in viewers. - -
- -### MassBank EU - high quality mass spectral reference database - -Quick stats: - -- **Accepted data types:** MassBank format -- **Used standards/ontologies:** [Internal MassBank Record Format](https://github.com/MassBank/MassBank-web/blob/main/Documentation/MassBankRecordFormat.md) -- **Access rights/licence information/embargo:** Copyright; individual licences based on [creative commons](https://creativecommons.org/); no embargo period -- **Recommended by Journals/Societies:** in progress, official database of the [Mass Spectrometry Society of Japan](https://www.mssj.jp/index_en.html) - -
- Click to expand for more details about MassBank EU! -

MassBank EU - High Quality Mass Spectral Reference Database

- MassBank EU is a field-specific repository and the first public repository - of mass spectral reference data for sharing them among the scientific - research community. 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 - - . GitHub is used as their current AAI environment (open read access, limited - write access), whereas - GitHub issues - serves as their curation tracking system. The curation itself is performed - by the - MassBank record validator - . 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 spectral data is hosted - in a revision control system with all spectral 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 - is provided as a separated data processing/analysis tool. -
+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. -### RADAR4Chem - research data repository +## Core Repositories -Quick stats: - -- **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 -- **Access rights/licence information/embargo:** Terms and conditions for both [data providers](https://radar.products.fiz-karlsruhe.de/sites/default/files/radar/docs/terms/License_and_User_Instructions_for_Data_Providers_RADAR4Chem.pdf) and [data users](https://radar.products.fiz-karlsruhe.de/sites/default/files/radar/docs/terms/RADAR_Terms_for_Data_Users.pdf), mandatory licences for datasets (e.g. Creative Commons), embargo period (1-12 months) -- **Recommended by Journals/Societies:** Recommended by [Angewandte Chemie](https://onlinelibrary.wiley.com/page/journal/15213773/homepage/notice-to-authors#sectFDataDeposition) and further Wiley journals. - -
- Click to expand for more details about RADAR4Chem! - -

RADAR4Chem - Research Data Repository

- -RADAR4Chem is a generic 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 serves as a catch-all repository, which 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, registration to RADAR4Chem, and consent to the RADAR4Chem licence and usage instructions. -Authentication is supported after self-registration and via DFN-AAI (Shibboleth). Metadata are recorded using the internal RADAR Metadata Schema (based on DataCite Metadata Schema 4.0), 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 licence 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. 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 (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. 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). - -Please note: currently, the free-of-charge use of RADAR4Chem is limited to a maximum of 10 GB storage volume per research project. Researchers from the NFDI4Chem community whose research data volume exceeds this free quota and are interested in using RADAR functions institution-wide or in archiving research data, can stipulate a regular RADAR Cloud contract. - -RADAR aims to ensure access to and long-term availability of archived and published datasets according to the FAIR criteria. Therefore, RADAR is intended as a generic infrastructure component in several NFDI consortia (e.g. NFDI4Culture next to NFDI4Chem). For interoperability purposes, it takes into account data types that are recommended by NFDI and supports discipline-specific metadata step-by-step. - -
- -### STRENDA DB - repository for reporting rnzymology data - -Quick stats: - -- **Accepted data types:** Currently none, EnzymeML (in development) -- **Used standards/ontologies:** DataCite, InChI, [EnzymeML (in development)](https://enzymeml.org/) -- **Access rights/licence information/embargo:** [Creative Commons Attribution 4.0 International (CC BY 4.0)](https://creativecommons.org/licenses/by/4.0/), [Term of Use](https://www.beilstein-strenda-db.org/strenda/termsConditions.xhtml); no embargo period possible -- **Recommended by Journals/Societies:** [Archives in Biochemistry and Biophysics](https://www.sciencedirect.com/journal/archives-of-biochemistry-and-biophysics), [Beilstein Journal of Organic Chemistry](https://www.beilstein-journals.org/bjoc/home), [eLife](https://elifesciences.org/), [Molecular Catalysis](https://www.sciencedirect.com/journal/molecular-catalysis), [Nature](https://www.nature.com/) (including Biotechnology, Chemistry, Microbiology, Pharmacology, Systems Biology), [PLoS](https://plos.org/) (relevant journals, e.g. One, Biology, Computational Biology, Medicine), [Scientific Data](https://www.nature.com/sdata/), [The Journal of Biological Chemistry](https://www.jbc.org/), recommended by [Angewandte Chemie](https://onlinelibrary.wiley.com/page/journal/15213773/homepage/notice-to-authors#sectFDataDeposition) and further Wiley journals. - -
- Click to expand for more details about STRENDA DB! -

STRENDA DB - Repository for Reporting Enzymology Data

- STRENDA DB is a field-specific repository for enzymology data operated since - 2016 and hosted at Beilstein Institute (BI) Frankfurt. It ensures that - datasets are complete and valid before scientists submit them as part of a - publication. Their target audience is biochemists, systems biologists, - biocatalysts in the fields of life sciences, biological, molecular, and food - chemists. The typical data contained in this repository consists of - functional enzymology data (kinetic and experimental data) from manuscripts - and publications. Data entered in the STRENDA DB are automatically checked - (according to STRENDA Guidelines and a PDF fact sheet with submittable input - data), allowing users to receive notifications for necessary but missing - information. Currently, more than{" "} - - 55 international biochemistry journals - {" "} - already include the STRENDA guidelines in their instructions for authors. - DOI is used as the identification system for citations and ORCID iD as the - identification system for authors. Data viewing is possible via open access - and data contribution is possible after a required registration where the - current AAI is provided through an internal user administration (user, - administrator). -
- -### SupraBank - -Quick stats: - -- **Accepted data types:** JSON (DataCite), CDX (for 2D/3D molecule structure), PNG, proprietary formats -- **Used standards/ontologies:** DataCite 4.0, Dublin Core for metadata tags -- **Access rights/licence information/embargo:** CC licences (CC0, BY, BY-SA), embargo period possible (unlimited) -- **Recommended by Journals/Societies:** Recommended by [Angewandte Chemie](https://onlinelibrary.wiley.com/page/journal/15213773/homepage/notice-to-authors#sectFDataDeposition) and further Wiley journals. - -
- Click to expand for more details about SupraBank! - -

SupraBank

- -SupraBank is hosted at KIT (Karlsruhe) since 2019 and is a curated database that provides project data on intermolecular interactions of molecular systems and supramolecular interactions which are not available in other repositories or databases. SupraBank is mainly aimed at supramolecular and physical chemists or biologists in the domain of organic chemistry who deal with binding, assembly, and interaction phenomena. Molecular properties are retrieved from PubChem, allowing the correlation of intermolecular interactions parameters to molecular properties of the interacting components. All molecules, solvents, and additives are searchable by their chemical identifiers. At present, SupraBank stores more than 3500 curated datasets of intermolecular interaction parameters. The data has open access for viewing and registered access for data download and contribution. It can be searched for experiments and related components, molecule interactions, and publications while being curated by non-judgemental plausibility checks. The current implementation of AAI consists of internal user administration (anonymous and non-anonymous user, data provider, administrator). DOI is used as the identification system for citations and ORCID iD as the identification system for authors. Its web interface offers file format compatibility with CSV, JSON, BibTex, RIS, and Endnote and its tool suite contains molecule representations as pictures, a structure editor, and a simulation modeller tool. -
- -### CSD, ICSD - Joint CCDC/FIZ access structures service - -Quick stats: - -ICSD quick stats: - -- **Accepted data types:** CIF -- **Used standards/ontologies:** none -- **Access rights/licence information/embargo:** usage terms, no embargo period -- **Recommended by Journals/Societies:** List of the [80 most important journals](https://icsd.products.fiz-karlsruhe.de/about/list-80-most-important-journals-covered-icsd) covered by ICSD - -CSD quick stats: - -- **Accepted data types:** primarily CIF but other supporting file formats accepted -- **Used standards/ontologies:** CIF, DataCite -- **Access rights/licence information/embargo:** usage terms, data embargoed until an associated article is published or researcher triggers publication -- **Recommended by Journals/Societies:** IUCr, Royal Society of Chemistry, American Chemical Society, Wiley, Elsevier, Springer Nature, Taylor & Francis, Hindawi, Chemical Society of Japan +- [Chemotion Repository](https://www.chemotion-repository.net/)
