From 45f9338394d37c44dc9bf666d197c3424d2c94f0 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 30 Jan 2024 13:48:21 +0000 Subject: [PATCH 01/44] edit: title --- docs/50_data_publication/00_data_publication.mdx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/50_data_publication/00_data_publication.mdx b/docs/50_data_publication/00_data_publication.mdx index 7dfb52ec..82fcc607 100644 --- a/docs/50_data_publication/00_data_publication.mdx +++ b/docs/50_data_publication/00_data_publication.mdx @@ -1,12 +1,12 @@ --- -title: "Data Publication" +title: "Publishing Data" slug: "/data_publication" id: "data_publication" --- import useBaseUrl from '@docusaurus/useBaseUrl'; -# Data Publication +# Publishing Data :::info Applies to: This page applies to all researchers who want to publish their data. From 581e399f03ad7c9c7ff64643480d260c3a7573e3 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 30 Jan 2024 16:03:14 +0000 Subject: [PATCH 02/44] add: rough draft of all standards --- .../70_publication_standards.mdx | 132 +++++++++++++++++- 1 file changed, 128 insertions(+), 4 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index d4c85247..bfec830f 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -14,8 +14,17 @@ This page is under construction, while you are welcome to read the already exist During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their article for interlinking in two main ways: -- For corresponding data, i.e. directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. If you believe that your data publication is as decisive as the article itself, add your dataset to the references as well and cite within the text. -- For datasets published by other researchers and reused within a study, add the PID to the reference section of the manuscript and cite within the text accordingly. +:::tip Standard +*Authors should add the PID of the corresponding dataset(s) to the data availability statement. In addition, authors corresponding datasets to the references.* +::: + +For corresponding data, i.e. directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. If you believe that your data publication is as decisive as the article itself, add your dataset to the references as well and cite within the text. + +:::tip Standard +*Authors should add PIDs to datasets by other researchers, which have been reused to the references rather than citing the corresponding article* +::: + +For datasets published by other researchers and reused within a study, add the PID to the reference section of the manuscript and cite within the text accordingly. @@ -27,10 +36,125 @@ For a set of reactions, samples, and analyses, to assemble a study, Collection P In addition, but second-tier, the PID of a related dataset could also be mentioned in the supplementary PDF, if such a document is generated. + +## More Standards in Scientific Publication with Respect to Research Data + +The below outlines a collection of standards for scientific publishing. It serves as a resource for journal editors and publishers as well as infrastructure providers, e.g. research data repositories. + +:::tip Standard +*Research data repositories should provide a Collection DOI to wrap datasets corresponding to one study.* +::: + +Research data repositories may use individual DOIs to reference individual chemical reactions, molecules, or analytical datasets. Thus, many DOIs will then be relevant to the published study results. In order to facilitate the manuscript submission process, a single DOI that wraps all relevant data should be available. Furthermore, this ensure all data underlying a published manuscript can be viewed and referenced as a single collection. + +:::tip Standard +*NFDI4Chem-supported research data repositories should contribute to Scholix.org (or a similar solution).* +::: + +Scholix provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing high-level interoperability framework for exchanging information about these links. Thus, Scholix hubs, such as DataCite or OpenAire, contribute information on their metadata records, which contain information on connected digital objects. + + + +:::tip Standard +*Journals should add data availability statements to their submission system.* +::: + +During manuscript submission, editable templates should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data, enabling the FAIR principles. + +:::tip Standard +*Datasets published with an embargo period should have inaccessible data but accessible metadata.* +::: + +While an embargo period restricts access to a published dataset, the metadata should still be accessible. This allows relevant information on the dataset to be retrieved, while guaranteeing first rights to the data to the authors. + + +:::tip Standard +*Articles should be linked in their DOI metadata with dataset(s) with relationship_type IsSupplementedBy and the dataset(s) should link with relationType IsSupplementTo.* +::: + +This agrees with Crossref's documentation on linking datasets to published items. This establishes a structured link between both DOIs and ensures humans and machine's alike can interpret the relationship between the published objects. + + + + +:::tip Standard +*URLs to access datasets under review should have the access credentials encoded in the URL.* +::: + +Review links for datasets should have the access credentials encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. + +:::tip Standard +*Repositories should register a DOI and populate main fields such as creator and contributor, if a dataset is under review.* +::: + +This ensures that journals may carry out automated quality control steps upon manuscript submission. Further details within the dataset's metadata and content may still be adjusted and updated before final publication. + +:::tip Standard +*Author guidelines of journals should explicitly encourage pre-submission of datasets.* +::: + + +:::tip Standard +*Research data repositories should provide the repository name as publisher in a dataset's metadata.* +::: + + +:::tip Standard +*Research data repositories should provide their repository identifier by re3data.org as a relatedIdentifier with relationType IsPublishedIn.* +::: + +To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide repository identifier from re3data.org. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. The relationship is as follows. + +In the case of RADAR4Chem the relationship would be described as follows: + +> relatedIdentifier -> relatedIdentifierType:DOI -> relationType:IsPublishedIn -> http://doi.org/10.17616/R3ZX96 + +This ensures humans as well as machines can trace and interpret where the data has been published. + +:::tip Standard +*Journals should recommend trusted, chemistry-friendly research data repositories.* +::: + +To assist authors in selecting well-established and community-specific repositories for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. + +:::tip Standard +*Research data repositories should allow researchers to update the metadata of the PID with their dataset.* +::: + +:::tip Standard +*Research data repositories should allow metadata corrections.* +::: + +(version control?) + +:::tip Standard +*Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the DataCite schema* +::: + +Dataset's should have their own description as an abstract. Copying the related text publication abstract can results in a rights conflict with the respective publisher. Authors and data curators should be informed about this conflict when filling out a dataset's metadata. + +:::tip Standard +*In research data repositories, licenses should be grouped in licenses for research data vs. licences for software.* +::: + +Licenses differ for datasets and software. Thus, providing a grouping greatly aids authors in selecting from the correct set. + +:::tip Standard +*Research data repositories should guide users to choose a creative commons license while not making the overall landscape too complicated* +::: + +In line with grouping licenses between software and datasets, pointing authors towards the selection of [creative commons (CC)](https://creativecommons.org/) license alleviates the selection process. + +:::tip Standard +*Research data repositories should pre-select licenses such as CC0 or CC BY 4.0 instead of more restrictive licenses such as CC BY-SA 4.0, which might highly complicate reuse.* +::: + +Licenses can be confusing to authors. Shared data should be as open as possible, as closed as necessary with the intend of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as [CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) as opposed to more restrictive licenses such as [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) or [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). + + *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.* ![CC0 badge](https://licensebuttons.net/l/zero/1.0/88x31.png) ---- -Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661) - +Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) From 0c18fe08ced1eaccbbf47915eca147b66340b2d4 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 30 Jan 2024 16:04:09 +0000 Subject: [PATCH 03/44] edit: section title --- docs/50_data_publication/_category_.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/50_data_publication/_category_.json b/docs/50_data_publication/_category_.json index 323ce918..bee603f7 100644 --- a/docs/50_data_publication/_category_.json +++ b/docs/50_data_publication/_category_.json @@ -1,5 +1,5 @@ { - "label": "Data Publication", + "label": "Publishing Data", "link": { "type" : "doc", "id" : "data_publication" From b17d381bec9f6775a8d0dcaa2203439a4692dc12 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:04:22 +0000 Subject: [PATCH 04/44] re-organize --- .../70_publication_standards.mdx | 58 ++++++++++--------- 1 file changed, 32 insertions(+), 26 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index bfec830f..c2f03d86 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -10,7 +10,9 @@ slug: "/publication_standards" This page is under construction, while you are welcome to read the already existing paragraphs. On this page we will summarise the standards for the publication of data, formulated as principles, developed within the NFDI4Chem project on Publication Standards. These standards should streamline the publication workflows. Authors, publishers and infrastructure operators are the audience for these standards. ::: -## How to use dataset PIDs in scientific articles +## For Authors + +### How to use dataset PIDs in scientific articles During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their article for interlinking in two main ways: @@ -37,9 +39,9 @@ For a set of reactions, samples, and analyses, to assemble a study, Collection P In addition, but second-tier, the PID of a related dataset could also be mentioned in the supplementary PDF, if such a document is generated. -## More Standards in Scientific Publication with Respect to Research Data +## For Research Data Repositories -The below outlines a collection of standards for scientific publishing. It serves as a resource for journal editors and publishers as well as infrastructure providers, e.g. research data repositories. +The below outlines a collection of standards for research data repositories. :::tip Standard *Research data repositories should provide a Collection DOI to wrap datasets corresponding to one study.* @@ -55,25 +57,12 @@ Scholix provides the framework for improving the links between scientific litera -:::tip Standard -*Journals should add data availability statements to their submission system.* -::: - -During manuscript submission, editable templates should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data, enabling the FAIR principles. - :::tip Standard *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: While an embargo period restricts access to a published dataset, the metadata should still be accessible. This allows relevant information on the dataset to be retrieved, while guaranteeing first rights to the data to the authors. - -:::tip Standard -*Articles should be linked in their DOI metadata with dataset(s) with relationship_type IsSupplementedBy and the dataset(s) should link with relationType IsSupplementTo.* -::: - -This agrees with Crossref's documentation on linking datasets to published items. This establishes a structured link between both DOIs and ensures humans and machine's alike can interpret the relationship between the published objects. - @@ -89,10 +78,6 @@ Review links for datasets should have the access credentials encoded in the URL, This ensures that journals may carry out automated quality control steps upon manuscript submission. Further details within the dataset's metadata and content may still be adjusted and updated before final publication. -:::tip Standard -*Author guidelines of journals should explicitly encourage pre-submission of datasets.* -::: - :::tip Standard *Research data repositories should provide the repository name as publisher in a dataset's metadata.* @@ -111,12 +96,6 @@ In the case of RADAR4Chem the relationship would be described as follows: This ensures humans as well as machines can trace and interpret where the data has been published. -:::tip Standard -*Journals should recommend trusted, chemistry-friendly research data repositories.* -::: - -To assist authors in selecting well-established and community-specific repositories for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. - :::tip Standard *Research data repositories should allow researchers to update the metadata of the PID with their dataset.* ::: @@ -151,6 +130,33 @@ In line with grouping licenses between software and datasets, pointing authors t Licenses can be confusing to authors. Shared data should be as open as possible, as closed as necessary with the intend of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as [CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) as opposed to more restrictive licenses such as [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) or [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). +## For Publishers and Journals + +:::tip Standard +*Articles should be linked in their DOI metadata with dataset(s) with relationship_type IsSupplementedBy and the dataset(s) should link with relationType IsSupplementTo.* +::: + + + +This agrees with Crossref's documentation on linking datasets to published items. This establishes a structured link between both DOIs and ensures humans and machine's alike can interpret the relationship between the published objects. + +:::tip Standard +*Journals should recommend trusted, chemistry-friendly research data repositories.* +::: + +To assist authors in selecting well-established and community-specific repositories for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. + +:::tip Standard +*Journals should add data availability statements to their submission system.* +::: + +During manuscript submission, editable templates should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data, enabling the FAIR principles. + +:::tip Standard +*Author guidelines of journals should explicitly encourage pre-submission of datasets.* +::: + + *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.* From 8c7060c716f863ac5955d4f45327010e2ae4d55c Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Mon, 15 Apr 2024 11:33:08 +0000 Subject: [PATCH 05/44] fix: nicer arrows --- docs/50_data_publication/70_publication_standards.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index c2f03d86..a26aed7a 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -92,7 +92,7 @@ To uniquely and persistently identify themselves within the dataset's metadata, In the case of RADAR4Chem the relationship would be described as follows: -> relatedIdentifier -> relatedIdentifierType:DOI -> relationType:IsPublishedIn -> http://doi.org/10.17616/R3ZX96 +> relatedIdentifier → relatedIdentifierType:DOI → relationType:IsPublishedIn → http://doi.org/10.17616/R3ZX96 This ensures humans as well as machines can trace and interpret where the data has been published. From 727dcffa36f49975b57adcf322b8f448b3ac71e5 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Mon, 15 Apr 2024 13:59:42 +0000 Subject: [PATCH 06/44] fix: small things and notes --- .../50_data_publication/70_publication_standards.mdx | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index a26aed7a..e4687927 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -3,6 +3,8 @@ title: "Publication Standards" slug: "/publication_standards" --- + + ![Under Construction](/img/Constr_2bl.png) @@ -17,10 +19,10 @@ This page is under construction, while you are welcome to read the already exist During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their article for interlinking in two main ways: :::tip Standard -*Authors should add the PID of the corresponding dataset(s) to the data availability statement. In addition, authors corresponding datasets to the references.* -::: +*Authors should add the PID of the corresponding dataset(s) to the data availability statement. In addition, authors should add corresponding datasets to the references, making them citable within the text of the article.* +::: -For corresponding data, i.e. directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. If you believe that your data publication is as decisive as the article itself, add your dataset to the references as well and cite within the text. +For corresponding data, i.e. data directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. If you believe that your data publication is as decisive as the article itself, add your dataset to the references as well and cite within the text. :::tip Standard *Authors should add PIDs to datasets by other researchers, which have been reused to the references rather than citing the corresponding article* @@ -28,10 +30,8 @@ For corresponding data, i.e. directly underlying the results reported in the art For datasets published by other researchers and reused within a study, add the PID to the reference section of the manuscript and cite within the text accordingly. - - :::info Notice: -This distinction is important, because the link to the dataset in the DOI metadata of scientific articles is differently set, depending on whether the dataset is a directly related source of information or a referenced source of other researchers and its information is reused. +This distinction is important, because the link to the dataset in the DOI metadata of scientific articles is differently set, depending on whether the dataset is a directly related source of information or a referenced source by other researchers and its information has been reused. ::: For a set of reactions, samples, and analyses, to assemble a study, Collection PIDs should be used rather than providing many separate PIDs. Such a study wrapped with a Collection PID can directly correspond to a published scientific article and can be referenced in a bundled manner within the [data availability statement](/docs/data_availability_statement) or references section. From 36acb5cce08089a39d7001409730dc950bb37435 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Mon, 15 Apr 2024 14:30:21 +0000 Subject: [PATCH 07/44] add: sec on dataset -> article link --- docs/50_data_publication/70_publication_standards.mdx | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index e4687927..90128363 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -38,6 +38,11 @@ For a set of reactions, samples, and analyses, to assemble a study, Collection P In addition, but second-tier, the PID of a related dataset could also be mentioned in the supplementary PDF, if such a document is generated. +### How to link scientific articles to thier corresponding dataset(s) + +Many data repositories will offer the option to add a related identifier. According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. As stressed [above](#how-to-use-dataset-pids-in-scientific-articles), while datasets _may_ be cited within the article, the data availability statement should include them, first and foremost. Hence, to ensure the correct linking on the side of the datset, the relation type `IsSupplementTo` should primarily used, while `IsCitedBy` can be used in addition if the dataset is indeed referenced. + + ## For Research Data Repositories From e837a1612588c8893962f48ad14f1c3bb5386b91 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 16 Apr 2024 08:28:19 +0000 Subject: [PATCH 08/44] re-worked: repos --- .../70_publication_standards.mdx | 75 ++++++++++++------- 1 file changed, 50 insertions(+), 25 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 90128363..9025ac01 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -34,7 +34,7 @@ For datasets published by other researchers and reused within a study, add the P This distinction is important, because the link to the dataset in the DOI metadata of scientific articles is differently set, depending on whether the dataset is a directly related source of information or a referenced source by other researchers and its information has been reused. ::: -For a set of reactions, samples, and analyses, to assemble a study, Collection PIDs should be used rather than providing many separate PIDs. Such a study wrapped with a Collection PID can directly correspond to a published scientific article and can be referenced in a bundled manner within the [data availability statement](/docs/data_availability_statement) or references section. +For a set of reactions, samples, and analyses, to assemble a study, **Collection PIDs** should be used rather than providing many separate PIDs. Such a study wrapped with a Collection PID can directly correspond to a published scientific article and can be referenced in a bundled manner within the [data availability statement](/docs/data_availability_statement) or references section. In addition, but second-tier, the PID of a related dataset could also be mentioned in the supplementary PDF, if such a document is generated. @@ -48,26 +48,31 @@ Many data repositories will offer the option to add a related identifier. Accord The below outlines a collection of standards for research data repositories. +--- + :::tip Standard *Research data repositories should provide a Collection DOI to wrap datasets corresponding to one study.* ::: Research data repositories may use individual DOIs to reference individual chemical reactions, molecules, or analytical datasets. Thus, many DOIs will then be relevant to the published study results. In order to facilitate the manuscript submission process, a single DOI that wraps all relevant data should be available. Furthermore, this ensure all data underlying a published manuscript can be viewed and referenced as a single collection. +--- + :::tip Standard *NFDI4Chem-supported research data repositories should contribute to Scholix.org (or a similar solution).* ::: -Scholix provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing high-level interoperability framework for exchanging information about these links. Thus, Scholix hubs, such as DataCite or OpenAire, contribute information on their metadata records, which contain information on connected digital objects. +[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. - +--- :::tip Standard *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: -While an embargo period restricts access to a published dataset, the metadata should still be accessible. This allows relevant information on the dataset to be retrieved, while guaranteeing first rights to the data to the authors. +While an embargo period restricts access to a published dataset, the **metadata should still be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. +--- @@ -75,74 +80,94 @@ While an embargo period restricts access to a published dataset, the metadata sh *URLs to access datasets under review should have the access credentials encoded in the URL.