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/)*
Field-specific ecosystem of databases and tools for mass spectrometry reference spectra. +- [nmrXiv](https://docs.nmrxiv.org/)
Field-specific repository for NMR data. +- [RADAR4Chem](https://radar4chem.radar-service.eu/)
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/)
Field-specific repository for enzymology data, which incorporates the STRENDA Guidelines for reporting enzymology data. +- [SUPRABANK](https://suprabank.org/)
Field-specific repository for intermolecular interactions data. -Joint CCDC/FIZ Access Structures Service quick stats: +*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). -- **Accepted data types:** primarily CIF but other supporting file formats accepted. -- **Used standards/ontologies:** CIF, DataCite -- **Access rights/licence information/embargo:** usage terms, data embargoed until an associated article is published or researcher triggers publication -- **Recommended by Journals/Societies:** IUCr, Royal Society of Chemistry, American Chemical Society, Wiley, Elsevier, Springer Nature, Taylor & Francis, Hindawi, Chemical Society of Japan +## Associated repositories -
- Click to expand for more details about CSD, ICSD and joint CCDC/FIZ Access Structures Service! +- [Cambridge Structural Database](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/)*
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/)*
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/)
Service that provides open access to the CSD Structure Depot, but not to all CSD data. -

CSD, ICSD and joint CCDC/FIZ Access Structures Service

+*Resource for which a licence agreement is required. -The Inorganic Crystal Structure Database (ICSD) provided by FIZ Karlsruhe is the world's largest database of completely identified inorganic crystal structures. It contains over 260,000 datases. Complimentarily, the CCDC provides the Cambridge Structural Database (CSD), a certified trusted database of fully curated and enhanced organic and metal-organic crystal structures. First established over fifty years ago it now contains over one million entries. ICSD and CSD support scientists in the field of crystallography, chemistry, material science, physics and structural biology. The joint CCDC/FIZ Access Structures Service, launched in 2018, serves to deposit, register, and preserve structure data of inorganic crystalline compounds at no charge. Crystal structures mentioned in scientific publications are stored in the crystal structure depot. Upon deposition, each dataset is assigned a Digital Object Identifier (DOI) so that the crystal structure is unambiguously identified and registered. The DOI enables third parties to cite and reference data according to the rules of good scientific practice. +## Further Repositories -Both institutions are world-leading experts in structural data and their combined databases contain every published organic, metal-organic, and inorganic crystal structure and are essential resources for the structural chemistry community. Each dataset has to pass rigorous quality checks with manual curation performed by scientific experts. These rich, high-quality data resources alongside advanced software provided by the two institutions enable scientists from industry and academia to extract new insights from the data and discover novel scientific trends. Researchers in structural chemistry rely on the data, it is relevant to industry, and used to teach chemistry concepts to new generations of scientists. Collectively, the licensed databases are installed in over 1,300 institutions worldwide. +- [NOMAD](https://nomad-lab.eu/)
Field-specific repository for computational materials science data. +- [ioChem-BD](https://www.iochem-bd.org/)
Field-specific repository for computational chemistry data. +- [RADAR](https://www.radar-service.eu/radar/en/home)*
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/)
Generic repository developed under the European OpenAIRE program, operated by CERN. +- [EUDAT B2SHARE](https://sp.eudat.eu/catalog/resources/709c053d-3b3f-4c54-8ef4-6efeea387816)
Generic repository operated by a pan-european network consisting of more than 25 research organisations, data and computing centers. -Prior to data deposition, ICSD requires registration, whereas CSD is open. The joint CCDC/FIZ Access Structures Service is open for depositing data and all datasets are freely available on an individual basis. Moreover, researchers can register, but registration is not required to deposit or retrieve data. DOIs are linked to the related publications in both cases. CIF (Crystallographic Information Framework) serves as the metadata standard and the accepted data type. The joint CCDC/FIZ Access Structures Service and CSD are CoreTrustSeal certified. +*Resource for which a licence agreement is required. -
+## Currently under Development within NFDI4Chem -### NOMAD +- [VibSpecDB](https://vibspecdb.k8s.photonicdata.science/)
Filed-specifc repository for IR and Raman data. -Quick stats: +:::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. +::: -- **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) -- **Access rights/licence information/embargo:** CC BY 4.0; Embargoes period definable up to 3 years -- **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. +:::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 +::: -
- Click to expand for more details about NOMAD! -

NOMAD

- 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 - {" "} - of the Nature publishing group. -
+--- -_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._ +_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) --- -Main author: [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) +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) diff --git a/static/img/data_pub/Repo_decision_tree.svg b/static/img/data_pub/Repo_decision_tree.svg deleted file mode 100644 index 8d4fae3f..00000000 --- a/static/img/data_pub/Repo_decision_tree.svg +++ /dev/null @@ -1,3998 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/static/img/data_pub/Repo_decision_tree_v2.svg b/static/img/data_pub/Repo_decision_tree_v2.svg new file mode 100644 index 00000000..d860aaf3 --- /dev/null +++ b/static/img/data_pub/Repo_decision_tree_v2.svg @@ -0,0 +1,917 @@ + +image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +molecules and theirproperties, iden-tification, reactions and experimentalinvestigationsnuclear magnetic resonance (NMR)inorganic crystalstructurescrystal structures oforganic, metal-organic,and organometallic molecules mass spectrometry reference spectramultidisciplinaryintermolecular andsupramolecularinteractions ofmolecular systemsenzyme kinetics datasimulations From 846442f8c51c5c41026ed37e5328dc9fc41aa146 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Thu, 25 Apr 2024 10:19:26 +0200 Subject: [PATCH 06/14] feat: added content to choose repo --- .../20_choose_repository/10_choose_repository.mdx | 2 +- .../20_choose_repository/20_common_data_and_formats.mdx | 3 ++- .../20_choose_repository/30_chemotion_repo.mdx | 1 + 3 files changed, 4 insertions(+), 2 deletions(-) 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 index 5f44a91c..bc924d9c 100644 --- a/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx +++ b/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx @@ -1,5 +1,5 @@ --- -title: "How to Choose the Right Repository" +title: "Choose a Repository" slug: "/choose_repository" --- diff --git a/docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx b/docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx index 975d6b2d..f9a66d44 100644 --- a/docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx +++ b/docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx @@ -1,5 +1,6 @@ --- -slug: /selection_criteria +title: "Data Types and Formats" +slug: /data_types_formats --- # Selection Criteria 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 index 9923f129..63b1330c 100644 --- a/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx +++ b/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx @@ -1,4 +1,5 @@ --- +title: "Chemotion Repository" slug: /chemotion_repo --- From 93e278f07d6a7124c6034f94f7c8372a54eabdbf Mon Sep 17 00:00:00 2001 From: tilfischer Date: Thu, 25 Apr 2024 15:00:39 +0200 Subject: [PATCH 07/14] feat: added content to repo subpages --- .../20_choose_repository/100_nmrxiv.mdx | 38 +++++++++++++++- .../10_choose_repository.mdx | 8 ++-- .../20_common_data_and_formats.mdx | 39 ++++++++++------ .../30_chemotion_repo.mdx | 34 +++++++++----- .../20_choose_repository/40_massbank_eu.mdx | 24 +++++++++- .../20_choose_repository/50_radar4chem.mdx | 26 ++++++++++- .../20_choose_repository/60_strenda_db.mdx | 21 ++++++++- .../20_choose_repository/70_suprabank.mdx | 22 ++++++++- .../20_choose_repository/80_csd_icsd.mdx | 45 ++++++++++++++++++- .../20_choose_repository/90_nomad.mdx | 21 ++++++++- 10 files changed, 242 insertions(+), 36 deletions(-) diff --git a/docs/50_data_publication/20_choose_repository/100_nmrxiv.mdx b/docs/50_data_publication/20_choose_repository/100_nmrxiv.mdx index b60b62c4..5d1459a6 100644 --- a/docs/50_data_publication/20_choose_repository/100_nmrxiv.mdx +++ b/docs/50_data_publication/20_choose_repository/100_nmrxiv.mdx @@ -5,4 +5,40 @@ slug: "/nmrxiv" import useBaseUrl from "@docusaurus/useBaseUrl"; -# Heading 1 \ No newline at end of file +# nmrXiv +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) + +## 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** +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** +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** +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** +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. + +--- + +Main authors: [ORCID:0000-0002-2564-3243](https://orcid.org/0000-0002-2564-3243), [ORCID:0009-0001-5998-5030](https://orcid.org/0009-0001-5998-5030) 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 index bc924d9c..a346e1e3 100644 --- a/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx +++ b/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx @@ -7,7 +7,7 @@ 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](LINK_TO_TABLE_PAGE) of the community has been compiled to suggests suitable trusted chemistry-friendly repositories. +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! @@ -62,10 +62,8 @@ Further details of the repositories listed above can be found on the sub-pages o --- +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) - ---- - -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) diff --git a/docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx b/docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx index f9a66d44..0f860029 100644 --- a/docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx +++ b/docs/50_data_publication/20_choose_repository/20_common_data_and_formats.mdx @@ -1,20 +1,33 @@ --- title: "Data Types and Formats" -slug: /data_types_formats +slug: /pub_data_types_formats --- -# Selection Criteria +# Common Data Types and Formats -The consortium for chemistry (NFDI4Chem) within the NFDI aims to support researchers in collecting, storing, processing, analysing, publishing, and reusing research data by establishing a federation of repositories. To identify the **core repositories** that are part of the federation and have potential for development, the TA3 repository team has selected the following criteria: +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 repository is suitable for the deposition of molecule-related data -- The repository contains reusable data or functionality such as viewers, editors, or analysis tools that fulfil the needs of the NFDI4Chem community -- The repository software is open source -- The operators of the repositories have declared their willingness to adapt their services to the standards developed by NFDI4Chem as well as the [FAIR data principles](/docs/fair/) -- The repository operators can be funded in accordance with the funding guidelines of the NFDI, i.e. the main operator is based in Germany and is a non-profit organisation +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. -The repositories that fulfil the above-mentioned criteria are reported in the following list as **core repositories**. Cases that do not meet all criteria are included as associated or relevant repositories, supplementing the following list of recommended and trusted, chemistry-friendly repositories. - -:::danger Notice: -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. -::: +| 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 | 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 index 63b1330c..e3414e7d 100644 --- a/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx +++ b/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx @@ -1,22 +1,34 @@ --- title: "Chemotion Repository" -slug: /chemotion_repo +slug: /chemotion_repository --- -# Chemotion Repository +# Chemotion Repository - Repository for Samples, Reactions and Research data -:::info Quick stats +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) -- **Accepted data types:** mass spectrometry: JCAMP-DX, mzMl, mzXML (open, visualisable and processable), RAW for selected mass data types (processed and converted in JCAMP-DX), NMR: Bruker XWIN-NMR format (zip) and 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. -- **Used standards/ontologies:** [DataCite Metadata Schema](https://schema.datacite.org/), InChI, SMILES, molfile V2000 and V3000 [CHMO Ontology](http://www.ontobee.org/ontology/CHMO), [RXNO Ontology](http://www.ontobee.org/ontology/RXNO) -- **Access rights/licence information/embargo:** CC0, CCBY, CCBY-SA, public domain; embargo period possible (unlimited) + +## 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 (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** 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**. Authors can be referenced by their ORCID iDs. 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 **(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. -## Chemotion - Repository for molecules and research data +Please note: Chemotion Repository accepts all data types and some of them can be also processed and edited in spectral viewers. -The Chemotion Repository is a field-specific repository and covers research data that is assigned to molecules, their properties and characterization as well as reactions and experimental investigations. It is hosted at Karlsruhe Institute for Technology (KIT) and is used by several groups in Germany and beyond. 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 but only few of them can be processed and edited in 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) 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 index 93d25953..f2bfe7d7 100644 --- a/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx +++ b/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx @@ -5,4 +5,26 @@ slug: "/massbank_eu" import useBaseUrl from "@docusaurus/useBaseUrl"; -# Heading 1 \ No newline at end of file +# MassBank EU - High Quality Mass Spectrometry Reference Database + +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 spectral data is hosted in a revision control system with all spectral 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) diff --git a/docs/50_data_publication/20_choose_repository/50_radar4chem.mdx b/docs/50_data_publication/20_choose_repository/50_radar4chem.mdx index 8e4e4303..5b44902a 100644 --- a/docs/50_data_publication/20_choose_repository/50_radar4chem.mdx +++ b/docs/50_data_publication/20_choose_repository/50_radar4chem.mdx @@ -5,4 +5,28 @@ slug: "/radar4chem" import useBaseUrl from "@docusaurus/useBaseUrl"; -# Heading 1 \ No newline at end of file +# RADAR4Chem - Research Data Repository for Chemistry + +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 + +- **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 licence 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 licence](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). + +Please note: currently, the free-of-charge use of RADAR4Chem is **limited to a maximum of 10 GB** storage volume per research project. Researchers from the NFDI4Chem community whose research data volume exceeds this free quota and are interested in using RADAR functions institution-wide or in archiving research data, can stipulate a [regular RADAR Cloud contract](https://radar.products.fiz-karlsruhe.de/en/radaragreementsprices/vertraege-preise). + +RADAR aims to ensure access to and long-term availability of archived and published datasets according to the FAIR criteria. Therefore, RADAR is intended as a generic infrastructure component in several NFDI consortia (e.g. [NFDI4Culture](https://nfdi4culture.de/de/aktuelles/nachrichten/radar4culture-neuer-service-fuer-kulturgueter.html) next to NFDI4Chem). For interoperability purposes, it takes into account data types that are recommended by NFDI and supports discipline-specific metadata step-by-step. + +--- + +Main authors: [ORCID:0000-0002-6368-1929](https://orcid.org/0000-0002-6368-1929), [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) diff --git a/docs/50_data_publication/20_choose_repository/60_strenda_db.mdx b/docs/50_data_publication/20_choose_repository/60_strenda_db.mdx index defdfb5a..c4fbf9fc 100644 --- a/docs/50_data_publication/20_choose_repository/60_strenda_db.mdx +++ b/docs/50_data_publication/20_choose_repository/60_strenda_db.mdx @@ -5,4 +5,23 @@ slug: "/strenda_db" import useBaseUrl from "@docusaurus/useBaseUrl"; -# Heading 1 \ No newline at end of file +# STRENDA DB - Repository for Reporting Enzymology Data + +Link to [STRENDA DB](https://www.beilstein-strenda-db.org/) +Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.ekj9zx) +Link to [re3data](http://doi.org/10.17616/R3536N) + +## Quick facts + +- **Accepted data types:** Currently none, EnzymeML (in development) +- **Used standards/ontologies:** DataCite, InChI, [EnzymeML (in development)](https://enzymeml.org/) +- **Data deposition condition:** open +- **Recommended by Journals/Societies:** [Archives