* ::: -Review links for datasets should have the access credentials encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. +**Review links** for datasets should have the **access credentials** encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. + +--- :::tip Standard *Repositories should register a DOI and populate main fields such as creator and contributor, if a dataset is under review.* ::: -This ensures that journals may carry out automated quality control steps upon manuscript submission. Further details within the dataset's metadata and content may still be adjusted and updated before final publication. +This ensures that journals may carry out automated **quality control steps upon manuscript submission**. Further details within the dataset's metadata and content may still be adjusted and updated prior to final publication. +--- :::tip Standard -*Research data repositories should provide the repository name as publisher in a dataset's metadata.* +*Research data repositories should provide the repository name as `publisher` in a dataset's metadata.* ::: +As stated by [**DataCite's documenation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), this field is used to formulate the citation of the data and thus should be the repository name. + +--- :::tip Standard -*Research data repositories should provide their repository identifier by re3data.org as a relatedIdentifier with relationType IsPublishedIn.* +*Research data repositories should provide their repository identifier by re3data.org as a `publisherIdentifier`.* ::: -To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide repository identifier from re3data.org. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. The relationship is as follows. +To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide **repository identifier from re3data.org**. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. + +In the case of RADAR4Chem the relationship would be described as follows (see also [DataCite's documenation on the publisher field](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher)): -In the case of RADAR4Chem the relationship would be described as follows: +>Publisher:RADAR4Chem +> +>publisherIdentifier:http://doi.org/10.17616/R3ZX96 +> +>publisherIdentifierScheme:re3data +> +>schemeURI:https://re3data.org/ -> relatedIdentifier → relatedIdentifierType:DOI → relationType:IsPublishedIn → http://doi.org/10.17616/R3ZX96 +```xml +RADAR4Chem +``` This ensures humans as well as machines can trace and interpret where the data has been published. -:::tip Standard -*Research data repositories should allow researchers to update the metadata of the PID with their dataset.* -::: +--- :::tip Standard -*Research data repositories should allow metadata corrections.* +*Research data repositories should allow researchers to update the research data's metadata.* ::: -(version control?) +This pertains to **corrections and updates** made both to the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. + +--- :::tip Standard *Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the DataCite schema* ::: -Dataset's should have their own description as an abstract. Copying the related text publication abstract can results in a rights conflict with the respective publisher. Authors and data curators should be informed about this conflict when filling out a dataset's metadata. +Dataset's should have their **own description as an abstract**. Copying the related text publication abstract can results in a **rights conflict** with the respective publisher. Authors and data curators should be informed about this conflict when filling out a dataset's metadata. + +--- :::tip Standard *In research data repositories, licenses should be grouped in licenses for research data vs. licences for software.* ::: -Licenses differ for datasets and software. Thus, providing a grouping greatly aids authors in selecting from the correct set. +**Licenses** differ for datasets and software. Thus, providing a **grouping** greatly aids authors in selecting from the correct set. + +--- :::tip Standard *Research data repositories should guide users to choose a creative commons license while not making the overall landscape too complicated* ::: -In line with grouping licenses between software and datasets, pointing authors towards the selection of [creative commons (CC)](https://creativecommons.org/) license alleviates the selection process. +In line with grouping licenses between software and datasets, pointing authors towards the selection of [**creative commons (CC)**](https://creativecommons.org/) license alleviates the selection process. + +--- :::tip Standard *Research data repositories should pre-select licenses such as CC0 or CC BY 4.0 instead of more restrictive licenses such as CC BY-SA 4.0, which might highly complicate reuse.* ::: -Licenses can be confusing to authors. Shared data should be as open as possible, as closed as necessary with the intend of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as [CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) as opposed to more restrictive licenses such as [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) or [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). +Licenses can be confusing to authors. Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)** as opposed to more restrictive licenses such as [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) or [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). ## For Publishers and Journals :::tip Standard -*Articles should be linked in their DOI metadata with dataset(s) with relationship_type IsSupplementedBy and the dataset(s) should link with relationType IsSupplementTo.* +*Articles should be linked within their DOI metadata to dataset(s) with the `relation` `type` `is-supplemented-by` and the dataset(s) should link with `relationType` `IsSupplementTo`.* ::: - - This agrees with Crossref's documentation on linking datasets to published items. This establishes a structured link between both DOIs and ensures humans and machine's alike can interpret the relationship between the published objects. :::tip Standard @@ -158,9 +183,9 @@ To assist authors in selecting well-established and community-specific repositor During manuscript submission, editable templates should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data, enabling the FAIR principles. :::tip Standard -*Author guidelines of journals should explicitly encourage pre-submission of datasets.* +*Journal author guidelines should explicitly encourage pre-submission of datasets.* ::: - + *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.* From aec82bfefdde151ece26fd2047f77162c3743589 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 16 Apr 2024 08:58:29 +0000 Subject: [PATCH 09/44] edit: additions to publishers and journals --- .../70_publication_standards.mdx | 20 +++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 9025ac01..902953b4 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -164,29 +164,41 @@ Licenses can be confusing to authors. Shared data should be as **open as possibl ## For Publishers and Journals +The below outlines a collection of standards for publishers and journals. + +--- + :::tip Standard -*Articles should be linked within their DOI metadata to dataset(s) with the `relation` `type` `is-supplemented-by` and the dataset(s) should link with `relationType` `IsSupplementTo`.* +*Articles should be linked within their DOI metadata to dataset(s) with the `relation` `type` `is-supplemented-by` and the dataset(s) should link to the article using the `relationType` `IsSupplementTo`.* ::: -This agrees with Crossref's documentation on linking datasets to published items. This establishes a structured link between both DOIs and ensures humans and machine's alike can interpret the relationship between the published objects. +This agrees with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/). It establishes a structured **link** between both PIDs and ensures humans and machines alike can interpret the relationship between the published objects. + +--- :::tip Standard *Journals should recommend trusted, chemistry-friendly research data repositories.* ::: -To assist authors in selecting well-established and community-specific repositories for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. +To assist authors in selecting **well-established and community-specific repositories** for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. These should be included within the author guidelines or the data policies. + +--- :::tip Standard *Journals should add data availability statements to their submission system.* ::: -During manuscript submission, editable templates should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data, enabling the FAIR principles. +During manuscript submission, editable [templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availabilty statements**](/docs/data_availability_statement) should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by inlcuding the DOI or other PID, enabling the FAIR principles (e.g., [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). + +--- :::tip Standard *Journal author guidelines should explicitly encourage pre-submission of datasets.* ::: +To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets should be published prior to the publication of the article**. Thus, once an article is accepted, the authors should publish the underlying data, ensuring that data is avilable when the article is published and that the journal editors can run quality control checks on the provided DOI. This process must be explicitely communicated with authors through the author guidelines, yet can also be in included within other communication upon acceptance. At this point, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to publication. +--- *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.* From 361a027fdefbc80f33ef298ccd4b3657d44996ef Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 16 Apr 2024 09:02:29 +0000 Subject: [PATCH 10/44] add: crossref info to author/linking datasets sections --- docs/50_data_publication/70_publication_standards.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 902953b4..fa37784c 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -42,7 +42,7 @@ In addition, but second-tier, the PID of a related dataset could also be mention Many data repositories will offer the option to add a related identifier. According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. As stressed [above](#how-to-use-dataset-pids-in-scientific-articles), while datasets _may_ be cited within the article, the data availability statement should include them, first and foremost. Hence, to ensure the correct linking on the side of the datset, the relation type `IsSupplementTo` should primarily used, while `IsCitedBy` can be used in addition if the dataset is indeed referenced. - +See also: [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) ## For Research Data Repositories From e5b46386ebd7e30abd8e3c6fa592bb5d850a88c3 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 16 Apr 2024 09:08:40 +0000 Subject: [PATCH 11/44] proof read: section repos --- .../70_publication_standards.mdx | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index fa37784c..8ad1ba40 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -54,7 +54,7 @@ The below outlines a collection of standards for research data repositories. *Research data repositories should provide a Collection DOI to wrap datasets corresponding to one study.* ::: -Research data repositories may use individual DOIs to reference individual chemical reactions, molecules, or analytical datasets. Thus, many DOIs will then be relevant to the published study results. In order to facilitate the manuscript submission process, a single DOI that wraps all relevant data should be available. Furthermore, this ensure all data underlying a published manuscript can be viewed and referenced as a single collection. +Research data repositories may use individual DOIs to reference individual chemical reactions, molecules, or analytical datasets. Thus, many DOIs will then be relevant to the published study results. In order to facilitate the manuscript submission process, a **single DOI** that wraps all relevant data should be available. Furthermore, this ensure all data underlying a published manuscript can be viewed and referenced as a single **collection**. --- @@ -70,7 +70,7 @@ Research data repositories may use individual DOIs to reference individual chemi *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: -While an embargo period restricts access to a published dataset, the **metadata should still be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. +While an **embargo** period restricts access to a published dataset, the **metadata should still be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. --- @@ -96,7 +96,7 @@ This ensures that journals may carry out automated **quality control steps upon *Research data repositories should provide the repository name as `publisher` in a dataset's metadata.* ::: -As stated by [**DataCite's documenation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), this field is used to formulate the citation of the data and thus should be the repository name. +As stated by [**DataCite's documenation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), this `publisher` field is used to formulate the citation of the data and thus should be the repository name. --- @@ -104,17 +104,17 @@ As stated by [**DataCite's documenation on the publisher field**](https://dataci *Research data repositories should provide their repository identifier by re3data.org as a `publisherIdentifier`.* ::: -To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide **repository identifier from re3data.org**. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. +To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide their **repository identifier from re3data.org**. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. In the case of RADAR4Chem the relationship would be described as follows (see also [DataCite's documenation on the publisher field](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher)): ->Publisher:RADAR4Chem +>Publisher: RADAR4Chem > ->publisherIdentifier:http://doi.org/10.17616/R3ZX96 +>publisherIdentifier: http://doi.org/10.17616/R3ZX96 > ->publisherIdentifierScheme:re3data +>publisherIdentifierScheme: re3data > ->schemeURI:https://re3data.org/ +>schemeURI: https://re3data.org/ ```xml RADAR4Chem From ff85dd794b81f60752a099a561dadb6c1647f300 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 30 Jan 2024 16:03:14 +0000 Subject: [PATCH 12/44] add: rough draft of all standards --- .../70_publication_standards.mdx | 134 +++++++++++++++++- 1 file changed, 129 insertions(+), 5 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index f7c73456..76e226ee 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -13,8 +13,17 @@ This page is under construction, while you are welcome to read the already exist During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their article for interlinking in two main ways: -- For corresponding data, i.e. directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. If you believe that your data publication is as decisive as the article itself, add your dataset to the references as well and cite within the text. -- For datasets published by other researchers and reused within a study, add the PID to the reference section of the manuscript and cite within the text accordingly. +:::tip Standard +*Authors should add the PID of the corresponding dataset(s) to the data availability statement. In addition, authors corresponding datasets to the references.* +::: + +For corresponding data, i.e. directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. If you believe that your data publication is as decisive as the article itself, add your dataset to the references as well and cite within the text. + +:::tip Standard +*Authors should add PIDs to datasets by other researchers, which have been reused to the references rather than citing the corresponding article* +::: + +For datasets published by other researchers and reused within a study, add the PID to the reference section of the manuscript and cite within the text accordingly. @@ -26,10 +35,125 @@ For a set of reactions, samples, and analyses, to assemble a study, Collection P In addition, but second-tier, the PID of a related dataset could also be mentioned in the supplementary PDF, if such a document is generated. -_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._ -![CC0 badge](/img/cc-zero.svg) +## More Standards in Scientific Publication with Respect to Research Data + +The below outlines a collection of standards for scientific publishing. It serves as a resource for journal editors and publishers as well as infrastructure providers, e.g. research data repositories. + +:::tip Standard +*Research data repositories should provide a Collection DOI to wrap datasets corresponding to one study.* +::: + +Research data repositories may use individual DOIs to reference individual chemical reactions, molecules, or analytical datasets. Thus, many DOIs will then be relevant to the published study results. In order to facilitate the manuscript submission process, a single DOI that wraps all relevant data should be available. Furthermore, this ensure all data underlying a published manuscript can be viewed and referenced as a single collection. + +:::tip Standard +*NFDI4Chem-supported research data repositories should contribute to Scholix.org (or a similar solution).* +::: + +Scholix provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing high-level interoperability framework for exchanging information about these links. Thus, Scholix hubs, such as DataCite or OpenAire, contribute information on their metadata records, which contain information on connected digital objects. + + + +:::tip Standard +*Journals should add data availability statements to their submission system.* +::: + +During manuscript submission, editable templates should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data, enabling the FAIR principles. + +:::tip Standard +*Datasets published with an embargo period should have inaccessible data but accessible metadata.* +::: + +While an embargo period restricts access to a published dataset, the metadata should still be accessible. This allows relevant information on the dataset to be retrieved, while guaranteeing first rights to the data to the authors. + + +:::tip Standard +*Articles should be linked in their DOI metadata with dataset(s) with relationship_type IsSupplementedBy and the dataset(s) should link with relationType IsSupplementTo.* +::: + +This agrees with Crossref's documentation on linking datasets to published items. This establishes a structured link between both DOIs and ensures humans and machine's alike can interpret the relationship between the published objects. + + + + +:::tip Standard +*URLs to access datasets under review should have the access credentials encoded in the URL.* +::: + +Review links for datasets should have the access credentials encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. + +:::tip Standard +*Repositories should register a DOI and populate main fields such as creator and contributor, if a dataset is under review.* +::: + +This ensures that journals may carry out automated quality control steps upon manuscript submission. Further details within the dataset's metadata and content may still be adjusted and updated before final publication. + +:::tip Standard +*Author guidelines of journals should explicitly encourage pre-submission of datasets.* +::: + + +:::tip Standard +*Research data repositories should provide the repository name as publisher in a dataset's metadata.* +::: + + +:::tip Standard +*Research data repositories should provide their repository identifier by re3data.org as a relatedIdentifier with relationType IsPublishedIn.* +::: + +To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide repository identifier from re3data.org. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. The relationship is as follows. + +In the case of RADAR4Chem the relationship would be described as follows: + +> relatedIdentifier -> relatedIdentifierType:DOI -> relationType:IsPublishedIn -> http://doi.org/10.17616/R3ZX96 + +This ensures humans as well as machines can trace and interpret where the data has been published. + +:::tip Standard +*Journals should recommend trusted, chemistry-friendly research data repositories.* +::: + +To assist authors in selecting well-established and community-specific repositories for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. + +:::tip Standard +*Research data repositories should allow researchers to update the metadata of the PID with their dataset.* +::: + +:::tip Standard +*Research data repositories should allow metadata corrections.* +::: + +(version control?) + +:::tip Standard +*Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the DataCite schema* +::: + +Dataset's should have their own description as an abstract. Copying the related text publication abstract can results in a rights conflict with the respective publisher. Authors and data curators should be informed about this conflict when filling out a dataset's metadata. + +:::tip Standard +*In research data repositories, licenses should be grouped in licenses for research data vs. licences for software.* +::: + +Licenses differ for datasets and software. Thus, providing a grouping greatly aids authors in selecting from the correct set. + +:::tip Standard +*Research data repositories should guide users to choose a creative commons license while not making the overall landscape too complicated* +::: + +In line with grouping licenses between software and datasets, pointing authors towards the selection of [creative commons (CC)](https://creativecommons.org/) license alleviates the selection process. + +:::tip Standard +*Research data repositories should pre-select licenses such as CC0 or CC BY 4.0 instead of more restrictive licenses such as CC BY-SA 4.0, which might highly complicate reuse.* +::: + +Licenses can be confusing to authors. Shared data should be as open as possible, as closed as necessary with the intend of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as [CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) as opposed to more restrictive licenses such as [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) or [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). + + +*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.