in Biochemistry and Biophysics](https://www.sciencedirect.com/journal/archives-of-biochemistry-and-biophysics), [Beilstein Journal of Organic Chemistry](https://www.beilstein-journals.org/bjoc/home), [eLife](https://elifesciences.org/), [Molecular Catalysis](https://www.sciencedirect.com/journal/molecular-catalysis), [Nature](https://www.nature.com/) (including Biotechnology, Chemistry, Microbiology, Pharmacology, Systems Biology), [PLoS](https://plos.org/) (relevant journals, e.g. One, Biology, Computational Biology, Medicine), [Scientific Data](https://www.nature.com/sdata/), [The Journal of Biological Chemistry](https://www.jbc.org/), recommended by [Angewandte Chemie](https://onlinelibrary.wiley.com/page/journal/15213773/homepage/notice-to-authors#sectFDataDeposition) and further Wiley journals. + +## Details + +STRENDA DB is a **field-specific** repository for **enzymology** data operated since 2016 and hosted at Beilstein Institute (BI) Frankfurt. It ensures that datasets are complete and valid before scientists submit them as part of a publication. Their target audience is biochemists, systems biologists, biocatalysts in the fields of life sciences, biological, molecular, and food chemists. The typical data contained in this repository consists of **functional enzymology data** (kinetic and experimental data) from manuscripts and publications. Data entered in the STRENDA DB are automatically checked (according to STRENDA Guidelines and a PDF fact sheet with submittable input data), allowing users to receive notifications for necessary but missing information. Currently, more than [55 international biochemistry journals](https://www.beilstein-institut.de/en/projects/strenda/journals/) already include the STRENDA guidelines in their instructions for authors. **DOI** is used as the identification system for citations and ORCID iD as the identification system for authors. Data viewing is possible via open access and data contribution is possible after a required registration where the current **AAI** is provided through an internal user administration (user, administrator). + +--- + +Main authors: [ORCID:0000-0002-8697-6842](https://orcid.org/0000-0002-8697-6842), [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) diff --git a/docs/50_data_publication/20_choose_repository/70_suprabank.mdx b/docs/50_data_publication/20_choose_repository/70_suprabank.mdx index 3dda8b09..5ebf6ff8 100644 --- a/docs/50_data_publication/20_choose_repository/70_suprabank.mdx +++ b/docs/50_data_publication/20_choose_repository/70_suprabank.mdx @@ -5,4 +5,24 @@ slug: "/suprabank" import useBaseUrl from "@docusaurus/useBaseUrl"; -# Heading 1 \ No newline at end of file +# SupraBank + +Link to [SupraBank](https://suprabank.org/) +Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.vjWUT7) +Link to [re3data](http://doi.org/10.17616/R31NJMQ9) + + +## Quick facts + +- **Accepted data types:** JSON (DataCite), CDX (for 2D/3D molecule structure), PNG, proprietary formats +- **Used standards/ontologies:** DataCite 4.0, Dublin Core for metadata tags +- **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 + +SupraBank is hosted at KIT (Karlsruhe) since 2019 and is a curated database that provides project data on **intermolecular interactions of molecular systems** and **supramolecular interactions** which are not available in other repositories or databases. SupraBank is mainly aimed at supramolecular and physical chemists or biologists in the domain of organic chemistry who deal with binding, assembly, and interaction phenomena. Molecular properties are retrieved from PubChem, allowing the correlation of intermolecular interactions parameters to molecular properties of the interacting components. All molecules, solvents, and additives are searchable by their chemical identifiers. At present, SupraBank stores more than 3500 curated datasets of intermolecular interaction parameters. The data has open access for viewing and registered access for data download and contribution. It can be searched for experiments and related components, molecule interactions, and publications while being curated by non-judgemental plausibility checks. The current implementation of AAI consists of internal user administration (anonymous and non-anonymous user, data provider, administrator). DOI is used as the identification system for citations and ORCID iD as the identification system for authors. Its web interface offers file format compatibility with CSV, JSON, BibTex, RIS, and Endnote and its tool suite contains molecule representations as pictures, a structure editor, and a simulation modeller tool. + +--- + +Main authors: [ORCID:0000-0002-1077-6529](https://orcid.org/0000-0002-1077-6529), [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) diff --git a/docs/50_data_publication/20_choose_repository/80_csd_icsd.mdx b/docs/50_data_publication/20_choose_repository/80_csd_icsd.mdx index d3ef0af4..0d804e2d 100644 --- a/docs/50_data_publication/20_choose_repository/80_csd_icsd.mdx +++ b/docs/50_data_publication/20_choose_repository/80_csd_icsd.mdx @@ -5,4 +5,47 @@ slug: "/csd_icsd" import useBaseUrl from "@docusaurus/useBaseUrl"; -# Heading 1 \ No newline at end of file +# CSD, ICSD - Joint CCDC/FIZ access structures service + +Link to [CSD](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/) (requires license) [ICSD](https://icsd.fiz-karlsruhe.de/) (requires license) and [Joint CCDC/FIZ Access Structure](https://www.ccdc.cam.ac.uk/structures/) that provides open access to the CSD Strcutrue Depot, but not all CSD data. + +CSD: +Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.vs7865) +Link to [re3data](http://doi.org/10.17616/R36011) + +ICSD: +Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.a95199) +Link to [re3data](http://doi.org/10.17616/R3GW2V) + +## ICSD quick facts: + +- **Accepted data types:** CIF +- **Used standards/ontologies:** none +- **Data deposition condition:** controlled +- **Recommended by Journals/Societies:** List of the [80 most important journals](https://icsd.products.fiz-karlsruhe.de/about/list-80-most-important-journals-covered-icsd) covered by ICSD + +## CSD quick facts: + +- **Accepted data types:** primarily CIF but other supporting file formats accepted +- **Used standards/ontologies:** CIF, DataCite +- **Data deposition condition:** partially open +- **Recommended by Journals/Societies:** IUCr, Royal Society of Chemistry, American Chemical Society, Wiley, Elsevier, Springer Nature, Taylor & Francis, Hindawi, Chemical Society of Japan + +## Joint CCDC/FIZ Access Structures Service quick facts: + +- **Accepted data types:** primarily CIF but other supporting file formats accepted. +- **Used standards/ontologies:** CIF, DataCite +- **Data deposition condition:** open +- **Recommended by Journals/Societies:** IUCr, Royal Society of Chemistry, American Chemical Society, Wiley, Elsevier, Springer Nature, Taylor & Francis, Hindawi, Chemical Society of Japan + +## CSD, ICSD and joint CCDC/FIZ Access Structures Service + +The [Inorganic Crystal Structure Database](https://icsd.fiz-karlsruhe.de/) (ICSD) provided by [FIZ Karlsruhe](https://www.fiz-karlsruhe.de/) is the world's largest database of completely identified **inorganic crystal structures**. It contains over 260,000 datases. Complimentarily, the CCDC provides the [Cambridge Structural Database](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/) (CSD), a [certified trusted](https://www.coretrustseal.org) database of fully curated and enhanced **organic** and **metal-organic crystal structures**. First established over fifty years ago it now contains over **one million** entries. ICSD and CSD support scientists in the field of crystallography, chemistry, material science, physics and structural biology. The [joint CCDC/FIZ Access Structures Service](https://www.ccdc.cam.ac.uk/structures/), launched in 2018, serves to deposit, register, and preserve structure data of inorganic crystalline compounds at **no charge**. Crystal structures mentioned in scientific publications are stored in the crystal structure depot. Upon deposition, each dataset is assigned a Digital Object Identifier (**DOI**) so that the crystal structure is unambiguously identified and registered. The DOI enables third parties to cite and reference data according to the rules of good scientific practice. + +Both institutions are world-leading experts in structural data and their combined databases contain every published organic, metal-organic, and inorganic crystal structure and are essential resources for the structural chemistry community. Each dataset has to pass rigorous quality checks with manual curation performed by scientific experts. These rich, high-quality data resources alongside advanced software provided by the two institutions enable scientists from industry and academia to extract new insights from the data and discover novel scientific trends. Researchers in structural chemistry rely on the data, it is relevant to industry, and used to teach chemistry concepts to new generations of scientists. Collectively, the licensed databases are installed in over 1,300 institutions worldwide. + +Prior to data deposition, ICSD requires registration, whereas CSD is open. The [joint CCDC/FIZ Access Structures Service is open](https://www.ccdc.cam.ac.uk/structures) for depositing data and all datasets are freely available on an individual basis. Moreover, researchers can register, but registration is not required to deposit or retrieve data. DOIs are linked to the related publications in both cases. CIF (Crystallographic Information Framework) serves as the metadata standard and the accepted data type. The joint CCDC/FIZ Access Structures Service and CSD are CoreTrustSeal certified. + +--- + +Main authors: [ORCID:0000-0002-6062-7492](https://orcid.org/0000-0002-6062-7492), [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) diff --git a/docs/50_data_publication/20_choose_repository/90_nomad.mdx b/docs/50_data_publication/20_choose_repository/90_nomad.mdx index b67b8282..fe56e92d 100644 --- a/docs/50_data_publication/20_choose_repository/90_nomad.mdx +++ b/docs/50_data_publication/20_choose_repository/90_nomad.mdx @@ -5,4 +5,23 @@ slug: "/nomad" import useBaseUrl from "@docusaurus/useBaseUrl"; -# Heading 1 \ No newline at end of file +# NOMAD - NOvel MAterials Discovery + +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) + +## 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. + +--- + +Main authors: [ORCID: -](https://orcid.org/tbd), [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) From 07d11907ef4488bf49a6599d24541937adf8ee43 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Thu, 25 Apr 2024 15:03:40 +0200 Subject: [PATCH 08/14] feat: ordering repo pages following intro page --- .../20_choose_repository/{100_nmrxiv.mdx => 50_nmrxiv.mdx} | 0 .../20_choose_repository/{90_nomad.mdx => 60_nomad.mdx} | 0 .../20_choose_repository/{50_radar4chem.mdx => 60_radar4chem.mdx} | 0 .../20_choose_repository/{60_strenda_db.mdx => 70_strenda_db.mdx} | 0 .../20_choose_repository/{70_suprabank.mdx => 80_suprabank.mdx} | 0 .../20_choose_repository/{80_csd_icsd.mdx => 90_csd_icsd.mdx} | 0 6 files changed, 0 insertions(+), 0 deletions(-) rename docs/50_data_publication/20_choose_repository/{100_nmrxiv.mdx => 50_nmrxiv.mdx} (100%) rename docs/50_data_publication/20_choose_repository/{90_nomad.mdx => 60_nomad.mdx} (100%) rename docs/50_data_publication/20_choose_repository/{50_radar4chem.mdx => 60_radar4chem.mdx} (100%) rename docs/50_data_publication/20_choose_repository/{60_strenda_db.mdx => 70_strenda_db.mdx} (100%) rename docs/50_data_publication/20_choose_repository/{70_suprabank.mdx => 80_suprabank.mdx} (100%) rename docs/50_data_publication/20_choose_repository/{80_csd_icsd.mdx => 90_csd_icsd.mdx} (100%) diff --git a/docs/50_data_publication/20_choose_repository/100_nmrxiv.mdx b/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx similarity index 100% rename from docs/50_data_publication/20_choose_repository/100_nmrxiv.mdx rename to docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx diff --git a/docs/50_data_publication/20_choose_repository/90_nomad.mdx b/docs/50_data_publication/20_choose_repository/60_nomad.mdx similarity index 100% rename from docs/50_data_publication/20_choose_repository/90_nomad.mdx rename to docs/50_data_publication/20_choose_repository/60_nomad.mdx diff --git a/docs/50_data_publication/20_choose_repository/50_radar4chem.mdx b/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx similarity index 100% rename from docs/50_data_publication/20_choose_repository/50_radar4chem.mdx rename to docs/50_data_publication/20_choose_repository/60_radar4chem.mdx diff --git a/docs/50_data_publication/20_choose_repository/60_strenda_db.mdx b/docs/50_data_publication/20_choose_repository/70_strenda_db.mdx similarity index 100% rename from docs/50_data_publication/20_choose_repository/60_strenda_db.mdx rename to docs/50_data_publication/20_choose_repository/70_strenda_db.mdx diff --git a/docs/50_data_publication/20_choose_repository/70_suprabank.mdx b/docs/50_data_publication/20_choose_repository/80_suprabank.mdx similarity index 100% rename from docs/50_data_publication/20_choose_repository/70_suprabank.mdx rename to docs/50_data_publication/20_choose_repository/80_suprabank.mdx diff --git a/docs/50_data_publication/20_choose_repository/80_csd_icsd.mdx b/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx similarity index 100% rename from docs/50_data_publication/20_choose_repository/80_csd_icsd.mdx rename to docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx From 0a1f993d0fae876a16425e98424b1b63968f2bca Mon Sep 17 00:00:00 2001 From: tilfischer Date: Thu, 25 Apr 2024 15:30:07 +0200 Subject: [PATCH 09/14] feat fix all: before pr --- .../20_choose_repository/30_chemotion_repo.mdx | 3 +-- .../20_choose_repository/40_massbank_eu.mdx | 10 +++++----- .../20_choose_repository/60_nomad.mdx | 4 ++-- 3 files changed, 8 insertions(+), 9 deletions(-) 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 index e3414e7d..9571463b 100644 --- a/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx +++ b/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx @@ -5,11 +5,10 @@ slug: /chemotion_repository # Chemotion Repository - Repository for Samples, Reactions and Research data -Link to [Chemotion Repository](https://www.chemotion-repository.net/) +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:** 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 index f2bfe7d7..e72ce34f 100644 --- a/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx +++ b/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx @@ -5,11 +5,11 @@ slug: "/massbank_eu" import useBaseUrl from "@docusaurus/useBaseUrl"; -# MassBank EU - High Quality Mass Spectrometry Reference Database +# MassBank EU - High Quality Mass Spectrometry Reference Database -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) +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 @@ -23,7 +23,7 @@ Link to [re3data](http://doi.org/10.17616/R3K05Z) 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 spectral data is hosted in a revision control system with all spectral 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. +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. --- diff --git a/docs/50_data_publication/20_choose_repository/60_nomad.mdx b/docs/50_data_publication/20_choose_repository/60_nomad.mdx index fe56e92d..51add3d9 100644 --- a/docs/50_data_publication/20_choose_repository/60_nomad.mdx +++ b/docs/50_data_publication/20_choose_repository/60_nomad.mdx @@ -1,5 +1,5 @@ --- -title: "NOMAD - NOvel MAterials Discovery" +title: "NOMAD" slug: "/nomad" --- @@ -24,4 +24,4 @@ Nomad is a public repository operating since 2015 that is hosted at the MPCDF (M --- -Main authors: [ORCID: -](https://orcid.org/tbd), [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) +Main authors: [ORCID: orcid.org/0000-0003-2637-6009](https://orcid.org/0000-0003-2637-6009), [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) From 807ae1a1d7c39fa29b862933d0ec352b3f980eac Mon Sep 17 00:00:00 2001 From: tilfischer Date: Fri, 26 Apr 2024 10:40:21 +0200 Subject: [PATCH 10/14] fix: typo --- .../20_choose_repository/10_choose_repository.mdx | 6 +++--- docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx | 2 +- .../20_choose_repository/60_radar4chem.mdx | 2 +- .../20_choose_repository/80_suprabank.mdx | 2 +- .../20_choose_repository/90_csd_icsd.mdx | 4 ++-- 5 files changed, 8 insertions(+), 8 deletions(-) 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 index a346e1e3..b0273459 100644 --- a/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx +++ b/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx @@ -36,7 +36,7 @@ Based on the [criteria](https://doi.org/10.3897/rio.6.e55852) chosen by Task Are - [Inorganic Crystal Structure Database](https://icsd.fiz-karlsruhe.de/)*
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/)
Service that provides open access to the CSD Structure Depot, but not to all CSD data. -*Resource for which a licence agreement is required. +*Resource for which a license agreement is required. ## Further Repositories @@ -46,11 +46,11 @@ Based on the [criteria](https://doi.org/10.3897/rio.6.e55852) chosen by Task Are - [Zenodo](https://zenodo.org/)
Generic repository developed under the European OpenAIRE program, operated by CERN. - [EUDAT B2SHARE](https://sp.eudat.eu/catalog/resources/709c053d-3b3f-4c54-8ef4-6efeea387816)
Generic repository operated by a pan-european network consisting of more than 25 research organisations, data and computing centers. -*Resource for which a licence agreement is required. +*Resource for which a license agreement is required. ## Currently under Development within NFDI4Chem -- [VibSpecDB](https://vibspecdb.k8s.photonicdata.science/)
Filed-specifc repository for IR and Raman data. +- [VibSpecDB](https://vibspecdb.k8s.photonicdata.science/)