* --- -Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661) +---- +Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) From 69c824c6b37f7aab2bf413e8998b9f956cdef855 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:04:22 +0000 Subject: [PATCH 13/44] re-organize --- .../70_publication_standards.mdx | 58 ++++++++++--------- 1 file changed, 32 insertions(+), 26 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 76e226ee..0063d18e 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -9,7 +9,9 @@ slug: "/publishing_standards" This page is under construction, while you are welcome to read the already existing paragraphs. On this page we will summarise the standards for the publication of data, formulated as principles, developed within the NFDI4Chem project on Publication Standards. These standards should streamline the publication workflows. Authors, publishers and infrastructure operators are the audience for these standards. ::: -## How to use dataset PIDs in scientific articles +## For Authors + +### How to use dataset PIDs in scientific articles During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their article for interlinking in two main ways: @@ -36,9 +38,9 @@ For a set of reactions, samples, and analyses, to assemble a study, Collection P In addition, but second-tier, the PID of a related dataset could also be mentioned in the supplementary PDF, if such a document is generated. -## More Standards in Scientific Publication with Respect to Research Data +## For Research Data Repositories -The below outlines a collection of standards for scientific publishing. It serves as a resource for journal editors and publishers as well as infrastructure providers, e.g. research data repositories. +The below outlines a collection of standards for research data repositories. :::tip Standard *Research data repositories should provide a Collection DOI to wrap datasets corresponding to one study.* @@ -54,25 +56,12 @@ Scholix provides the framework for improving the links between scientific litera -:::tip Standard -*Journals should add data availability statements to their submission system.* -::: - -During manuscript submission, editable templates should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data, enabling the FAIR principles. - :::tip Standard *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: While an embargo period restricts access to a published dataset, the metadata should still be accessible. This allows relevant information on the dataset to be retrieved, while guaranteeing first rights to the data to the authors. - -:::tip Standard -*Articles should be linked in their DOI metadata with dataset(s) with relationship_type IsSupplementedBy and the dataset(s) should link with relationType IsSupplementTo.* -::: - -This agrees with Crossref's documentation on linking datasets to published items. This establishes a structured link between both DOIs and ensures humans and machine's alike can interpret the relationship between the published objects. - @@ -88,10 +77,6 @@ Review links for datasets should have the access credentials encoded in the URL, This ensures that journals may carry out automated quality control steps upon manuscript submission. Further details within the dataset's metadata and content may still be adjusted and updated before final publication. -:::tip Standard -*Author guidelines of journals should explicitly encourage pre-submission of datasets.* -::: - :::tip Standard *Research data repositories should provide the repository name as publisher in a dataset's metadata.* @@ -110,12 +95,6 @@ In the case of RADAR4Chem the relationship would be described as follows: This ensures humans as well as machines can trace and interpret where the data has been published. -:::tip Standard -*Journals should recommend trusted, chemistry-friendly research data repositories.* -::: - -To assist authors in selecting well-established and community-specific repositories for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. - :::tip Standard *Research data repositories should allow researchers to update the metadata of the PID with their dataset.* ::: @@ -150,6 +129,33 @@ In line with grouping licenses between software and datasets, pointing authors t Licenses can be confusing to authors. Shared data should be as open as possible, as closed as necessary with the intend of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as [CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) as opposed to more restrictive licenses such as [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) or [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). +## For Publishers and Journals + +:::tip Standard +*Articles should be linked in their DOI metadata with dataset(s) with relationship_type IsSupplementedBy and the dataset(s) should link with relationType IsSupplementTo.* +::: + + + +This agrees with Crossref's documentation on linking datasets to published items. This establishes a structured link between both DOIs and ensures humans and machine's alike can interpret the relationship between the published objects. + +:::tip Standard +*Journals should recommend trusted, chemistry-friendly research data repositories.* +::: + +To assist authors in selecting well-established and community-specific repositories for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. + +:::tip Standard +*Journals should add data availability statements to their submission system.* +::: + +During manuscript submission, editable templates should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data, enabling the FAIR principles. + +:::tip Standard +*Author guidelines of journals should explicitly encourage pre-submission of datasets.* +::: + + *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.* From 8e434edfd863e55fc6e3faa173d0b5588346eb0f Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Mon, 15 Apr 2024 11:33:08 +0000 Subject: [PATCH 14/44] fix: nicer arrows --- docs/50_data_publication/70_publication_standards.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 0063d18e..086ff162 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -91,7 +91,7 @@ To uniquely and persistently identify themselves within the dataset's metadata, In the case of RADAR4Chem the relationship would be described as follows: -> relatedIdentifier -> relatedIdentifierType:DOI -> relationType:IsPublishedIn -> http://doi.org/10.17616/R3ZX96 +> relatedIdentifier → relatedIdentifierType:DOI → relationType:IsPublishedIn → http://doi.org/10.17616/R3ZX96 This ensures humans as well as machines can trace and interpret where the data has been published. From a7407cfa975cce88949e5de2b7319982b16c7c0c Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Mon, 15 Apr 2024 13:59:42 +0000 Subject: [PATCH 15/44] fix: small things and notes --- .../70_publication_standards.mdx | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 086ff162..5add7f96 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -3,6 +3,9 @@ title: "Publishing Standards" slug: "/publishing_standards" --- + + + ![Under Construction](/img/Constr_2bl.png) :::info Info: @@ -16,10 +19,10 @@ This page is under construction, while you are welcome to read the already exist During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their article for interlinking in two main ways: :::tip Standard -*Authors should add the PID of the corresponding dataset(s) to the data availability statement. In addition, authors corresponding datasets to the references.* -::: +*Authors should add the PID of the corresponding dataset(s) to the data availability statement. In addition, authors should add corresponding datasets to the references, making them citable within the text of the article.* +::: -For corresponding data, i.e. directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. If you believe that your data publication is as decisive as the article itself, add your dataset to the references as well and cite within the text. +For corresponding data, i.e. data directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. If you believe that your data publication is as decisive as the article itself, add your dataset to the references as well and cite within the text. :::tip Standard *Authors should add PIDs to datasets by other researchers, which have been reused to the references rather than citing the corresponding article* @@ -27,10 +30,8 @@ For corresponding data, i.e. directly underlying the results reported in the art For datasets published by other researchers and reused within a study, add the PID to the reference section of the manuscript and cite within the text accordingly. - - :::info Notice: -This distinction is important, because the link to the dataset in the DOI metadata of scientific articles is differently set, depending on whether the dataset is a directly related source of information or a referenced source of other researchers and its information is reused. +This distinction is important, because the link to the dataset in the DOI metadata of scientific articles is differently set, depending on whether the dataset is a directly related source of information or a referenced source by other researchers and its information has been reused. ::: For a set of reactions, samples, and analyses, to assemble a study, Collection PIDs should be used rather than providing many separate PIDs. Such a study wrapped with a Collection PID can directly correspond to a published scientific article and can be referenced in a bundled manner within the [data availability statement](/docs/data_availability_statement) or references section. From 2b53f52f15ff55b39f28441304489629d7ad310b Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Mon, 15 Apr 2024 14:30:21 +0000 Subject: [PATCH 16/44] add: sec on dataset -> article link --- docs/50_data_publication/70_publication_standards.mdx | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 5add7f96..e6433901 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -38,6 +38,11 @@ For a set of reactions, samples, and analyses, to assemble a study, Collection P In addition, but second-tier, the PID of a related dataset could also be mentioned in the supplementary PDF, if such a document is generated. +### How to link scientific articles to thier corresponding dataset(s) + +Many data repositories will offer the option to add a related identifier. According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. As stressed [above](#how-to-use-dataset-pids-in-scientific-articles), while datasets _may_ be cited within the article, the data availability statement should include them, first and foremost. Hence, to ensure the correct linking on the side of the datset, the relation type `IsSupplementTo` should primarily used, while `IsCitedBy` can be used in addition if the dataset is indeed referenced. + + ## For Research Data Repositories From 639379a8459ac2db493c54dd806c6b30a0ad503c Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 16 Apr 2024 08:28:19 +0000 Subject: [PATCH 17/44] re-worked: repos --- .../70_publication_standards.mdx | 75 ++++++++++++------- 1 file changed, 50 insertions(+), 25 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index e6433901..3ccbf62a 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -34,7 +34,7 @@ For datasets published by other researchers and reused within a study, add the P This distinction is important, because the link to the dataset in the DOI metadata of scientific articles is differently set, depending on whether the dataset is a directly related source of information or a referenced source by other researchers and its information has been reused. ::: -For a set of reactions, samples, and analyses, to assemble a study, Collection PIDs should be used rather than providing many separate PIDs. Such a study wrapped with a Collection PID can directly correspond to a published scientific article and can be referenced in a bundled manner within the [data availability statement](/docs/data_availability_statement) or references section. +For a set of reactions, samples, and analyses, to assemble a study, **Collection PIDs** should be used rather than providing many separate PIDs. Such a study wrapped with a Collection PID can directly correspond to a published scientific article and can be referenced in a bundled manner within the [data availability statement](/docs/data_availability_statement) or references section. In addition, but second-tier, the PID of a related dataset could also be mentioned in the supplementary PDF, if such a document is generated. @@ -48,26 +48,31 @@ Many data repositories will offer the option to add a related identifier. Accord The below outlines a collection of standards for research data repositories. +--- + :::tip Standard *Research data repositories should provide a Collection DOI to wrap datasets corresponding to one study.* ::: Research data repositories may use individual DOIs to reference individual chemical reactions, molecules, or analytical datasets. Thus, many DOIs will then be relevant to the published study results. In order to facilitate the manuscript submission process, a single DOI that wraps all relevant data should be available. Furthermore, this ensure all data underlying a published manuscript can be viewed and referenced as a single collection. +--- + :::tip Standard *NFDI4Chem-supported research data repositories should contribute to Scholix.org (or a similar solution).* ::: -Scholix provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing high-level interoperability framework for exchanging information about these links. Thus, Scholix hubs, such as DataCite or OpenAire, contribute information on their metadata records, which contain information on connected digital objects. +[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. - +--- :::tip Standard *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: -While an embargo period restricts access to a published dataset, the metadata should still be accessible. This allows relevant information on the dataset to be retrieved, while guaranteeing first rights to the data to the authors. +While an embargo period restricts access to a published dataset, the **metadata should still be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. +--- @@ -75,74 +80,94 @@ While an embargo period restricts access to a published dataset, the metadata sh *URLs to access datasets under review should have the access credentials encoded in the URL.* ::: -Review links for datasets should have the access credentials encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. +**Review links** for datasets should have the **access credentials** encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. + +--- :::tip Standard *Repositories should register a DOI and populate main fields such as creator and contributor, if a dataset is under review.* ::: -This ensures that journals may carry out automated quality control steps upon manuscript submission. Further details within the dataset's metadata and content may still be adjusted and updated before final publication. +This ensures that journals may carry out automated **quality control steps upon manuscript submission**. Further details within the dataset's metadata and content may still be adjusted and updated prior to final publication. +--- :::tip Standard -*Research data repositories should provide the repository name as publisher in a dataset's metadata.* +*Research data repositories should provide the repository name as `publisher` in a dataset's metadata.* ::: +As stated by [**DataCite's documenation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), this field is used to formulate the citation of the data and thus should be the repository name. + +--- :::tip Standard -*Research data repositories should provide their repository identifier by re3data.org as a relatedIdentifier with relationType IsPublishedIn.* +*Research data repositories should provide their repository identifier by re3data.org as a `publisherIdentifier`.* ::: -To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide repository identifier from re3data.org. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. The relationship is as follows. +To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide **repository identifier from re3data.org**. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. + +In the case of RADAR4Chem the relationship would be described as follows (see also [DataCite's documenation on the publisher field](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher)): -In the case of RADAR4Chem the relationship would be described as follows: +>Publisher:RADAR4Chem +> +>publisherIdentifier:http://doi.org/10.17616/R3ZX96 +> +>publisherIdentifierScheme:re3data +> +>schemeURI:https://re3data.org/ -> relatedIdentifier → relatedIdentifierType:DOI → relationType:IsPublishedIn → http://doi.org/10.17616/R3ZX96 +```xml +RADAR4Chem +``` This ensures humans as well as machines can trace and interpret where the data has been published. -:::tip Standard -*Research data repositories should allow researchers to update the metadata of the PID with their dataset.* -::: +--- :::tip Standard -*Research data repositories should allow metadata corrections.* +*Research data repositories should allow researchers to update the research data's metadata.* ::: -(version control?) +This pertains to **corrections and updates** made both to the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. + +--- :::tip Standard *Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the DataCite schema* ::: -Dataset's should have their own description as an abstract. Copying the related text publication abstract can results in a rights conflict with the respective publisher. Authors and data curators should be informed about this conflict when filling out a dataset's metadata. +Dataset's should have their **own description as an abstract**. Copying the related text publication abstract can results in a **rights conflict** with the respective publisher. Authors and data curators should be informed about this conflict when filling out a dataset's metadata. + +--- :::tip Standard *In research data repositories, licenses should be grouped in licenses for research data vs. licences for software.* ::: -Licenses differ for datasets and software. Thus, providing a grouping greatly aids authors in selecting from the correct set. +**Licenses** differ for datasets and software. Thus, providing a **grouping** greatly aids authors in selecting from the correct set. + +--- :::tip Standard *Research data repositories should guide users to choose a creative commons license while not making the overall landscape too complicated* ::: -In line with grouping licenses between software and datasets, pointing authors towards the selection of [creative commons (CC)](https://creativecommons.org/) license alleviates the selection process. +In line with grouping licenses between software and datasets, pointing authors towards the selection of [**creative commons (CC)**](https://creativecommons.org/) license alleviates the selection process. + +--- :::tip Standard *Research data repositories should pre-select licenses such as CC0 or CC BY 4.0 instead of more restrictive licenses such as CC BY-SA 4.0, which might highly complicate reuse.* ::: -Licenses can be confusing to authors. Shared data should be as open as possible, as closed as necessary with the intend of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as [CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) as opposed to more restrictive licenses such as [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) or [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). +Licenses can be confusing to authors. Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)** as opposed to more restrictive licenses such as [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) or [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). ## For Publishers and Journals :::tip Standard -*Articles should be linked in their DOI metadata with dataset(s) with relationship_type IsSupplementedBy and the dataset(s) should link with relationType IsSupplementTo.* +*Articles should be linked within their DOI metadata to dataset(s) with the `relation` `type` `is-supplemented-by` and the dataset(s) should link with `relationType` `IsSupplementTo`.* ::: - - This agrees with Crossref's documentation on linking datasets to published items. This establishes a structured link between both DOIs and ensures humans and machine's alike can interpret the relationship between the published objects. :::tip Standard @@ -158,9 +183,9 @@ To assist authors in selecting well-established and community-specific repositor During manuscript submission, editable templates should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data, enabling the FAIR principles. :::tip Standard -*Author guidelines of journals should explicitly encourage pre-submission of datasets.* +*Journal author guidelines should explicitly encourage pre-submission of datasets.* ::: - + *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.* From 1bfa13bc5eb17a06474f60ac6c5a31c82e2206dd Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 16 Apr 2024 08:58:29 +0000 Subject: [PATCH 18/44] edit: additions to publishers and journals --- .../70_publication_standards.mdx | 20 +++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 3ccbf62a..28a1d465 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -164,29 +164,41 @@ Licenses can be confusing to authors. Shared data should be as **open as possibl ## For Publishers and Journals +The below outlines a collection of standards for publishers and journals. + +--- + :::tip Standard -*Articles should be linked within their DOI metadata to dataset(s) with the `relation` `type` `is-supplemented-by` and the dataset(s) should link with `relationType` `IsSupplementTo`.* +*Articles should be linked within their DOI metadata to dataset(s) with the `relation` `type` `is-supplemented-by` and the dataset(s) should link to the article using the `relationType` `IsSupplementTo`.* ::: -This agrees with Crossref's documentation on linking datasets to published items. This establishes a structured link between both DOIs and ensures humans and machine's alike can interpret the relationship between the published objects. +This agrees with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/). It establishes a structured **link** between both PIDs and ensures humans and machines alike can interpret the relationship between the published objects. + +--- :::tip Standard *Journals should recommend trusted, chemistry-friendly research data repositories.* ::: -To assist authors in selecting well-established and community-specific repositories for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. +To assist authors in selecting **well-established and community-specific repositories** for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. These should be included within the author guidelines or the data policies. + +--- :::tip Standard *Journals should add data availability statements to their submission system.* ::: -During manuscript submission, editable templates should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data, enabling the FAIR principles. +During manuscript submission, editable [templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availabilty statements**](/docs/data_availability_statement) should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by inlcuding the DOI or other PID, enabling the FAIR principles (e.g., [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). + +--- :::tip Standard *Journal author guidelines should explicitly encourage pre-submission of datasets.* ::: +To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets should be published prior to the publication of the article**. Thus, once an article is accepted, the authors should publish the underlying data, ensuring that data is avilable when the article is published and that the journal editors can run quality control checks on the provided DOI. This process must be explicitely communicated with authors through the author guidelines, yet can also be in included within other communication upon acceptance. At this point, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to publication. +--- *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.* From 6bef6f9c2b087ac381afa7210cf99025f724ddd1 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 16 Apr 2024 09:02:29 +0000 Subject: [PATCH 19/44] add: crossref info to author/linking datasets sections --- docs/50_data_publication/70_publication_standards.