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. diff --git a/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx b/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx index 5d1459a6..aecf112a 100644 --- a/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx +++ b/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx @@ -20,7 +20,7 @@ Link to [re3data](http://doi.org/10.17616/R31NJNGJ) ## Details **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. +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. diff --git a/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx b/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx index 5b44902a..38996065 100644 --- a/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx +++ b/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx @@ -21,7 +21,7 @@ Link to [re3data](http://doi.org/10.17616/R31NJNAY) ## 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 licence 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 licence](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). +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). Please note: currently, the free-of-charge use of RADAR4Chem is **limited to a maximum of 10 GB** storage volume per research project. Researchers from the NFDI4Chem community whose research data volume exceeds this free quota and are interested in using RADAR functions institution-wide or in archiving research data, can stipulate a [regular RADAR Cloud contract](https://radar.products.fiz-karlsruhe.de/en/radaragreementsprices/vertraege-preise). diff --git a/docs/50_data_publication/20_choose_repository/80_suprabank.mdx b/docs/50_data_publication/20_choose_repository/80_suprabank.mdx index 5ebf6ff8..e4fc567a 100644 --- a/docs/50_data_publication/20_choose_repository/80_suprabank.mdx +++ b/docs/50_data_publication/20_choose_repository/80_suprabank.mdx @@ -21,7 +21,7 @@ Link to [re3data](http://doi.org/10.17616/R31NJMQ9) ## Details -SupraBank is hosted at KIT (Karlsruhe) since 2019 and is a curated database that provides project data on **intermolecular interactions of molecular systems** and **supramolecular interactions** which are not available in other repositories or databases. SupraBank is mainly aimed at supramolecular and physical chemists or biologists in the domain of organic chemistry who deal with binding, assembly, and interaction phenomena. Molecular properties are retrieved from PubChem, allowing the correlation of intermolecular interactions parameters to molecular properties of the interacting components. All molecules, solvents, and additives are searchable by their chemical identifiers. At present, SupraBank stores more than 3500 curated datasets of intermolecular interaction parameters. The data has open access for viewing and registered access for data download and contribution. It can be searched for experiments and related components, molecule interactions, and publications while being curated by non-judgemental plausibility checks. The current implementation of AAI consists of internal user administration (anonymous and non-anonymous user, data provider, administrator). DOI is used as the identification system for citations and ORCID iD as the identification system for authors. Its web interface offers file format compatibility with CSV, JSON, BibTex, RIS, and Endnote and its tool suite contains molecule representations as pictures, a structure editor, and a simulation modeller tool. +SupraBank is hosted at KIT (Karlsruhe) since 2019 and is a curated database that provides project data on **intermolecular interactions of molecular systems** and **supramolecular interactions** which are not available in other repositories or databases. SupraBank is mainly aimed at supramolecular and physical chemists or biologists in the domain of organic chemistry who deal with binding, assembly, and interaction phenomena. Molecular properties are retrieved from PubChem, allowing the correlation of intermolecular interactions parameters to molecular properties of the interacting components. All molecules, solvents, and additives are searchable by their chemical identifiers. At present, SupraBank stores more than 3500 curated datasets of intermolecular interaction parameters. The data has open access for viewing and registered access for data download and contribution. It can be searched for experiments and related components, molecule interactions, and publications while being curated by non-judgemental plausibility checks. The current implementation of AAI consists of internal user administration (anonymous and non-anonymous user, data provider, administrator). DOI is used as the identification system for citations and ORCID iD as the identification system for authors. Its web interface offers file format compatibility with CSV, JSON, BibTex, RIS, and Endnote and its tool suite contains molecule representations as pictures, a structure editor, and a simulation modell tool. --- diff --git a/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx b/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx index 0d804e2d..f4dafb0e 100644 --- a/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx +++ b/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx @@ -7,7 +7,7 @@ import useBaseUrl from "@docusaurus/useBaseUrl"; # CSD, ICSD - Joint CCDC/FIZ access structures service -Link to [CSD](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/) (requires license) [ICSD](https://icsd.fiz-karlsruhe.de/) (requires license) and [Joint CCDC/FIZ Access Structure](https://www.ccdc.cam.ac.uk/structures/) that provides open access to the CSD Strcutrue Depot, but not all CSD data. +Link to [CSD](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/) (requires license) [ICSD](https://icsd.fiz-karlsruhe.de/) (requires license) and [Joint CCDC/FIZ Access Structure](https://www.ccdc.cam.ac.uk/structures/) that provides open access to the CSD Structure Depot, but not all CSD data. CSD: Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.vs7865) @@ -40,7 +40,7 @@ Link to [re3data](http://doi.org/10.17616/R3GW2V) ## CSD, ICSD and joint CCDC/FIZ Access Structures Service -The [Inorganic Crystal Structure Database](https://icsd.fiz-karlsruhe.de/) (ICSD) provided by [FIZ Karlsruhe](https://www.fiz-karlsruhe.de/) is the world's largest database of completely identified **inorganic crystal structures**. It contains over 260,000 datases. Complimentarily, the CCDC provides the [Cambridge Structural Database](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/) (CSD), a [certified trusted](https://www.coretrustseal.org) database of fully curated and enhanced **organic** and **metal-organic crystal structures**. First established over fifty years ago it now contains over **one million** entries. ICSD and CSD support scientists in the field of crystallography, chemistry, material science, physics and structural biology. The [joint CCDC/FIZ Access Structures Service](https://www.ccdc.cam.ac.uk/structures/), launched in 2018, serves to deposit, register, and preserve structure data of inorganic crystalline compounds at **no charge**. Crystal structures mentioned in scientific publications are stored in the crystal structure depot. Upon deposition, each dataset is assigned a Digital Object Identifier (**DOI**) so that the crystal structure is unambiguously identified and registered. The DOI enables third parties to cite and reference data according to the rules of good scientific practice. +The [Inorganic Crystal Structure Database](https://icsd.fiz-karlsruhe.de/) (ICSD) provided by [FIZ Karlsruhe](https://www.fiz-karlsruhe.de/) is the world's largest database of completely identified **inorganic crystal structures**. It contains over 260,000 datasets. Complimentarily, the CCDC provides the [Cambridge Structural Database](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/) (CSD), a [certified trusted](https://www.coretrustseal.org) database of fully curated and enhanced **organic** and **metal-organic crystal structures**. First established over fifty years ago it now contains over **one million** entries. ICSD and CSD support scientists in the field of crystallography, chemistry, material science, physics and structural biology. The [joint CCDC/FIZ Access Structures Service](https://www.ccdc.cam.ac.uk/structures/), launched in 2018, serves to deposit, register, and preserve structure data of inorganic crystalline compounds at **no charge**. Crystal structures mentioned in scientific publications are stored in the crystal structure depot. Upon deposition, each dataset is assigned a Digital Object Identifier (**DOI**) so that the crystal structure is unambiguously identified and registered. The DOI enables third parties to cite and reference data according to the rules of good scientific practice. Both institutions are world-leading experts in structural data and their combined databases contain every published organic, metal-organic, and inorganic crystal structure and are essential resources for the structural chemistry community. Each dataset has to pass rigorous quality checks with manual curation performed by scientific experts. These rich, high-quality data resources alongside advanced software provided by the two institutions enable scientists from industry and academia to extract new insights from the data and discover novel scientific trends. Researchers in structural chemistry rely on the data, it is relevant to industry, and used to teach chemistry concepts to new generations of scientists. Collectively, the licensed databases are installed in over 1,300 institutions worldwide. From 70f63207f4c950a05f39c0da1f468d5255963506 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Fri, 26 Apr 2024 10:46:14 +0200 Subject: [PATCH 11/14] feat: added info box for links to repo, fs and rd --- .../20_choose_repository/30_chemotion_repo.mdx | 6 +++--- .../20_choose_repository/40_massbank_eu.mdx | 7 +++---- .../20_choose_repository/50_nmrxiv.mdx | 9 +++++---- .../20_choose_repository/60_nomad.mdx | 6 +++--- .../20_choose_repository/60_radar4chem.mdx | 7 +++---- .../20_choose_repository/70_strenda_db.mdx | 6 +++--- .../20_choose_repository/80_suprabank.mdx | 7 +++---- .../20_choose_repository/90_csd_icsd.mdx | 5 +++-- 8 files changed, 26 insertions(+), 27 deletions(-) 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 index 9571463b..3d524485 100644 --- a/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx +++ b/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx @@ -5,9 +5,9 @@ slug: /chemotion_repository # Chemotion Repository - Repository for Samples, Reactions and Research data -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) +:::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 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 index e72ce34f..46cfbd79 100644 --- a/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx +++ b/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx @@ -7,10 +7,9 @@ import useBaseUrl from "@docusaurus/useBaseUrl"; # MassBank EU - High Quality Mass Spectrometry Reference Database -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). - +:::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 diff --git a/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx b/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx index aecf112a..b9e1c29f 100644 --- a/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx +++ b/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx @@ -5,10 +5,11 @@ slug: "/nmrxiv" import useBaseUrl from "@docusaurus/useBaseUrl"; -# nmrXiv -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) +# nmrXiv + +:::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). +::: ## Quick facts diff --git a/docs/50_data_publication/20_choose_repository/60_nomad.mdx b/docs/50_data_publication/20_choose_repository/60_nomad.mdx index 51add3d9..1042f0d5 100644 --- a/docs/50_data_publication/20_choose_repository/60_nomad.mdx +++ b/docs/50_data_publication/20_choose_repository/60_nomad.mdx @@ -7,9 +7,9 @@ import useBaseUrl from "@docusaurus/useBaseUrl"; # NOMAD - NOvel MAterials Discovery -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) +:::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). +::: ## Quick facts diff --git a/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx b/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx index 38996065..b22f3b7f 100644 --- a/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx +++ b/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx @@ -7,10 +7,9 @@ import useBaseUrl from "@docusaurus/useBaseUrl"; # RADAR4Chem - Research Data Repository for Chemistry -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) - +:::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 diff --git a/docs/50_data_publication/20_choose_repository/70_strenda_db.mdx b/docs/50_data_publication/20_choose_repository/70_strenda_db.mdx index c4fbf9fc..d3957b93 100644 --- a/docs/50_data_publication/20_choose_repository/70_strenda_db.mdx +++ b/docs/50_data_publication/20_choose_repository/70_strenda_db.mdx @@ -7,9 +7,9 @@ import useBaseUrl from "@docusaurus/useBaseUrl"; # STRENDA DB - Repository for Reporting Enzymology Data -Link to [STRENDA DB](https://www.beilstein-strenda-db.org/) -Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.ekj9zx) -Link to [re3data](http://doi.org/10.17616/R3536N) +:::info Note: +Link to [STRENDA DB](https://www.beilstein-strenda-db.org/), Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.ekj9zx), Link to [re3data](http://doi.org/10.17616/R3536N). +::: ## Quick facts diff --git a/docs/50_data_publication/20_choose_repository/80_suprabank.mdx b/docs/50_data_publication/20_choose_repository/80_suprabank.mdx index e4fc567a..58652db7 100644 --- a/docs/50_data_publication/20_choose_repository/80_suprabank.mdx +++ b/docs/50_data_publication/20_choose_repository/80_suprabank.mdx @@ -7,10 +7,9 @@ import useBaseUrl from "@docusaurus/useBaseUrl"; # SupraBank -Link to [SupraBank](https://suprabank.org/) -Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.vjWUT7) -Link to [re3data](http://doi.org/10.17616/R31NJMQ9) - +:::info Note: +Link to [SupraBank](https://suprabank.org/), Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.vjWUT7), Link to [re3data](http://doi.org/10.17616/R31NJMQ9). +::: ## Quick facts diff --git a/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx b/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx index f4dafb0e..615ae153 100644 --- a/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx +++ b/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx @@ -7,15 +7,16 @@ import useBaseUrl from "@docusaurus/useBaseUrl"; # CSD, ICSD - Joint CCDC/FIZ access structures service +:::info Note: Link to [CSD](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/) (requires license) [ICSD](https://icsd.fiz-karlsruhe.de/) (requires license) and [Joint CCDC/FIZ Access Structure](https://www.ccdc.cam.ac.uk/structures/) that provides open access to the CSD Structure Depot, but not all CSD data. -CSD: -Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.vs7865) +CSD: Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.vs7865) Link to [re3data](http://doi.org/10.17616/R36011) ICSD: Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.a95199) Link to [re3data](http://doi.org/10.17616/R3GW2V) +::: ## ICSD quick facts: From 15da3713727a30d47c1d9a75472a5b542199e340 Mon Sep 17 00:00:00 2001 From: Johannes Liermann Date: Tue, 30 Apr 2024 12:04:00 +0200 Subject: [PATCH 12/14] refactor: remove html links --- .../20_choose_repository/30_chemotion_repo.mdx | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) 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 index 3d524485..97fd34dc 100644 --- a/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx +++ b/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx @@ -11,20 +11,20 @@ Link to [Chemotion Repository](https://www.chemotion-repository.net/), Link to [ ## Quick facts -- **Accepted data types:** +- **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. + - NMR: Bruker format (as ZIP) and JCAMP-DX. - IR and Raman: JCAMP-DX - - XRD: JCAMP-DX, - - UV-VIS: 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 (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** 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**. Authors can be referenced by their ORCID iDs. 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 **(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. + +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. From 7bcf67435aa690ffd44071aa58cee2ccee76f488 Mon Sep 17 00:00:00 2001 From: Johannes Liermann Date: Tue, 30 Apr 2024 12:06:27 +0200 Subject: [PATCH 13/14] fix: no bold links --- .../20_choose_repository/30_chemotion_repo.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 index 97fd34dc..eb82bd5c 100644 --- a/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx +++ b/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx @@ -24,7 +24,7 @@ Link to [Chemotion Repository](https://www.chemotion-repository.net/), Link to [ ## 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. +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. From c2bffc534189c29c3626d6f0ea1e6c7e6af7d49b Mon Sep 17 00:00:00 2001 From: Johannes Liermann Date: Tue, 30 Apr 2024 12:17:39 +0200 Subject: [PATCH 14/14] fix: en-dashes --- .../10_choose_repository.mdx | 18 +++++++++--------- .../20_choose_repository/30_chemotion_repo.mdx | 2 +- .../20_choose_repository/40_massbank_eu.mdx | 4 ++-- .../20_choose_repository/50_nmrxiv.mdx | 7 +++---- .../20_choose_repository/60_nomad.mdx | 4 ++-- .../20_choose_repository/60_radar4chem.mdx | 6 +++--- .../20_choose_repository/70_strenda_db.mdx | 4 ++-- .../20_choose_repository/90_csd_icsd.mdx | 6 +++--- 8 files changed, 25 insertions(+), 26 deletions(-) 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 index b0273459..14f43954 100644 --- a/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx +++ b/docs/50_data_publication/20_choose_repository/10_choose_repository.mdx @@ -22,31 +22,31 @@ Based on the [criteria](https://doi.org/10.3897/rio.6.e55852) chosen by Task Are ## Core Repositories - [Chemotion Repository](https://www.chemotion-repository.net/)
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/)*
Field-specific ecosystem of databases and tools for mass spectrometry reference spectra. +- [MassBank EU](https://massbank.eu/MassBank/)\*
Field-specific ecosystem of databases and tools for mass spectrometry reference spectra. - [nmrXiv](https://docs.nmrxiv.org/)
Field-specific repository for NMR data. - [RADAR4Chem](https://radar4chem.radar-service.eu/)
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/)
Field-specific repository for enzymology data, which incorporates the STRENDA Guidelines for reporting enzymology data. - [SUPRABANK](https://suprabank.org/)
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). +\*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/)*
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/)*
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/)