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 28a1d465..7d3b1b11 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -42,7 +42,7 @@ In addition, but second-tier, the PID of a related dataset could also be mention Many data repositories will offer the option to add a related identifier. According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. As stressed [above](#how-to-use-dataset-pids-in-scientific-articles), while datasets _may_ be cited within the article, the data availability statement should include them, first and foremost. Hence, to ensure the correct linking on the side of the datset, the relation type `IsSupplementTo` should primarily used, while `IsCitedBy` can be used in addition if the dataset is indeed referenced. - +See also: [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) ## For Research Data Repositories From f81fdb974461efb9896f4de8e9240661569f9d95 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Tue, 16 Apr 2024 09:08:40 +0000 Subject: [PATCH 20/44] proof read: section repos --- .../70_publication_standards.mdx | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 7d3b1b11..e06f7a1d 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -54,7 +54,7 @@ The below outlines a collection of standards for research data repositories. *Research data repositories should provide a Collection DOI to wrap datasets corresponding to one study.* ::: -Research data repositories may use individual DOIs to reference individual chemical reactions, molecules, or analytical datasets. Thus, many DOIs will then be relevant to the published study results. In order to facilitate the manuscript submission process, a single DOI that wraps all relevant data should be available. Furthermore, this ensure all data underlying a published manuscript can be viewed and referenced as a single collection. +Research data repositories may use individual DOIs to reference individual chemical reactions, molecules, or analytical datasets. Thus, many DOIs will then be relevant to the published study results. In order to facilitate the manuscript submission process, a **single DOI** that wraps all relevant data should be available. Furthermore, this ensure all data underlying a published manuscript can be viewed and referenced as a single **collection**. --- @@ -70,7 +70,7 @@ Research data repositories may use individual DOIs to reference individual chemi *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: -While an embargo period restricts access to a published dataset, the **metadata should still be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. +While an **embargo** period restricts access to a published dataset, the **metadata should still be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. --- @@ -96,7 +96,7 @@ This ensures that journals may carry out automated **quality control steps upon *Research data repositories should provide the repository name as `publisher` in a dataset's metadata.* ::: -As stated by [**DataCite's documenation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), this field is used to formulate the citation of the data and thus should be the repository name. +As stated by [**DataCite's documenation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), this `publisher` field is used to formulate the citation of the data and thus should be the repository name. --- @@ -104,17 +104,17 @@ As stated by [**DataCite's documenation on the publisher field**](https://dataci *Research data repositories should provide their repository identifier by re3data.org as a `publisherIdentifier`.* ::: -To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide **repository identifier from re3data.org**. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. +To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide their **repository identifier from re3data.org**. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. In the case of RADAR4Chem the relationship would be described as follows (see also [DataCite's documenation on the publisher field](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher)): ->Publisher:RADAR4Chem +>Publisher: RADAR4Chem > ->publisherIdentifier:http://doi.org/10.17616/R3ZX96 +>publisherIdentifier: http://doi.org/10.17616/R3ZX96 > ->publisherIdentifierScheme:re3data +>publisherIdentifierScheme: re3data > ->schemeURI:https://re3data.org/ +>schemeURI: https://re3data.org/ ```xml RADAR4Chem From 3644933b4009951b7a305a3c9be93f32f83a9675 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Fri, 7 Jun 2024 14:44:37 +0200 Subject: [PATCH 21/44] fix: for research infrastructure providers --- .../70_publication_standards.mdx | 91 ++++++++----------- 1 file changed, 37 insertions(+), 54 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index e06f7a1d..d6c85f42 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -3,8 +3,7 @@ title: "Publishing Standards" slug: "/publishing_standards" --- - - + ![Under Construction](/img/Constr_2bl.png) @@ -16,6 +15,9 @@ This page is under construction, while you are welcome to read the already exist ### How to use dataset PIDs in scientific articles + + + During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their article for interlinking in two main ways: :::tip Standard @@ -44,45 +46,39 @@ Many data repositories will offer the option to add a related identifier. Accord See also: [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) -## For Research Data Repositories - -The below outlines a collection of standards for research data repositories. - ---- +## For Research Data Infrastructure and Resource Providers :::tip Standard -*Research data repositories should provide a Collection DOI to wrap datasets corresponding to one study.* +*Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to an article to be published.* ::: -Research data repositories may use individual DOIs to reference individual chemical reactions, molecules, or analytical datasets. Thus, many DOIs will then be relevant to the published study results. In order to facilitate the manuscript submission process, a **single DOI** that wraps all relevant data should be available. Furthermore, this ensure all data underlying a published manuscript can be viewed and referenced as a single **collection**. - ---- +Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole datasets published, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. :::tip Standard -*NFDI4Chem-supported research data repositories should contribute to Scholix.org (or a similar solution).* +*Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: -[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. - ---- +While an **embargo** period restricts access to a published dataset, the **metadata should be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accesible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. :::tip Standard -*Datasets published with an embargo period should have inaccessible data but accessible metadata.* +*Research data repositories should contribute to Scholix.org.* ::: -While an **embargo** period restricts access to a published dataset, the **metadata should still be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. +[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing an **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information is used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset. ---- - +:::tip Standard +*Research data repositories should provide access to datasets under review.* +::: +In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* beside of the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via an URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset is not yet published. :::tip Standard *URLs to access datasets under review should have the access credentials encoded in the URL.* ::: -**Review links** for datasets should have the **access credentials** encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. +**Review links** for datasets *under review* should have the **access credentials** encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. ---- + :::tip Standard -*Research data repositories should provide their repository identifier by re3data.org as a `publisherIdentifier`.* +*Research data repositories should provide the repository name as 'publisher' as well as a 'publisherIdentifier' in a dataset's DataCite metadata.* ::: -To uniquely and persistently identify themselves within the dataset's metadata, repositories should provide their **repository identifier from re3data.org**. These should be automatically populated metadata fields. If data has originally been published in another repository, the respective repository identifier should be used. +DOI prefixes are specific to each registrant. As each registrant may host more than one repository, the prefix is not neccesarily specific to an individual repository. As stated by [**DataCite's documenation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), the required `publisher` field is used to formulate the citation of the data and should therefore be the repository name. In addition, a repository identifier such as the re3data identifier should be provided to unambiguously identify the repository. Both fields should be automatically populated by the repository and should not be editable by the submitter. -In the case of RADAR4Chem the relationship would be described as follows (see also [DataCite's documenation on the publisher field](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher)): +In the case of RADAR4Chem the relationship would be described as follows: >Publisher: RADAR4Chem > ->publisherIdentifier: http://doi.org/10.17616/R3ZX96 +>publisherIdentifier: http://doi.org/10.17616/R31NJNAY > >publisherIdentifierScheme: re3data > >schemeURI: https://re3data.org/ +In XML: ```xml -RADAR4Chem +RADAR4Chem ``` This ensures humans as well as machines can trace and interpret where the data has been published. ---- - :::tip Standard -*Research data repositories should allow researchers to update the research data's metadata.* +*Research data repositories should allow researchers to update the metadata of datasets.* ::: -This pertains to **corrections and updates** made both to the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. - ---- +As the process of adding metadata via a metadata editor can be error-prone, creators should be allowed to **correct and update** the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. Updating of metadata contributes to [FAIR](/docs/fair) ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) by enhancing the richness of metadata, and also allows creators to add additional related identifiers for recently published related datasets and articles. :::tip Standard -*Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the DataCite schema* +*Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the datasets DataCite metadata.* ::: -Dataset's should have their **own description as an abstract**. Copying the related text publication abstract can results in a **rights conflict** with the respective publisher. Authors and data curators should be informed about this conflict when filling out a dataset's metadata. - ---- +Dataset's should have their **own description as an abstract**. Copying the related article abstract can results in a **rights conflict** with the respective acedemic publisher. This is particularly the case in German law. Authors and data curators should be informed of this conflict, e.g. via a **tooltip** when adding metadata using a metadata editor. :::tip Standard -*In research data repositories, licenses should be grouped in licenses for research data vs. licences for software.* +*In research data repositories, licences should be grouped into research data licenses and software licenses.* ::: -**Licenses** differ for datasets and software. Thus, providing a **grouping** greatly aids authors in selecting from the correct set. - ---- +Repositories often tend to provide confusingly long lists of licences. Furthermore, **licenses** differ for datasets and software. Providing a **grouping** will greatly assit authors in selecting from the correct set. :::tip Standard -*Research data repositories should guide users to choose a creative commons license while not making the overall landscape too complicated* +*Research data repositories should encourage researchers to choose a Creative Commons licence to simplify the landscape of licences and their choice.* ::: -In line with grouping licenses between software and datasets, pointing authors towards the selection of [**creative commons (CC)**](https://creativecommons.org/) license alleviates the selection process. - ---- +In line with grouping licences between software and datasets, pointing authors towards the selection of [**Creative Commons (CC)**](https://creativecommons.org/) license alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. :::tip Standard -*Research data repositories should pre-select licenses such as CC0 or CC BY 4.0 instead of more restrictive licenses such as CC BY-SA 4.0, which might highly complicate reuse.* +*Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can make reuse very difficult.* ::: -Licenses can be confusing to authors. Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/) and [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)** as opposed to more restrictive licenses such as [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/) or [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/). +Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licenses/by/4.0/)** as opposed to more restrictive licenses such as [CC BY-SA](https://creativecommons.org/licenses/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licenses/by-nc-nd/4.0/). ## For Publishers and Journals + + The below outlines a collection of standards for publishers and journals. --- From 8f78afe3eed2a27196837a6f9eef1d660b99ea3d Mon Sep 17 00:00:00 2001 From: tilfischer Date: Fri, 7 Jun 2024 15:13:48 +0200 Subject: [PATCH 22/44] fix: remove CC0 --- docs/50_data_publication/70_publication_standards.mdx | 6 ------ 1 file changed, 6 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index d6c85f42..9917ac1d 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -181,11 +181,5 @@ During manuscript submission, editable [templates](/docs/data_availability_state To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets should be published prior to the publication of the article**. Thus, once an article is accepted, the authors should publish the underlying data, ensuring that data is avilable when the article is published and that the journal editors can run quality control checks on the provided DOI. This process must be explicitely communicated with authors through the author guidelines, yet can also be in included within other communication upon acceptance. At this point, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to publication. ---- - -*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.* - ---- - ---- Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) From e19c63f2ee1a2a8c8829b72e415653c6384276da Mon Sep 17 00:00:00 2001 From: tilfischer Date: Fri, 7 Jun 2024 15:21:28 +0200 Subject: [PATCH 23/44] feat: headlines standards for infrastructure --- .../70_publication_standards.mdx | 24 ++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 9917ac1d..14fff2fc 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -48,30 +48,40 @@ See also: [Crossref's documentation on **linking datasets** to published items]( ## For Research Data Infrastructure and Resource Providers +### Collection DOIs + :::tip Standard *Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to an article to be published.* ::: Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole datasets published, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. +### Embargo Periode and Metadata Accessibility + :::tip Standard *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: While an **embargo** period restricts access to a published dataset, the **metadata should be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accesible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. +### Scholix.org + :::tip Standard *Research data repositories should contribute to Scholix.org.* ::: [**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing an **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information is used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset. +### Datasets under Review + :::tip Standard *Research data repositories should provide access to datasets under review.* ::: In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* beside of the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via an URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset is not yet published. +### Reviewer Access to Datasets under Review + :::tip Standard *URLs to access datasets under review should have the access credentials encoded in the URL.* ::: @@ -90,6 +100,8 @@ I commented this out, as the DOI should be registered when something gets publis --> +### Publisher and PublisherIdentifier in DataCite Metadata + :::tip Standard *Research data repositories should provide the repository name as 'publisher' as well as a 'publisherIdentifier' in a dataset's DataCite metadata.* ::: @@ -113,30 +125,40 @@ In XML: This ensures humans as well as machines can trace and interpret where the data has been published. +### Metadata Corrections and Updates + :::tip Standard -*Research data repositories should allow researchers to update the metadata of datasets.* +*Research data repositories should allow researchers to correct and update the metadata of datasets.* ::: As the process of adding metadata via a metadata editor can be error-prone, creators should be allowed to **correct and update** the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. Updating of metadata contributes to [FAIR](/docs/fair) ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) by enhancing the richness of metadata, and also allows creators to add additional related identifiers for recently published related datasets and articles. +### Legal Issues on Dataset Abstract + :::tip Standard *Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the datasets DataCite metadata.* ::: Dataset's should have their **own description as an abstract**. Copying the related article abstract can results in a **rights conflict** with the respective acedemic publisher. This is particularly the case in German law. Authors and data curators should be informed of this conflict, e.g. via a **tooltip** when adding metadata using a metadata editor. +### Group Licenes + :::tip Standard *In research data repositories, licences should be grouped into research data licenses and software licenses.* ::: Repositories often tend to provide confusingly long lists of licences. Furthermore, **licenses** differ for datasets and software. Providing a **grouping** will greatly assit authors in selecting from the correct set. +### Encourage Creative Commons Licences + :::tip Standard *Research data repositories should encourage researchers to choose a Creative Commons licence to simplify the landscape of licences and their choice.* ::: In line with grouping licences between software and datasets, pointing authors towards the selection of [**Creative Commons (CC)**](https://creativecommons.org/) license alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. +### Promote Least Restrictive Creative Commons Licences + :::tip Standard *Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can make reuse very difficult.* ::: From 83832983283e18c37b3c893704417bd9bb1b49df Mon Sep 17 00:00:00 2001 From: tilfischer Date: Fri, 7 Jun 2024 15:56:29 +0200 Subject: [PATCH 24/44] fix: pub standards, infrastructure, typo --- .../70_publication_standards.mdx | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 14fff2fc..4a2c6db9 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -54,7 +54,7 @@ See also: [Crossref's documentation on **linking datasets** to published items]( *Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to an article to be published.* ::: -Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole datasets published, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. +Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. ### Embargo Periode and Metadata Accessibility @@ -62,7 +62,7 @@ Field-specific research data repositories may provide DOIs to reference individu *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: -While an **embargo** period restricts access to a published dataset, the **metadata should be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accesible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. +While an **embargo** period restricts access to a published dataset, the **metadata should be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accessible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. ### Scholix.org @@ -70,7 +70,7 @@ While an **embargo** period restricts access to a published dataset, the **metad *Research data repositories should contribute to Scholix.org.* ::: -[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing an **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information is used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset. +[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information is used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset. ### Datasets under Review @@ -78,7 +78,7 @@ While an **embargo** period restricts access to a published dataset, the **metad *Research data repositories should provide access to datasets under review.* ::: -In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* beside of the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via an URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset is not yet published. +In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* beside of the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via a URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset is not yet published. ### Reviewer Access to Datasets under Review @@ -106,7 +106,7 @@ I commented this out, as the DOI should be registered when something gets publis *Research data repositories should provide the repository name as 'publisher' as well as a 'publisherIdentifier' in a dataset's DataCite metadata.* ::: -DOI prefixes are specific to each registrant. As each registrant may host more than one repository, the prefix is not neccesarily specific to an individual repository. As stated by [**DataCite's documenation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), the required `publisher` field is used to formulate the citation of the data and should therefore be the repository name. In addition, a repository identifier such as the re3data identifier should be provided to unambiguously identify the repository. Both fields should be automatically populated by the repository and should not be editable by the submitter. +DOI prefixes are specific to each registrant. As each registrant may host more than one repository, the prefix is not necessarily specific to an individual repository. As stated by [**DataCite's documentation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), the required `publisher` field is used to formulate the citation of the data and should therefore be the repository name. In addition, a repository identifier such as the re3data identifier should be provided to unambiguously identify the repository. Both fields should be automatically populated by the repository and should not be editable by the submitter. In the case of RADAR4Chem the relationship would be described as follows: @@ -139,15 +139,15 @@ As the process of adding metadata via a metadata editor can be error-prone, crea *Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the datasets DataCite metadata.* ::: -Dataset's should have their **own description as an abstract**. Copying the related article abstract can results in a **rights conflict** with the respective acedemic publisher. This is particularly the case in German law. Authors and data curators should be informed of this conflict, e.g. via a **tooltip** when adding metadata using a metadata editor. +Dataset's should have their **own description as an abstract**. Copying the related article abstract can result in a **rights conflict** with the respective academic publisher. This is particularly the case in German law. Authors and data curators should be informed of this conflict, e.g. via a **tooltip** when adding metadata using a metadata editor. -### Group Licenes +### Group Licences :::tip Standard -*In research data repositories, licences should be grouped into research data licenses and software licenses.* +*In research data repositories, licences should be grouped into research data licences and software licences.* ::: -Repositories often tend to provide confusingly long lists of licences. Furthermore, **licenses** differ for datasets and software. Providing a **grouping** will greatly assit authors in selecting from the correct set. +Repositories often tend to provide confusingly long lists of licences. Furthermore, **licences** differ for datasets and software. Providing a **grouping** will greatly assist authors in selecting from the correct set. ### Encourage Creative Commons Licences @@ -155,7 +155,7 @@ Repositories often tend to provide confusingly long lists of licences. Furthermo *Research data repositories should encourage researchers to choose a Creative Commons licence to simplify the landscape of licences and their choice.* ::: -In line with grouping licences between software and datasets, pointing authors towards the selection of [**Creative Commons (CC)**](https://creativecommons.org/) license alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. +In line with grouping licences between software and datasets, pointing authors towards the selection of [**Creative Commons (CC)**](https://creativecommons.org/) licence alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. ### Promote Least Restrictive Creative Commons Licences @@ -163,7 +163,7 @@ In line with grouping licences between software and datasets, pointing authors t *Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can make reuse very difficult.* ::: -Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licenses/by/4.0/)** as opposed to more restrictive licenses such as [CC BY-SA](https://creativecommons.org/licenses/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licenses/by-nc-nd/4.0/). +Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licences/by/4.0/)** as opposed to more restrictive licences such as [CC BY-SA](https://creativecommons.org/licences/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licences/by-nc-nd/4.0/). ## For Publishers and Journals From 8e74eba95a9d248994af6a082eec256baf3ed75c Mon Sep 17 00:00:00 2001 From: tilfischer Date: Tue, 11 Jun 2024 13:00:56 +0200 Subject: [PATCH 25/44] feat/fix: for publishers and journals --- .../70_publication_standards.mdx | 76 +++++++++++++++---- 1 file changed, 62 insertions(+), 14 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 4a2c6db9..8944e758 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -16,7 +16,7 @@ This page is under construction, while you are welcome to read the already exist ### How to use dataset PIDs in scientific articles - + During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their article for interlinking in two main ways: @@ -167,41 +167,89 @@ Shared data should be as **open as possible, as closed as necessary** with the i ## For Publishers and Journals - +### Recommendations for Trusted, Chemistry-friendly Repositories -The below outlines a collection of standards for publishers and journals. +:::tip Standard +*Journals should recommend trusted, chemistry-friendly research data repositories.* +::: ---- +To assist authors in selecting **well-established and community-specific [repositories](/docs/repositories/)** for their research data, [trusted chemistry friendly repositories](/docs/choose_repository/) should be recommended by journals. These should be included within the author guidelines or the data policies. + +### Recommendations to Include Data Availability Statements :::tip Standard -*Articles should be linked within their DOI metadata to dataset(s) with the `relation` `type` `is-supplemented-by` and the dataset(s) should link to the article using the `relationType` `IsSupplementTo`.* +Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.* ::: -This agrees with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/). It establishes a structured **link** between both PIDs and ensures humans and machines alike can interpret the relationship between the published objects. +[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or similarly termed section should be made available to authors in author guidelines of journals. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned if templates are selectable and information should be provided via the manuscript submission system. ---- +### Data Availability Statements and Manuscript Submission Systems :::tip Standard -*Journals should recommend trusted, chemistry-friendly research data repositories.* +*Journals should add a data availability statement to published articles and collect the necessary information through their submission systems.* ::: -To assist authors in selecting **well-established and community-specific repositories** for the research data, [trusted chemistry friendly repositories](docs/choose_repository) should be recommended by journals. These should be included within the author guidelines or the data policies. +[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for data [**availability statements**](/docs/data_availability_statement) or similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used. ---- +### Link Datasets to Articles in CrossRef DOI Metadata :::tip Standard -*Journals should add data availability statements to their submission system.* +*Journals should use the information available in data availability statements to enhance CrossRef DOI metadata by linking articles to datasets.* ::: -During manuscript submission, editable [templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availabilty statements**](/docs/data_availability_statement) should be provided to authors. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by inlcuding the DOI or other PID, enabling the FAIR principles (e.g., [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). +With the DOI and repository name in hand, journals should enrich CrossRef DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. For CrossRef metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata). ---- +In XML: +```xml + + + + Dataset in . + + 10.prefix/suffix + + + +``` + +In agreement with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/), the relationship type `isSupplementedBy` should be used. + +### Add Data Publications to Prior Publication Policy :::tip Standard *Journal author guidelines should explicitly encourage pre-submission of datasets.* ::: -To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets should be published prior to the publication of the article**. Thus, once an article is accepted, the authors should publish the underlying data, ensuring that data is avilable when the article is published and that the journal editors can run quality control checks on the provided DOI. This process must be explicitely communicated with authors through the author guidelines, yet can also be in included within other communication upon acceptance. At this point, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to publication. +Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of dataset are registered, DOIs can be validated and datasets can be included in the review process. + +:::danger Danger +A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset need to be manually updated by the authors after the article got published. Datasets with status *under review* are one way to overcome this disadvantage (see below). +::: + +### Recommendations to Include Research Data in the Review Process + +:::tip Standard +*Journal author guidelines should explicitly encourage to include research data in the review process.* +::: + +Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not published, i.e. it does not have a DOI registered, which can be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers. + +### Encourage to Publish Datasets prio Publishing Articles + +:::tip Standard +*Journal author guidelines should require that datasets under review get published prior an article gets published.* +::: + +To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published prior to the publication of the article**. Once a manuscript is accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journal can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article gets published, and its DOI gets registered. + +### Scholix.org + +:::tip Standard +*Journals and publishers should use Scholix.org.* +::: + +[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above). ---- Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) From 69855cfca476a09bf6dd58ebdaf9538d19f9eff4 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Tue, 11 Jun 2024 13:01:43 +0200 Subject: [PATCH 26/44] feat: move publisher up --- .../70_publication_standards.mdx | 172 +++++++++--------- 1 file changed, 86 insertions(+), 86 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 8944e758..51e6333c 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -46,6 +46,92 @@ Many data repositories will offer the option to add a related identifier. Accord See also: [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) +## For Publishers and Journals + +### Recommendations for Trusted, Chemistry-friendly Repositories + +:::tip Standard +*Journals should recommend trusted, chemistry-friendly research data repositories.* +::: + +To assist authors in selecting **well-established and community-specific [repositories](/docs/repositories/)** for their research data, [trusted chemistry friendly repositories](/docs/choose_repository/) should be recommended by journals. These should be included within the author guidelines or the data policies. + +### Recommendations to Include Data Availability Statements + +:::tip Standard +Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.* +::: + +[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or similarly termed section should be made available to authors in author guidelines of journals. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned if templates are selectable and information should be provided via the manuscript submission system. + +### Data Availability Statements and Manuscript Submission Systems + +:::tip Standard +*Journals should add a data availability statement to published articles and collect the necessary information through their submission systems.* +::: + +[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for data [**availability statements**](/docs/data_availability_statement) or similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used. + +### Link Datasets to Articles in CrossRef DOI Metadata + +:::tip Standard +*Journals should use the information available in data availability statements to enhance CrossRef DOI metadata by linking articles to datasets.* +::: + +With the DOI and repository name in hand, journals should enrich CrossRef DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. For CrossRef metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata). + +In XML: +```xml + + + + Dataset in . + + 10.prefix/suffix + + + +``` + +In agreement with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/), the relationship type `isSupplementedBy` should be used. + +### Add Data Publications to Prior Publication Policy + +:::tip Standard +*Journal author guidelines should explicitly encourage pre-submission of datasets.* +::: + +Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of dataset are registered, DOIs can be validated and datasets can be included in the review process. + +:::danger Danger +A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset need to be manually updated by the authors after the article got published. Datasets with status *under review* are one way to overcome this disadvantage (see below). +::: + +### Recommendations to Include Research Data in the Review Process + +:::tip Standard +*Journal author guidelines should explicitly encourage to include research data in the review process.* +::: + +Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not published, i.e. it does not have a DOI registered, which can be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers. + +### Encourage to Publish Datasets prio Publishing Articles + +:::tip Standard +*Journal author guidelines should require that datasets under review get published prior an article gets published.* +::: + +To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published prior to the publication of the article**. Once a manuscript is accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journal can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article gets published, and its DOI gets registered. + +### Scholix.org + +:::tip Standard +*Journals and publishers should use Scholix.org.* +::: + +[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above). + ## For Research Data Infrastructure and Resource Providers ### Collection DOIs @@ -165,91 +251,5 @@ In line with grouping licences between software and datasets, pointing authors t Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licences/by/4.0/)** as opposed to more restrictive licences such as [CC BY-SA](https://creativecommons.org/licences/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licences/by-nc-nd/4.0/). -## For Publishers and Journals - -### Recommendations for Trusted, Chemistry-friendly Repositories - -:::tip Standard -*Journals should recommend trusted, chemistry-friendly research data repositories.* -::: - -To assist authors in selecting **well-established and community-specific [repositories](/docs/repositories/)** for their research data, [trusted chemistry friendly repositories](/docs/choose_repository/) should be recommended by journals. These should be included within the author guidelines or the data policies. - -### Recommendations to Include Data Availability Statements - -:::tip Standard -Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.* -::: - -[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or similarly termed section should be made available to authors in author guidelines of journals. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned if templates are selectable and information should be provided via the manuscript submission system. - -### Data Availability Statements and Manuscript Submission Systems - -:::tip Standard -*Journals should add a data availability statement to published articles and collect the necessary information through their submission systems.* -::: - -[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for data [**availability statements**](/docs/data_availability_statement) or similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used. - -### Link Datasets to Articles in CrossRef DOI Metadata - -:::tip Standard -*Journals should use the information available in data availability statements to enhance CrossRef DOI metadata by linking articles to datasets.* -::: - -With the DOI and repository name in hand, journals should enrich CrossRef DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. For CrossRef metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata). - -In XML: -```xml - - - - Dataset in . - - 10.prefix/suffix - - - -``` - -In agreement with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/), the relationship type `isSupplementedBy` should be used. - -### Add Data Publications to Prior Publication Policy - -:::tip Standard -*Journal author guidelines should explicitly encourage pre-submission of datasets.* -::: - -Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of dataset are registered, DOIs can be validated and datasets can be included in the review process. - -:::danger Danger -A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset need to be manually updated by the authors after the article got published. Datasets with status *under review* are one way to overcome this disadvantage (see below). -::: - -### Recommendations to Include Research Data in the Review Process - -:::tip Standard -*Journal author guidelines should explicitly encourage to include research data in the review process.* -::: - -Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not published, i.e. it does not have a DOI registered, which can be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers. - -### Encourage to Publish Datasets prio Publishing Articles - -:::tip Standard -*Journal author guidelines should require that datasets under review get published prior an article gets published.* -::: - -To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published prior to the publication of the article**. Once a manuscript is accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journal can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article gets published, and its DOI gets registered. - -### Scholix.org - -:::tip Standard -*Journals and publishers should use Scholix.org.* -::: - -[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above). - ---- Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) From cfb13455544a66d4f7146f09fec389e6308ed4ff Mon Sep 17 00:00:00 2001 From: tilfischer Date: Tue, 11 Jun 2024 13:05:37 +0200 Subject: [PATCH 27/44] fix: removed DOI registration for under review --- .../70_publication_standards.mdx | 14 +------------- 1 file changed, 1 insertion(+), 13 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 51e6333c..94dd7edb 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -102,7 +102,7 @@ In agreement with [Crossref's documentation on **linking datasets** to published *Journal author guidelines should explicitly encourage pre-submission of datasets.* ::: -Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of dataset are registered, DOIs can be validated and datasets can be included in the review process. +Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is also already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of dataset are registered, DOIs can be validated and datasets can be included in the review process. :::danger Danger A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset need to be manually updated by the authors after the article got published. Datasets with status *under review* are one way to overcome this disadvantage (see below). @@ -174,18 +174,6 @@ In order to include datasets in the review process of manuscripts, repositories **Review links** for datasets *under review* should have the **access credentials** encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. - - ### Publisher and PublisherIdentifier in DataCite Metadata :::tip Standard From e937ce7bb5ecd566744b63997c3cf1ab146937a8 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Tue, 11 Jun 2024 13:07:09 +0200 Subject: [PATCH 28/44] fix: typo --- docs/50_data_publication/70_publication_standards.mdx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 94dd7edb..fd71ac7d 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -142,7 +142,7 @@ To assist in automated workflows, such as linking the datasets to the published Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. -### Embargo Periode and Metadata Accessibility +### Embargo Period and Metadata Accessibility :::tip Standard *Datasets published with an embargo period should have inaccessible data but accessible metadata.* @@ -231,7 +231,7 @@ Repositories often tend to provide confusingly long lists of licences. Furthermo In line with grouping licences between software and datasets, pointing authors towards the selection of [**Creative Commons (CC)**](https://creativecommons.org/) licence alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. -### Promote Least Restrictive Creative Commons Licences +### Promote the least Restrictive Creative Commons Licences :::tip Standard *Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can make reuse very difficult.* From 77e12c5e9cb145bdd2d82cf2320f4151c6c193ca Mon Sep 17 00:00:00 2001 From: tilfischer Date: Wed, 12 Jun 2024 11:38:07 +0200 Subject: [PATCH 29/44] feat/fix: pub standards, for authors --- .../70_publication_standards.mdx | 59 ++++++++++++------- 1 file changed, 39 insertions(+), 20 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index fd71ac7d..c964f3b2 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -3,48 +3,67 @@ title: "Publishing Standards" slug: "/publishing_standards" --- - +On this page we collect a non-exhaustive list of standards for data publication, formulated as principles, developed within the NFDI4Chem Publication Standards project. These standards are intended to streamline publication workflows, including the review process of manuscripts with corresponding datasets published in research data repositories. -![Under Construction](/img/Constr_2bl.png) - -:::info Info: -This page is under construction, while you are welcome to read the already existing paragraphs. On this page we will summarise the standards for the publication of data, formulated as principles, developed within the NFDI4Chem project on Publication Standards. These standards should streamline the publication workflows. Authors, publishers and infrastructure operators are the audience for these standards. +:::info Applies to: +Authors, publishers and infrastructure operators are the target audiences for these standards. ::: ## For Authors -### How to use dataset PIDs in scientific articles +### How to use Dataset PIDs in Scientific Articles - - +During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their scientific article for interlinking and referencing in **two main ways**: -During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their article for interlinking in two main ways: +#### How to use Dataset PIDs of own Datasets in Scientific Articles :::tip Standard -*Authors should add the PID of the corresponding dataset(s) to the data availability statement. In addition, authors should add corresponding datasets to the references, making them citable within the text of the article.* +*Authors should add the PID of their corresponding dataset(s) to the data availability statement and should add PIDs of dataset(s) to the reference section in order to specifically cite dataset(s).* ::: -For corresponding data, i.e. data directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. If you believe that your data publication is as decisive as the article itself, add your dataset to the references as well and cite within the text. +For corresponding data, i.e. directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. In order to specifically reference and cite your data within the text, add your dataset to the references as well. + +:::danger Notice: +This distinction is important, because **the link** to the dataset in CrossRef's DOI metadata of scientific articles **is differently set**, depending on whether the dataset is a directly related source of information or a specifically referenced resource. +::: + +#### How to use Dataset PIDs of Datasets of other Researchers in Scientific Articles :::tip Standard -*Authors should add PIDs to datasets by other researchers, which have been reused to the references rather than citing the corresponding article* +*Authors should include PIDs for datasets published by other researchers that have been reused in the references, rather than citing the corresponding article.