Service that provides open access to the CSD Structure Depot, but not to all CSD data. +- [Cambridge Structural Database](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/)\*
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/)\*
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/)
Service that provides open access to the CSD Structure Depot, but not to all CSD data. -*Resource for which a license agreement is required. +\*Resource for which a license agreement is required. ## Further Repositories - [NOMAD](https://nomad-lab.eu/)
Field-specific repository for computational materials science data. - [ioChem-BD](https://www.iochem-bd.org/)
Field-specific repository for computational chemistry data. -- [RADAR](https://www.radar-service.eu/radar/en/home)*
Generic, multidisciplinary repository for all types of chemical research data that do not meet the specifications of any field-specific repository. +- [RADAR](https://www.radar-service.eu/radar/en/home)\*
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/)
Generic repository developed under the European OpenAIRE program, operated by CERN. - [EUDAT B2SHARE](https://sp.eudat.eu/catalog/resources/709c053d-3b3f-4c54-8ef4-6efeea387816)
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. +\*Resource for which a license agreement is required. ## Currently under Development within NFDI4Chem @@ -64,6 +64,6 @@ Further details of the repositories listed above can be found on the sub-pages o 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._ +_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) 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 index eb82bd5c..2f0a97a4 100644 --- a/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx +++ b/docs/50_data_publication/20_choose_repository/30_chemotion_repo.mdx @@ -3,7 +3,7 @@ title: "Chemotion Repository" slug: /chemotion_repository --- -# Chemotion Repository - Repository for Samples, Reactions and Research data +# 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). 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 index 46cfbd79..2c55040d 100644 --- a/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx +++ b/docs/50_data_publication/20_choose_repository/40_massbank_eu.mdx @@ -5,7 +5,7 @@ slug: "/massbank_eu" import useBaseUrl from "@docusaurus/useBaseUrl"; -# MassBank EU - High Quality Mass Spectrometry Reference Database +# 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). @@ -23,7 +23,7 @@ Link to [MassBank EU](https://massbank.eu/) and [RMassBank](https://bioconductor 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) diff --git a/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx b/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx index b9e1c29f..038650ae 100644 --- a/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx +++ b/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx @@ -1,5 +1,4 @@ --- -title: "nmrXiv" slug: "/nmrxiv" --- @@ -13,7 +12,7 @@ Link to [nmrXiv](https://nmrxiv.org/), Link to [FAIRsharing](https://doi.org/10. ## Quick facts -- **Accepted data types:** all major NMR data formats - NMReData, Bruker +- **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) @@ -28,12 +27,12 @@ The immediate goal of nmrXiv is to integrate and execute the following objective **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) +More details about the platform architecture and related topics – [here](https://docs.nmrxiv.org/developer-guides/architecture.html) **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) +More details about the data standards and related topics – [here](https://docs.nmrxiv.org/category/data.html) **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. diff --git a/docs/50_data_publication/20_choose_repository/60_nomad.mdx b/docs/50_data_publication/20_choose_repository/60_nomad.mdx index 1042f0d5..0ad6975b 100644 --- a/docs/50_data_publication/20_choose_repository/60_nomad.mdx +++ b/docs/50_data_publication/20_choose_repository/60_nomad.mdx @@ -5,7 +5,7 @@ slug: "/nomad" import useBaseUrl from "@docusaurus/useBaseUrl"; -# NOMAD - NOvel MAterials Discovery +# NOMAD – 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). @@ -21,7 +21,7 @@ Link to [NOMAD](https://nomad-lab.eu/), Link to [FAIRsharing](https://doi.org/10 ## 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. - + --- Main authors: [ORCID: orcid.org/0000-0003-2637-6009](https://orcid.org/0000-0003-2637-6009), [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) diff --git a/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx b/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx index b22f3b7f..a8960c71 100644 --- a/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx +++ b/docs/50_data_publication/20_choose_repository/60_radar4chem.mdx @@ -5,7 +5,7 @@ slug: "/radar4chem" import useBaseUrl from "@docusaurus/useBaseUrl"; -# RADAR4Chem - Research Data Repository for Chemistry +# 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). @@ -18,9 +18,9 @@ Link to [RADAR4Chem](https://radar4chem.radar-service.eu/), Link to [FAIRsharing - **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 +## 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). +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). Please note: currently, the free-of-charge use of RADAR4Chem is **limited to a maximum of 10 GB** storage volume per research project. Researchers from the NFDI4Chem community whose research data volume exceeds this free quota and are interested in using RADAR functions institution-wide or in archiving research data, can stipulate a [regular RADAR Cloud contract](https://radar.products.fiz-karlsruhe.de/en/radaragreementsprices/vertraege-preise). diff --git a/docs/50_data_publication/20_choose_repository/70_strenda_db.mdx b/docs/50_data_publication/20_choose_repository/70_strenda_db.mdx index d3957b93..00d88f86 100644 --- a/docs/50_data_publication/20_choose_repository/70_strenda_db.mdx +++ b/docs/50_data_publication/20_choose_repository/70_strenda_db.mdx @@ -5,7 +5,7 @@ slug: "/strenda_db" import useBaseUrl from "@docusaurus/useBaseUrl"; -# STRENDA DB - Repository for Reporting Enzymology Data +# STRENDA DB – Repository for Reporting Enzymology Data :::info Note: Link to [STRENDA DB](https://www.beilstein-strenda-db.org/), Link to [FAIRsharing](https://doi.org/10.25504/FAIRsharing.ekj9zx), Link to [re3data](http://doi.org/10.17616/R3536N). @@ -21,7 +21,7 @@ Link to [STRENDA DB](https://www.beilstein-strenda-db.org/), Link to [FAIRsharin ## Details STRENDA DB is a **field-specific** repository for **enzymology** data operated since 2016 and hosted at Beilstein Institute (BI) Frankfurt. It ensures that datasets are complete and valid before scientists submit them as part of a publication. Their target audience is biochemists, systems biologists, biocatalysts in the fields of life sciences, biological, molecular, and food chemists. The typical data contained in this repository consists of **functional enzymology data** (kinetic and experimental data) from manuscripts and publications. Data entered in the STRENDA DB are automatically checked (according to STRENDA Guidelines and a PDF fact sheet with submittable input data), allowing users to receive notifications for necessary but missing information. Currently, more than [55 international biochemistry journals](https://www.beilstein-institut.de/en/projects/strenda/journals/) already include the STRENDA guidelines in their instructions for authors. **DOI** is used as the identification system for citations and ORCID iD as the identification system for authors. Data viewing is possible via open access and data contribution is possible after a required registration where the current **AAI** is provided through an internal user administration (user, administrator). - + --- Main authors: [ORCID:0000-0002-8697-6842](https://orcid.org/0000-0002-8697-6842), [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) diff --git a/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx b/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx index 615ae153..af9d8a72 100644 --- a/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx +++ b/docs/50_data_publication/20_choose_repository/90_csd_icsd.mdx @@ -1,11 +1,11 @@ --- -title: "CSD, ICSD - Joint CCDC/FIZ Access Structure Service" +title: "CSD/ICSD" slug: "/csd_icsd" --- import useBaseUrl from "@docusaurus/useBaseUrl"; -# CSD, ICSD - Joint CCDC/FIZ access structures service +# CSD, ICSD – Joint CCDC/FIZ access structures service :::info Note: Link to [CSD](https://www.ccdc.cam.ac.uk/solutions/software/webcsd/) (requires license) [ICSD](https://icsd.fiz-karlsruhe.de/) (requires license) and [Joint CCDC/FIZ Access Structure](https://www.ccdc.cam.ac.uk/structures/) that provides open access to the CSD Structure Depot, but not all CSD data. @@ -36,7 +36,7 @@ Link to [re3data](http://doi.org/10.17616/R3GW2V) - **Accepted data types:** primarily CIF but other supporting file formats accepted. - **Used standards/ontologies:** CIF, DataCite -- **Data deposition condition:** open +- **Data deposition condition:** open - **Recommended by Journals/Societies:** IUCr, Royal Society of Chemistry, American Chemical Society, Wiley, Elsevier, Springer Nature, Taylor & Francis, Hindawi, Chemical Society of Japan ## CSD, ICSD and joint CCDC/FIZ Access Structures Service