* ::: -For datasets published by other researchers and reused within a study, add the PID to the reference section of the manuscript and cite within the text accordingly. +For datasets published by other researchers and reused in a study, include the dataset PID in the reference section of the manuscript and cite within the text accordingly. -:::info Notice: -This distinction is important, because the link to the dataset in the DOI metadata of scientific articles is differently set, depending on whether the dataset is a directly related source of information or a referenced source by other researchers and its information has been reused. +### How to Link Datasets to their Corresponding Scientific Article + +:::tip Standard +*Researchers should link their datasets to be published to their corresponding articles by adding the article DOI to the dataset's DataCite metadata as a related identifier.* ::: -For a set of reactions, samples, and analyses, to assemble a study, **Collection PIDs** should be used rather than providing many separate PIDs. Such a study wrapped with a Collection PID can directly correspond to a published scientific article and can be referenced in a bundled manner within the [data availability statement](/docs/data_availability_statement) or references section. +Research data repositories offer the option to add a related identifier to link datasets to related resources, such as a corresponding article. This considerably enhances the [FAIRness](/docs/fair/) of datasets, mainly the findability ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) as well as the interoperability ([I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). -In addition, but second-tier, the PID of a related dataset could also be mentioned in the supplementary PDF, if such a document is generated. +### Usage of Relation Type for Linking Datasets with Scientific Articles -### How to link scientific articles to thier corresponding dataset(s) +:::tip Standard +*Researchers should link their datasets to be published to their corresponding articles using the relation type `IsSupplementTo` .* +::: -Many data repositories will offer the option to add a related identifier. According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. As stressed [above](#how-to-use-dataset-pids-in-scientific-articles), while datasets _may_ be cited within the article, the data availability statement should include them, first and foremost. Hence, to ensure the correct linking on the side of the datset, the relation type `IsSupplementTo` should primarily used, while `IsCitedBy` can be used in addition if the dataset is indeed referenced. +According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. On the other side of the pond, [CrossRef's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmenetTo` should be used to link datasets generated as part of research results. -See also: [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) +### Usage of Collection DOIs + +:::tip Standard +*Researchers should use the Collection DOI provided by a repository in the data availability statements of their corresponding manuscript to wrap research data objects that are relevant to that an article to be published.* +::: + +Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. + +To facilitate the process of manuscript submission and article publication, researchers should add the **Collection DOI** provided by the repository to the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. + +If individual reactions, molecules or analytical data should be referenced, add the DOIs of these individual research objects to the reference section and cite within the text accordingly. + + ## For Publishers and Journals From 937dcdf029fee02d83ca6c9638310cf53b9164e6 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Wed, 12 Jun 2024 16:39:38 +0200 Subject: [PATCH 30/44] feat: more standards --- .../70_publication_standards.mdx | 32 +++++++++++++++++-- 1 file changed, 30 insertions(+), 2 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index c964f3b2..21c59667 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -3,7 +3,9 @@ title: "Publishing Standards" slug: "/publishing_standards" --- -On this page we collect a non-exhaustive list of standards for data publication, formulated as principles, developed within the NFDI4Chem Publication Standards project. These standards are intended to streamline publication workflows, including the review process of manuscripts with corresponding datasets published in research data repositories. +On this page we collect a non-exhaustive list of data publication standards, formulated as principles, that have been developed within the NFDI4Chem Publication Standards project. These standards are intended to improve the quality of metadata and streamline publication workflows, including the review process of manuscripts with corresponding datasets published in research data repositories. + +For more generic information on publishing in field-specific and generic, multidisciplinary repositories such as publishing data in open formats or providing machine-readable chemical structures alongside the analytical data, please have a look to our page on [Best-Practices](/docs/best_practice/). :::info Applies to: Authors, publishers and infrastructure operators are the target audiences for these standards. @@ -11,6 +13,14 @@ Authors, publishers and infrastructure operators are the target audiences for th ## For Authors +### Use ORCID iD to Identifiy Authors and ROR to Identifiy Institutions + +:::tip Standard +*Authors should provide their ORCID iD to identify the authors/creators and contributors, and their ROR identifier to identify the institution to which they are affiliated.* +::: + +ORCID iDs allow authors to be uniquely identified, whereas author names may not be unique, may change, or may have different ordering conventions depending on cultural differences. Similarly, affiliations can vary according to style and granularity. In order to uniquely identify the institutions to which authors are affiliated, the ROR identifier should be provided. Please note that the ROR identifier is not intended to resolve down to the departmental level. Nevertheless, both identifiers improve findability. + ### How to use Dataset PIDs in Scientific Articles During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their scientific article for interlinking and referencing in **two main ways**: @@ -153,6 +163,16 @@ To assist in automated workflows, such as linking the datasets to the published ## For Research Data Infrastructure and Resource Providers +### Metadata Should be Part of the Dataset Downloaded + +:::tip Standard +*Research data repositories should include the metadata in datasets downloaded by researchers.* +::: + + + + + ### Collection DOIs :::tip Standard @@ -167,7 +187,7 @@ Field-specific research data repositories may provide DOIs to reference individu *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: -While an **embargo** period restricts access to a published dataset, the **metadata should be accessible**. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accessible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. +While an **embargo** period restricts access to a published dataset, the **metadata should be accessible** – *publish* with embargo. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accessible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. ### Scholix.org @@ -258,5 +278,13 @@ In line with grouping licences between software and datasets, pointing authors t Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licences/by/4.0/)** as opposed to more restrictive licences such as [CC BY-SA](https://creativecommons.org/licences/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licences/by-nc-nd/4.0/). +### Creators and Contributors + +:::tip Standard +*Research data repositories should label fields for creators in their (DataCite) metadata editor as authors/creators.* +::: + +Researchers are used to talking about authors when it comes to the publication of results with one of the scientific publishers. On the other hand, DataCite distinguishes between authors and contributors, with the latter also being assigned a role. To avoid confusion for researchers who want to publish their data, metadata editors of repositories should guide researchers when adding metadata by labelling the field for creators in their (DataCite) metadata editors as authors/creators. + ---- Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) From f1bd0d25ad38605c1f74dd25b353d5434977b6ba Mon Sep 17 00:00:00 2001 From: tilfischer Date: Wed, 12 Jun 2024 16:59:43 +0200 Subject: [PATCH 31/44] feat: pub std, orcid, ror, bagit, ro-crate --- .../70_publication_standards.mdx | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 16d66c99..d5f500f4 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -5,7 +5,7 @@ slug: "/publishing_standards" On this page we collect a non-exhaustive list of data publication standards, formulated as principles, that have been developed within the NFDI4Chem Publication Standards project. These standards are intended to improve the quality of metadata and streamline publication workflows, including the review process of manuscripts with corresponding datasets published in research data repositories. -For more generic information on publishing in field-specific and generic, multidisciplinary repositories such as publishing data in open formats or providing machine-readable chemical structures alongside the analytical data, please have a look to our page on [Best-Practices](/docs/best_practice/). +For more generic information for authors on publishing in field-specific and generic, multidisciplinary repositories such as publishing data in open formats or providing machine-readable chemical structures alongside the analytical data, please have a look to our page on [Best-Practices](/docs/best_practice/). :::info Applies to: Authors, publishers and infrastructure operators are the target audiences for these standards. @@ -165,15 +165,25 @@ To assist in automated workflows, such as linking the datasets to the published ## For Research Data Infrastructure and Resource Providers -### Metadata Should be Part of the Dataset Downloaded +### Metadata Should be Part of a Dataset :::tip Standard *Research data repositories should include the metadata in datasets downloaded by researchers.* ::: +While researchers upload their data, metadata is attached. For generic, multidisciplinary repositories, additional metadata is provided via a metadata editor. For field-specific repositories, the metadata is extracted from the analytical data files and provided by researcher along their lab workflows, as this is the case for Chemotion ELN. Once data is retrieved from a repository, this metadata should not be lost but should be included in the downloaded package. The minimum to include is the descriptive DataCite metadata. +[BagIt](https://www.rfc-editor.org/rfc/rfc8493.html), a set of hierarchical file system conventions, is one solution for including metadata in downloaded dataset. +### Structured Domain-Specific Metadata Should be Part of a Dataset +:::tip Standard +*Research data repositories should include structured, domain-specific metadata in datasets downloaded by researchers.* +::: + +Beside of metadata following generic schemes such as DataCite's metadata scheme, domain-specific metadata should be part of each dataset. This metadata should also be provided in datasets downloaded by researchers for reuse. + +One solution to this is to include Schema.org metadata by [combining RO-Crate and BagIt](https://www.researchobject.org/ro-crate/specification/1.1/appendix/implementation-notes.html#adding-ro-crate-to-bagit). ### Collection DOIs From 96fc8d31ae533facbc459aa91c01d967f1a103ff Mon Sep 17 00:00:00 2001 From: tilfischer Date: Wed, 17 Jul 2024 12:05:48 +0200 Subject: [PATCH 32/44] fix: replace dx.doi.org by doi.org in lbe json --- static/assets/lbe.json | 186 ++++++++++++++++++++--------------------- 1 file changed, 93 insertions(+), 93 deletions(-) diff --git a/static/assets/lbe.json b/static/assets/lbe.json index 0b590b31..a251a791 100644 --- a/static/assets/lbe.json +++ b/static/assets/lbe.json @@ -29,11 +29,11 @@ "linkdata": [ { "name": "RADAR4Chem", - "url": "https://dx.doi.org/10.22000/786" + "url": "https://doi.org/10.22000/786" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/LMVGRKPOXLBIFQ-UHFFFAOYSA-N.1" + "url": "https://doi.org/10.14272/LMVGRKPOXLBIFQ-UHFFFAOYSA-N.1" }, { "name": "nmrXiv", @@ -60,11 +60,11 @@ "linkdata": [ { "name": "RADAR4Chem", - "url": "https://dx.doi.org/10.22000/785" + "url": "https://doi.org/10.22000/785" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/NZGWDASTMWDZIW-MRVPVSSYSA-N.1" + "url": "https://doi.org/10.14272/NZGWDASTMWDZIW-MRVPVSSYSA-N.1" }, { "name": "nmrXiv", @@ -91,11 +91,11 @@ "linkdata": [ { "name": "RADAR4Chem", - "url": "https://dx.doi.org/10.22000/795" + "url": "https://doi.org/10.22000/795" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/DGQLVPJVXFOQEV-JNVSTXMASA-N.1" + "url": "https://doi.org/10.14272/DGQLVPJVXFOQEV-JNVSTXMASA-N.1" }, { "name": "nmrXiv", @@ -122,11 +122,11 @@ "linkdata": [ { "name": "RADAR4Chem", - "url": "https://dx.doi.org/10.22000/604" + "url": "https://doi.org/10.22000/604" }, { "name": "ILL Data Portal", - "url": "http://dx.doi.org/10.5291/ILL-DATA.9-11-2067" + "url": "http://doi.org/10.5291/ILL-DATA.9-11-2067" } ], "linkcomment": "curated by the publishing authors", @@ -151,115 +151,115 @@ }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-JHIAOWGCGN-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-JHIAOWGCGN-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-XNDIRRNFWB-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-XNDIRRNFWB-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-YLBKXSDEWV-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-YLBKXSDEWV-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-MTPUXEIATO-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-MTPUXEIATO-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-DYIBODSCVM-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-DYIBODSCVM-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-YSUUDYJLPD-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-YSUUDYJLPD-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-BRNGTXITIQ-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-BRNGTXITIQ-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-ACOFZHHYLN-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-ACOFZHHYLN-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-QLLLYNCAUW-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-QLLLYNCAUW-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-YKNRUBPOGQ-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-YKNRUBPOGQ-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-ZJSFNHZUYT-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-ZJSFNHZUYT-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-HXVOLPKNEJ-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-HXVOLPKNEJ-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - 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Schmidt, Walter Richtering, Andrea Scotti", "journal": "Nature Communications", "pubyear": 2022, - "linkpub": "https://dx.doi.org/10.1038/s41467-022-31209-3", + "linkpub": "https://doi.org/10.1038/s41467-022-31209-3", "linkdata": [ { "name": "RADAR4Chem", - "url": "https://dx.doi.org/10.22000/603" + "url": "https://doi.org/10.22000/603" }, { "name": "ILL Data Portal", @@ -461,11 +461,11 @@ }, { "name": "CSD/CCDC", - "url": "https://dx.doi.org/10.5517/ccdc.csd.cc25b961" + "url": "https://doi.org/10.5517/ccdc.csd.cc25b961" }, { "name": "CSD/CCDC", - "url": "https://dx.doi.org/10.5517/ccdc.csd.cc25b972" + "url": "https://doi.org/10.5517/ccdc.csd.cc25b972" } ], "linkcomment": "curated by the publishing authors", @@ -486,35 +486,35 @@ "linkdata": [ { "name": "CSD/CCDC", - "url": "https://dx.doi.org/10.5517/ccdc.csd.cc23hkz5" + "url": "https://doi.org/10.5517/ccdc.csd.cc23hkz5" }, { "name": "CSD/CCDC", - "url": "https://dx.doi.org/10.5517/ccdc.csd.cc23hl07" + "url": "https://doi.org/10.5517/ccdc.csd.cc23hl07" }, { "name": "CSD/CCDC", - 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"url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-LLIFZWKYAN-UHFFFADPSC-NUHFF-NHDGP-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-LLIFZWKYAN-UHFFFADPSC-NUHFF-NHDGP-NUHFF-ZZZ" }, { "name": "Chemotion Repository", - "url": "https://dx.doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-LHQKMJBXIU-UHFFFADPSC-NUHFF-NLTSL-NUHFF-ZZZ" + "url": "https://doi.org/10.14272/reaction/SA-FUHFF-UHFFFADPSC-LHQKMJBXIU-UHFFFADPSC-NUHFF-NLTSL-NUHFF-ZZZ" }, { "name": "CSD/CCDC", - "url": "https://dx.doi.org/10.5517/ccdc.csd.cc216k3y" + "url": "https://doi.org/10.5517/ccdc.csd.cc216k3y" } ], "linkcomment": "curated by the publishing authors", @@ -895,7 +895,7 @@ "linkdata": [ { "name": "RADAR4Chem", - "url": "https://dx.doi.org/10.22000/1865" + "url": "https://doi.org/10.22000/1865" }, { "name": "nmrXiv", From a0526996c5622f92db7b07e22b6e7b2087d09f6d Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Wed, 17 Jul 2024 14:35:54 +0000 Subject: [PATCH 33/44] edit: small en fix --- docs/50_data_publication/70_publication_standards.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index d5f500f4..432a9a54 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -3,7 +3,7 @@ title: "Publishing Standards" slug: "/publishing_standards" --- -On this page we collect a non-exhaustive list of data publication standards, formulated as principles, that have been developed within the NFDI4Chem Publication Standards project. These standards are intended to improve the quality of metadata and streamline publication workflows, including the review process of manuscripts with corresponding datasets published in research data repositories. +On this page we collect a non-exhaustive list of data publication standards, formulated as principles, that have been developed within the NFDI4Chem Publication Standards project. These standards are intended to improve the quality of metadata and streamline publication workflows, including the manuscript review process with corresponding datasets published in research data repositories. For more generic information for authors on publishing in field-specific and generic, multidisciplinary repositories such as publishing data in open formats or providing machine-readable chemical structures alongside the analytical data, please have a look to our page on [Best-Practices](/docs/best_practice/). From e2a0cb8c6682421e268005d91240ad90eab34c5f Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Wed, 17 Jul 2024 14:43:46 +0000 Subject: [PATCH 34/44] edited for authors section --- docs/50_data_publication/70_publication_standards.mdx | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 432a9a54..9ccdff6f 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -38,7 +38,7 @@ For corresponding data, i.e. directly underlying the results reported in the art This distinction is important, because **the link** to the dataset in CrossRef's DOI metadata of scientific articles **is differently set**, depending on whether the dataset is a directly related source of information or a specifically referenced resource. ::: -#### How to use Dataset PIDs of Datasets of other Researchers in Scientific Articles +#### How to use Dataset PIDs for Datasets by other Researchers in Scientific Articles :::tip Standard @@ -58,22 +58,22 @@ Research data repositories offer the option to add a related identifier to link ### Usage of Relation Type for Linking Datasets with Scientific Articles :::tip Standard -*Researchers should link their datasets to be published to their corresponding articles using the relation type `IsSupplementTo` .* +*Researchers should link their datasets to be published to their corresponding articles using the relation type `IsSupplementTo`.* ::: -According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. On the other side of the pond, [CrossRef's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmenetTo` should be used to link datasets generated as part of research results. +According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. For published articles, [CrossRef's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmenetTo` should be used to link datasets generated as part of research results. ### Usage of Collection DOIs :::tip Standard -*Researchers should use the Collection DOI provided by a repository in the data availability statements of their corresponding manuscript to wrap research data objects that are relevant to that an article to be published.* +*Researchers should use the Collection DOI provided by a repository in the data availability statements of their corresponding manuscript to wrap research data objects that are relevant to that of an article to be published.* ::: Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, researchers should add the **Collection DOI** provided by the repository to the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. -If individual reactions, molecules or analytical data should be referenced, add the DOIs of these individual research objects to the reference section and cite within the text accordingly. +If individual reactions, molecules, or analytical data should be referenced, add the DOIs of these individual research objects to the reference section and cite within the text accordingly. From 39c8df5ad9f957d4593f28dd3137ee1e6807b698 Mon Sep 17 00:00:00 2001 From: Nikki Parks <60778202+nap84@users.noreply.github.com> Date: Thu, 18 Jul 2024 09:05:29 +0000 Subject: [PATCH 35/44] Proofreding/edits --- .../70_publication_standards.mdx | 48 +++++++++---------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx index 9ccdff6f..fc3b3d11 100644 --- a/docs/50_data_publication/70_publication_standards.mdx +++ b/docs/50_data_publication/70_publication_standards.mdx @@ -90,10 +90,10 @@ To assist authors in selecting **well-established and community-specific [reposi ### Recommendations to Include Data Availability Statements :::tip Standard -Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.* +*Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.* ::: -[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or similarly termed section should be made available to authors in author guidelines of journals. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned if templates are selectable and information should be provided via the manuscript submission system. +[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should be made available to authors in the journal's author guidelines. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned whether templates are selectable and information should be provided via the manuscript submission system. ### Data Availability Statements and Manuscript Submission Systems @@ -101,7 +101,7 @@ Journals should recommend that authors provide a data availability statement. Au *Journals should add a data availability statement to published articles and collect the necessary information through their submission systems.* ::: -[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for data [**availability statements**](/docs/data_availability_statement) or similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used. +[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g. `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used. ### Link Datasets to Articles in CrossRef DOI Metadata @@ -133,27 +133,27 @@ In agreement with [Crossref's documentation on **linking datasets** to published *Journal author guidelines should explicitly encourage pre-submission of datasets.* ::: -Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is also already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of dataset are registered, DOIs can be validated and datasets can be included in the review process. +Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is also already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of datasets are registered. DOIs can therefore be validated and datasets can be included in the review process. :::danger Danger -A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset need to be manually updated by the authors after the article got published. Datasets with status *under review* are one way to overcome this disadvantage (see below). +A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset must then be manually updated by the authors after the article has been published. Datasets with status *under review* are one way to overcome this disadvantage (see below). ::: ### Recommendations to Include Research Data in the Review Process :::tip Standard -*Journal author guidelines should explicitly encourage to include research data in the review process.* +*Journal author guidelines should explicitly encourage research data to be included in the review process.* ::: -Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not published, i.e. it does not have a DOI registered, which can be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers. +Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not yet published, i.e. it does not have a DOI registered. Therefore, the DOI cannot be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers. -### Encourage to Publish Datasets prio Publishing Articles +### Encourage Authors to Publish Datasets prior Publishing Articles :::tip Standard -*Journal author guidelines should require that datasets under review get published prior an article gets published.* +*Journal author guidelines should require that datasets under review to be published prior to the publication of the associated article.* ::: -To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published prior to the publication of the article**. Once a manuscript is accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journal can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article gets published, and its DOI gets registered. +To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published prior to the publication of the article**. Once a manuscript has been accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journals can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet, can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article is published, and its DOI is registered. ### Scholix.org @@ -161,7 +161,7 @@ To assist in automated workflows, such as linking the datasets to the published *Journals and publishers should use Scholix.org.* ::: -[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above). +[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above). ## For Research Data Infrastructure and Resource Providers @@ -171,9 +171,9 @@ To assist in automated workflows, such as linking the datasets to the published *Research data repositories should include the metadata in datasets downloaded by researchers.* ::: -While researchers upload their data, metadata is attached. For generic, multidisciplinary repositories, additional metadata is provided via a metadata editor. For field-specific repositories, the metadata is extracted from the analytical data files and provided by researcher along their lab workflows, as this is the case for Chemotion ELN. Once data is retrieved from a repository, this metadata should not be lost but should be included in the downloaded package. The minimum to include is the descriptive DataCite metadata. +While researchers upload their data, metadata is attached. For generic, multidisciplinary repositories, additional metadata is provided via a metadata editor. For field-specific repositories, the metadata is extracted from the analytical data files and provided by researchers along their lab workflows, as this is the case for Chemotion ELN. Once data is retrieved from a repository, this metadata should not be lost but should be included in the downloaded package. The minimum to include is the descriptive DataCite metadata. -[BagIt](https://www.rfc-editor.org/rfc/rfc8493.html), a set of hierarchical file system conventions, is one solution for including metadata in downloaded dataset. +[BagIt](https://www.rfc-editor.org/rfc/rfc8493.html), a set of hierarchical file system conventions, is one solution for including metadata in downloaded dataset. ### Structured Domain-Specific Metadata Should be Part of a Dataset @@ -188,10 +188,10 @@ One solution to this is to include Schema.org metadata by [combining RO-Crate an ### Collection DOIs :::tip Standard -*Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to an article to be published.* +*Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to a single article that is to be published.* ::: -Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. +Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. ### Embargo Period and Metadata Accessibility @@ -199,7 +199,7 @@ Field-specific research data repositories may provide DOIs to reference individu *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: -While an **embargo** period restricts access to a published dataset, the **metadata should be accessible** – *publish* with embargo. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accessible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. +While an **embargo** period restricts access to a published dataset, the **metadata should be accessible**—*publish* with embargo. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accessible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. ### Scholix.org @@ -215,12 +215,12 @@ While an **embargo** period restricts access to a published dataset, the **metad *Research data repositories should provide access to datasets under review.* ::: -In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* beside of the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via a URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset is not yet published. +In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* in addition to the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via a URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset has not yet been published. ### Reviewer Access to Datasets under Review :::tip Standard -*URLs to access datasets under review should have the access credentials encoded in the URL.* +*URLs to access datasets under review should have the access credentials encoded within the URL.* ::: **Review links** for datasets *under review* should have the **access credentials** encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. @@ -256,7 +256,7 @@ This ensures humans as well as machines can trace and interpret where the data h *Research data repositories should allow researchers to correct and update the metadata of datasets.* ::: -As the process of adding metadata via a metadata editor can be error-prone, creators should be allowed to **correct and update** the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. Updating of metadata contributes to [FAIR](/docs/fair) ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) by enhancing the richness of metadata, and also allows creators to add additional related identifiers for recently published related datasets and articles. +As the process of adding metadata via a metadata editor can be error-prone, creators should be allowed to **correct and update** the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. Updating metadata contributes to [FAIR](/docs/fair) ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) by enhancing the richness of metadata, and also allows creators to add additional related identifiers for recently published related datasets and articles. ### Legal Issues on Dataset Abstract @@ -280,23 +280,23 @@ Repositories often tend to provide confusingly long lists of licences. Furthermo *Research data repositories should encourage researchers to choose a Creative Commons licence to simplify the landscape of licences and their choice.* ::: -In line with grouping licences between software and datasets, pointing authors towards the selection of [**Creative Commons (CC)**](https://creativecommons.org/) licence alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. +In line with grouping licences between software and datasets, pointing authors towards the selection of a [**Creative Commons (CC)**](https://creativecommons.org/) licence alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. ### Promote the least Restrictive Creative Commons Licences :::tip Standard -*Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can make reuse very difficult.* +*Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can inhibit reuse.* ::: -Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licences/by/4.0/)** as opposed to more restrictive licences such as [CC BY-SA](https://creativecommons.org/licences/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licences/by-nc-nd/4.0/). +Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licences/by/4.0/)** as opposed to more restrictive licences such as [CC BY-SA](https://creativecommons.org/licences/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licences/by-nc-nd/4.0/). Such restrictive licenses can make data reuse difficult. ### Creators and Contributors :::tip Standard -*Research data repositories should label fields for creators in their (DataCite) metadata editor as authors/creators.* +*Research data repositories should label fields for creators in their (DataCite) metadata editor as* Authors/Creators. ::: -Researchers are used to talking about authors when it comes to the publication of results with one of the scientific publishers. On the other hand, DataCite distinguishes between authors and contributors, with the latter also being assigned a role. To avoid confusion for researchers who want to publish their data, metadata editors of repositories should guide researchers when adding metadata by labelling the field for creators in their (DataCite) metadata editors as authors/creators. +Researchers are used to talking about authors when it comes to the publication of results with one of the scientific publishers. On the other hand, DataCite distinguishes between authors and contributors, with the latter also being assigned a role. To avoid confusion for researchers who want to publish their data, repositories should guide researchers when adding metadata by labelling the field for creators in their (DataCite) metadata editors as *Authors/Creators*. ---- Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) From 92e340f071ccce5cfb153efaaaa274f6f7db747b Mon Sep 17 00:00:00 2001 From: tilfischer Date: Fri, 19 Jul 2024 11:01:33 +0200 Subject: [PATCH 36/44] feat: split pub standards page by stakeholders --- .../70_publication_standards.mdx | 302 ------------------ .../10_publishing_standards_authors.mdx | 73 +++++ .../20_publishing_standards_publishers.mdx | 93 ++++++ ...30_publishing_standards_infrastructure.mdx | 142 ++++++++ .../70_publishing_standards_intro.mdx | 24 ++ .../70_publishing_standards/_category_.json | 7 + src/components/N4CFeatures.js | 17 + 7 files changed, 356 insertions(+), 302 deletions(-) delete mode 100644 docs/50_data_publication/70_publication_standards.mdx create mode 100644 docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx create mode 100644 docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx create mode 100644 docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx create mode 100644 docs/50_data_publication/70_publishing_standards/70_publishing_standards_intro.mdx create mode 100644 docs/50_data_publication/70_publishing_standards/_category_.json diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx deleted file mode 100644 index d5f500f4..00000000 --- a/docs/50_data_publication/70_publication_standards.mdx +++ /dev/null @@ -1,302 +0,0 @@ ---- -title: "Publishing Standards" -slug: "/publishing_standards" ---- - -On this page we collect a non-exhaustive list of data publication standards, formulated as principles, that have been developed within the NFDI4Chem Publication Standards project. These standards are intended to improve the quality of metadata and streamline publication workflows, including the review process of manuscripts with corresponding datasets published in research data repositories. - -For more generic information for authors on publishing in field-specific and generic, multidisciplinary repositories such as publishing data in open formats or providing machine-readable chemical structures alongside the analytical data, please have a look to our page on [Best-Practices](/docs/best_practice/). - -:::info Applies to: -Authors, publishers and infrastructure operators are the target audiences for these standards. -::: - -## For Authors - -### Use ORCID iD to Identifiy Authors and ROR to Identifiy Institutions - -:::tip Standard -*Authors should provide their ORCID iD to identify the authors/creators and contributors, and their ROR identifier to identify the institution to which they are affiliated.* -::: - -ORCID iDs allow authors to be uniquely identified, whereas author names may not be unique, may change, or may have different ordering conventions depending on cultural differences. Similarly, affiliations can vary according to style and granularity. In order to uniquely identify the institutions to which authors are affiliated, the ROR identifier should be provided. Please note that the ROR identifier is not intended to resolve down to the departmental level. Nevertheless, both identifiers improve findability. - -### How to use Dataset PIDs in Scientific Articles - -During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their scientific article for interlinking and referencing in **two main ways**: - -#### How to use Dataset PIDs of own Datasets in Scientific Articles - - -:::tip Standard -*Authors should add the PID of their corresponding dataset(s) to the data availability statement and should add PIDs of dataset(s) to the reference section in order to specifically cite dataset(s).* -::: - -For corresponding data, i.e. directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. In order to specifically reference and cite your data within the text, add your dataset to the references as well. - -:::danger Notice: -This distinction is important, because **the link** to the dataset in CrossRef's DOI metadata of scientific articles **is differently set**, depending on whether the dataset is a directly related source of information or a specifically referenced resource. -::: - -#### How to use Dataset PIDs of Datasets of other Researchers in Scientific Articles - - -:::tip Standard -*Authors should include PIDs for datasets published by other researchers that have been reused in the references, rather than citing the corresponding article.* -::: - -For datasets published by other researchers and reused in a study, include the dataset PID in the reference section of the manuscript and cite within the text accordingly. - -### How to Link Datasets to their Corresponding Scientific Article - -:::tip Standard -*Researchers should link their datasets to be published to their corresponding articles by adding the article DOI to the dataset's DataCite metadata as a related identifier.* -::: - -Research data repositories offer the option to add a related identifier to link datasets to related resources, such as a corresponding article. This considerably enhances the [FAIRness](/docs/fair/) of datasets, mainly the findability ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) as well as the interoperability ([I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). - -### Usage of Relation Type for Linking Datasets with Scientific Articles - -:::tip Standard -*Researchers should link their datasets to be published to their corresponding articles using the relation type `IsSupplementTo` .* -::: - -According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. On the other side of the pond, [CrossRef's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmenetTo` should be used to link datasets generated as part of research results. - -### Usage of Collection DOIs - -:::tip Standard -*Researchers should use the Collection DOI provided by a repository in the data availability statements of their corresponding manuscript to wrap research data objects that are relevant to that an article to be published.* -::: - -Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. - -To facilitate the process of manuscript submission and article publication, researchers should add the **Collection DOI** provided by the repository to the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. - -If individual reactions, molecules or analytical data should be referenced, add the DOIs of these individual research objects to the reference section and cite within the text accordingly. - - - -## For Publishers and Journals - -### Recommendations for Trusted, Chemistry-friendly Repositories - -:::tip Standard -*Journals should recommend trusted, chemistry-friendly research data repositories.* -::: - -To assist authors in selecting **well-established and community-specific [repositories](/docs/repositories/)** for their research data, [trusted chemistry friendly repositories](/docs/choose_repository/) should be recommended by journals. These should be included within the author guidelines or the data policies. - -### Recommendations to Include Data Availability Statements - -:::tip Standard -Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.* -::: - -[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or similarly termed section should be made available to authors in author guidelines of journals. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned if templates are selectable and information should be provided via the manuscript submission system. - -### Data Availability Statements and Manuscript Submission Systems - -:::tip Standard -*Journals should add a data availability statement to published articles and collect the necessary information through their submission systems.* -::: - -[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for data [**availability statements**](/docs/data_availability_statement) or similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used. - -### Link Datasets to Articles in CrossRef DOI Metadata - -:::tip Standard -*Journals should use the information available in data availability statements to enhance CrossRef DOI metadata by linking articles to datasets.* -::: - -With the DOI and repository name in hand, journals should enrich CrossRef DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. For CrossRef metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata). - -In XML: -```xml - - - - Dataset in . - - 10.prefix/suffix - - - -``` - -In agreement with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/), the relationship type `isSupplementedBy` should be used. - -### Add Data Publications to Prior Publication Policy - -:::tip Standard -*Journal author guidelines should explicitly encourage pre-submission of datasets.* -::: - -Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is also already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of dataset are registered, DOIs can be validated and datasets can be included in the review process. - -:::danger Danger -A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset need to be manually updated by the authors after the article got published. Datasets with status *under review* are one way to overcome this disadvantage (see below). -::: - -### Recommendations to Include Research Data in the Review Process - -:::tip Standard -*Journal author guidelines should explicitly encourage to include research data in the review process.* -::: - -Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not published, i.e. it does not have a DOI registered, which can be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers. - -### Encourage to Publish Datasets prio Publishing Articles - -:::tip Standard -*Journal author guidelines should require that datasets under review get published prior an article gets published.* -::: - -To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published prior to the publication of the article**. Once a manuscript is accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journal can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article gets published, and its DOI gets registered. - -### Scholix.org - -:::tip Standard -*Journals and publishers should use Scholix.org.* -::: - -[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above). - -## For Research Data Infrastructure and Resource Providers - -### Metadata Should be Part of a Dataset - -:::tip Standard -*Research data repositories should include the metadata in datasets downloaded by researchers.* -::: - -While researchers upload their data, metadata is attached. For generic, multidisciplinary repositories, additional metadata is provided via a metadata editor. For field-specific repositories, the metadata is extracted from the analytical data files and provided by researcher along their lab workflows, as this is the case for Chemotion ELN. Once data is retrieved from a repository, this metadata should not be lost but should be included in the downloaded package. The minimum to include is the descriptive DataCite metadata. - -[BagIt](https://www.rfc-editor.org/rfc/rfc8493.html), a set of hierarchical file system conventions, is one solution for including metadata in downloaded dataset. - -### Structured Domain-Specific Metadata Should be Part of a Dataset - -:::tip Standard -*Research data repositories should include structured, domain-specific metadata in datasets downloaded by researchers.* -::: - -Beside of metadata following generic schemes such as DataCite's metadata scheme, domain-specific metadata should be part of each dataset. This metadata should also be provided in datasets downloaded by researchers for reuse. - -One solution to this is to include Schema.org metadata by [combining RO-Crate and BagIt](https://www.researchobject.org/ro-crate/specification/1.1/appendix/implementation-notes.html#adding-ro-crate-to-bagit). - -### Collection DOIs - -:::tip Standard -*Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to an article to be published.* -::: - -Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. - -### Embargo Period and Metadata Accessibility - -:::tip Standard -*Datasets published with an embargo period should have inaccessible data but accessible metadata.* -::: - -While an **embargo** period restricts access to a published dataset, the **metadata should be accessible** – *publish* with embargo. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accessible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. - -### Scholix.org - -:::tip Standard -*Research data repositories should contribute to Scholix.org.* -::: - -[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information is used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset. - -### Datasets under Review - -:::tip Standard -*Research data repositories should provide access to datasets under review.* -::: - -In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* beside of the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via a URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset is not yet published. - -### Reviewer Access to Datasets under Review - -:::tip Standard -*URLs to access datasets under review should have the access credentials encoded in the URL.* -::: - -**Review links** for datasets *under review* should have the **access credentials** encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. - -### Publisher and PublisherIdentifier in DataCite Metadata - -:::tip Standard -*Research data repositories should provide the repository name as 'publisher' as well as a 'publisherIdentifier' in a dataset's DataCite metadata.* -::: - -DOI prefixes are specific to each registrant. As each registrant may host more than one repository, the prefix is not necessarily specific to an individual repository. As stated by [**DataCite's documentation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), the required `publisher` field is used to formulate the citation of the data and should therefore be the repository name. In addition, a repository identifier such as the re3data identifier should be provided to unambiguously identify the repository. Both fields should be automatically populated by the repository and should not be editable by the submitter. - -In the case of RADAR4Chem the relationship would be described as follows: - ->Publisher: RADAR4Chem -> ->publisherIdentifier: http://doi.org/10.17616/R31NJNAY -> ->publisherIdentifierScheme: re3data -> ->schemeURI: https://re3data.org/ - -In XML: -```xml -RADAR4Chem -``` - -This ensures humans as well as machines can trace and interpret where the data has been published. - -### Metadata Corrections and Updates - -:::tip Standard -*Research data repositories should allow researchers to correct and update the metadata of datasets.* -::: - -As the process of adding metadata via a metadata editor can be error-prone, creators should be allowed to **correct and update** the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. Updating of metadata contributes to [FAIR](/docs/fair) ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) by enhancing the richness of metadata, and also allows creators to add additional related identifiers for recently published related datasets and articles. - -### Legal Issues on Dataset Abstract - -:::tip Standard -*Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the datasets DataCite metadata.* -::: - -Dataset's should have their **own description as an abstract**. Copying the related article abstract can result in a **rights conflict** with the respective academic publisher. This is particularly the case in German law. Authors and data curators should be informed of this conflict, e.g. via a **tooltip** when adding metadata using a metadata editor. - -### Group Licences - -:::tip Standard -*In research data repositories, licences should be grouped into research data licences and software licences.* -::: - -Repositories often tend to provide confusingly long lists of licences. Furthermore, **licences** differ for datasets and software. Providing a **grouping** will greatly assist authors in selecting from the correct set. - -### Encourage Creative Commons Licences - -:::tip Standard -*Research data repositories should encourage researchers to choose a Creative Commons licence to simplify the landscape of licences and their choice.* -::: - -In line with grouping licences between software and datasets, pointing authors towards the selection of [**Creative Commons (CC)**](https://creativecommons.org/) licence alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. - -### Promote the least Restrictive Creative Commons Licences - -:::tip Standard -*Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can make reuse very difficult.* -::: - -Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licences/by/4.0/)** as opposed to more restrictive licences such as [CC BY-SA](https://creativecommons.org/licences/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licences/by-nc-nd/4.0/). - -### Creators and Contributors - -:::tip Standard -*Research data repositories should label fields for creators in their (DataCite) metadata editor as authors/creators.* -::: - -Researchers are used to talking about authors when it comes to the publication of results with one of the scientific publishers. On the other hand, DataCite distinguishes between authors and contributors, with the latter also being assigned a role. To avoid confusion for researchers who want to publish their data, metadata editors of repositories should guide researchers when adding metadata by labelling the field for creators in their (DataCite) metadata editors as authors/creators. - ----- -Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) diff --git a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx new file mode 100644 index 00000000..3a93cb0e --- /dev/null +++ b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx @@ -0,0 +1,73 @@ +--- +title: "Authors" +slug: "/publishing_standards_authors" +--- + +## For Authors + +### Use ORCID iD to Identifiy Authors and ROR to Identifiy Institutions + +:::tip Standard +*Authors should provide their ORCID iD to identify the authors/creators and contributors, and their ROR identifier to identify the institution to which they are affiliated.* +::: + +ORCID iDs allow authors to be uniquely identified, whereas author names may not be unique, may change, or may have different ordering conventions depending on cultural differences. Similarly, affiliations can vary according to style and granularity. In order to uniquely identify the institutions to which authors are affiliated, the ROR identifier should be provided. Please note that the ROR identifier is not intended to resolve down to the departmental level. Nevertheless, both identifiers improve findability. + +### How to use Dataset PIDs in Scientific Articles + +During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their scientific article for interlinking and referencing in **two main ways**: + +#### How to use Dataset PIDs of own Datasets in Scientific Articles + + +:::tip Standard +*Authors should add the PID of their corresponding dataset(s) to the data availability statement and should add PIDs of dataset(s) to the reference section in order to specifically cite dataset(s).* +::: + +For corresponding data, i.e. directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. In order to specifically reference and cite your data within the text, add your dataset to the references as well. + +:::danger Notice: +This distinction is important, because **the link** to the dataset in CrossRef's DOI metadata of scientific articles **is differently set**, depending on whether the dataset is a directly related source of information or a specifically referenced resource. +::: + +#### How to use Dataset PIDs of Datasets of other Researchers in Scientific Articles + + +:::tip Standard +*Authors should include PIDs for datasets published by other researchers that have been reused in the references, rather than citing the corresponding article.* +::: + +For datasets published by other researchers and reused in a study, include the dataset PID in the reference section of the manuscript and cite within the text accordingly. + +### How to Link Datasets to their Corresponding Scientific Article + +:::tip Standard +*Researchers should link their datasets to be published to their corresponding articles by adding the article DOI to the dataset's DataCite metadata as a related identifier.* +::: + +Research data repositories offer the option to add a related identifier to link datasets to related resources, such as a corresponding article. This considerably enhances the [FAIRness](/docs/fair/) of datasets, mainly the findability ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) as well as the interoperability ([I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). + +### Usage of Relation Type for Linking Datasets with Scientific Articles + +:::tip Standard +*Researchers should link their datasets to be published to their corresponding articles using the relation type `IsSupplementTo` .* +::: + +According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. On the other side of the pond, [CrossRef's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmenetTo` should be used to link datasets generated as part of research results. + +### Usage of Collection DOIs + +:::tip Standard +*Researchers should use the Collection DOI provided by a repository in the data availability statements of their corresponding manuscript to wrap research data objects that are relevant to that an article to be published.* +::: + +Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. + +To facilitate the process of manuscript submission and article publication, researchers should add the **Collection DOI** provided by the repository to the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. + +If individual reactions, molecules or analytical data should be referenced, add the DOIs of these individual research objects to the reference section and cite within the text accordingly. + + + +---- +Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) \ No newline at end of file diff --git a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx new file mode 100644 index 00000000..fe7583ae --- /dev/null +++ b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx @@ -0,0 +1,93 @@ +--- +title: "Academic Publishers" +slug: "/publishing_standards_publishers" +--- + +## For Publishers and Journals + +### Recommendations for Trusted, Chemistry-friendly Repositories + +:::tip Standard +*Journals should recommend trusted, chemistry-friendly research data repositories.* +::: + +To assist authors in selecting **well-established and community-specific [repositories](/docs/repositories/)** for their research data, [trusted chemistry friendly repositories](/docs/choose_repository/) should be recommended by journals. These should be included within the author guidelines or the data policies. + +### Recommendations to Include Data Availability Statements + +:::tip Standard +Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.* +::: + +[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or similarly termed section should be made available to authors in author guidelines of journals. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned if templates are selectable and information should be provided via the manuscript submission system. + +### Data Availability Statements and Manuscript Submission Systems + +:::tip Standard +*Journals should add a data availability statement to published articles and collect the necessary information through their submission systems.* +::: + +[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for data [**availability statements**](/docs/data_availability_statement) or similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used. + +### Link Datasets to Articles in CrossRef DOI Metadata + +:::tip Standard +*Journals should use the information available in data availability statements to enhance CrossRef DOI metadata by linking articles to datasets.* +::: + +With the DOI and repository name in hand, journals should enrich CrossRef DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. For CrossRef metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata). + +In XML: +```xml + + + + Dataset in . + + 10.prefix/suffix + + + +``` + +In agreement with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/), the relationship type `isSupplementedBy` should be used. + +### Add Data Publications to Prior Publication Policy + +:::tip Standard +*Journal author guidelines should explicitly encourage pre-submission of datasets.* +::: + +Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is also already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of dataset are registered, DOIs can be validated and datasets can be included in the review process. + +:::danger Danger +A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset need to be manually updated by the authors after the article got published. Datasets with status *under review* are one way to overcome this disadvantage (see below). +::: + +### Recommendations to Include Research Data in the Review Process + +:::tip Standard +*Journal author guidelines should explicitly encourage to include research data in the review process.* +::: + +Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not published, i.e. it does not have a DOI registered, which can be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers. + +### Encourage to Publish Datasets prio Publishing Articles + +:::tip Standard +*Journal author guidelines should require that datasets under review get published prior an article gets published.* +::: + +To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published prior to the publication of the article**. Once a manuscript is accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journal can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article gets published, and its DOI gets registered. + +### Scholix.org + +:::tip Standard +*Journals and publishers should use Scholix.org.* +::: + +[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above). + +---- +Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) \ No newline at end of file diff --git a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx new file mode 100644 index 00000000..ba68d470 --- /dev/null +++ b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx @@ -0,0 +1,142 @@ +--- +title: "Infrastructure Providers" +slug: "/publishing_standards_infrastructure" +--- + +## For Research Data Infrastructure and Resource Providers + +### Metadata Should be Part of a Dataset + +:::tip Standard +*Research data repositories should include the metadata in datasets downloaded by researchers.* +::: + +While researchers upload their data, metadata is attached. For generic, multidisciplinary repositories, additional metadata is provided via a metadata editor. For field-specific repositories, the metadata is extracted from the analytical data files and provided by researcher along their lab workflows, as this is the case for Chemotion ELN. Once data is retrieved from a repository, this metadata should not be lost but should be included in the downloaded package. The minimum to include is the descriptive DataCite metadata. + +[BagIt](https://www.rfc-editor.org/rfc/rfc8493.html), a set of hierarchical file system conventions, is one solution for including metadata in downloaded dataset. + +### Structured Domain-Specific Metadata Should be Part of a Dataset + +:::tip Standard +*Research data repositories should include structured, domain-specific metadata in datasets downloaded by researchers.* +::: + +Beside of metadata following generic schemes such as DataCite's metadata scheme, domain-specific metadata should be part of each dataset. This metadata should also be provided in datasets downloaded by researchers for reuse. + +One solution to this is to include Schema.org metadata by [combining RO-Crate and BagIt](https://www.researchobject.org/ro-crate/specification/1.1/appendix/implementation-notes.html#adding-ro-crate-to-bagit). + +### Collection DOIs + +:::tip Standard +*Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to an article to be published.* +::: + +Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. + +### Embargo Period and Metadata Accessibility + +:::tip Standard +*Datasets published with an embargo period should have inaccessible data but accessible metadata.* +::: + +While an **embargo** period restricts access to a published dataset, the **metadata should be accessible** – *publish* with embargo. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accessible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. + +### Scholix.org + +:::tip Standard +*Research data repositories should contribute to Scholix.org.* +::: + +[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information is used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset. + +### Datasets under Review + +:::tip Standard +*Research data repositories should provide access to datasets under review.* +::: + +In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* beside of the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via a URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset is not yet published. + +### Reviewer Access to Datasets under Review + +:::tip Standard +*URLs to access datasets under review should have the access credentials encoded in the URL.* +::: + +**Review links** for datasets *under review* should have the **access credentials** encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. + +### Publisher and PublisherIdentifier in DataCite Metadata + +:::tip Standard +*Research data repositories should provide the repository name as 'publisher' as well as a 'publisherIdentifier' in a dataset's DataCite metadata.* +::: + +DOI prefixes are specific to each registrant. As each registrant may host more than one repository, the prefix is not necessarily specific to an individual repository. As stated by [**DataCite's documentation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), the required `publisher` field is used to formulate the citation of the data and should therefore be the repository name. In addition, a repository identifier such as the re3data identifier should be provided to unambiguously identify the repository. Both fields should be automatically populated by the repository and should not be editable by the submitter. + +In the case of RADAR4Chem the relationship would be described as follows: + +>Publisher: RADAR4Chem +> +>publisherIdentifier: http://doi.org/10.17616/R31NJNAY +> +>publisherIdentifierScheme: re3data +> +>schemeURI: https://re3data.org/ + +In XML: +```xml +RADAR4Chem +``` + +This ensures humans as well as machines can trace and interpret where the data has been published. + +### Metadata Corrections and Updates + +:::tip Standard +*Research data repositories should allow researchers to correct and update the metadata of datasets.* +::: + +As the process of adding metadata via a metadata editor can be error-prone, creators should be allowed to **correct and update** the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. Updating of metadata contributes to [FAIR](/docs/fair) ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) by enhancing the richness of metadata, and also allows creators to add additional related identifiers for recently published related datasets and articles. + +### Legal Issues on Dataset Abstract + +:::tip Standard +*Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the datasets DataCite metadata.* +::: + +Dataset's should have their **own description as an abstract**. Copying the related article abstract can result in a **rights conflict** with the respective academic publisher. This is particularly the case in German law. Authors and data curators should be informed of this conflict, e.g. via a **tooltip** when adding metadata using a metadata editor. + +### Group Licences + +:::tip Standard +*In research data repositories, licences should be grouped into research data licences and software licences.* +::: + +Repositories often tend to provide confusingly long lists of licences. Furthermore, **licences** differ for datasets and software. Providing a **grouping** will greatly assist authors in selecting from the correct set. + +### Encourage Creative Commons Licences + +:::tip Standard +*Research data repositories should encourage researchers to choose a Creative Commons licence to simplify the landscape of licences and their choice.* +::: + +In line with grouping licences between software and datasets, pointing authors towards the selection of [**Creative Commons (CC)**](https://creativecommons.org/) licence alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. + +### Promote the least Restrictive Creative Commons Licences + +:::tip Standard +*Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can make reuse very difficult.* +::: + +Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licences/by/4.0/)** as opposed to more restrictive licences such as [CC BY-SA](https://creativecommons.org/licences/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licences/by-nc-nd/4.0/). + +### Creators and Contributors + +:::tip Standard +*Research data repositories should label fields for creators in their (DataCite) metadata editor as authors/creators.* +::: + +Researchers are used to talking about authors when it comes to the publication of results with one of the scientific publishers. On the other hand, DataCite distinguishes between authors and contributors, with the latter also being assigned a role. To avoid confusion for researchers who want to publish their data, metadata editors of repositories should guide researchers when adding metadata by labelling the field for creators in their (DataCite) metadata editors as authors/creators. + +---- +Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) \ No newline at end of file diff --git a/docs/50_data_publication/70_publishing_standards/70_publishing_standards_intro.mdx b/docs/50_data_publication/70_publishing_standards/70_publishing_standards_intro.mdx new file mode 100644 index 00000000..a8f06ee1 --- /dev/null +++ b/docs/50_data_publication/70_publishing_standards/70_publishing_standards_intro.mdx @@ -0,0 +1,24 @@ +--- +title: "Publishing Standards" +slug: "/publishing_standards" +id: "publishing_standards_intro" +--- + +import N4CFeatures from '/src/components/N4CFeatures.js'; + +:::info Info: +Authors, academic publishers and research data infrastructure and resource providers are the target audiences for these standards. +::: + +On this page we collect a non-exhaustive list of data publication standards, formulated as principles, that have been developed within the NFDI4Chem Publication Standards project. These standards are intended to implement the [FAIR Data Principles](/docs/fair/) with repect to data publication workflows. The main objective of these standards is to improve the quality of metadata and streamline publication workflows, including the peer-review process for manuscripts with corresponding datasets published in research data repositories. + +Click on a button below to get started with with standards for authors, academic publishers and infrastructure providers. These standards will be continously updated. + + + +:::danger Notice: +For more generic information for authors on publishing in field-specific and generic, multidisciplinary repositories such as publishing data in open formats or providing machine-readable chemical structures alongside the analytical data, please have a look to our page on [Best-Practices](/docs/best_practice/). +::: + +---- +Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) diff --git a/docs/50_data_publication/70_publishing_standards/_category_.json b/docs/50_data_publication/70_publishing_standards/_category_.json new file mode 100644 index 00000000..7653c3c7 --- /dev/null +++ b/docs/50_data_publication/70_publishing_standards/_category_.json @@ -0,0 +1,7 @@ +{ + "label": "Publishing Standards", + "link": { + "type" : "doc", + "id" : "publishing_standards_intro" + } +} \ No newline at end of file diff --git a/src/components/N4CFeatures.js b/src/components/N4CFeatures.js index b5c73094..7fdcadab 100644 --- a/src/components/N4CFeatures.js +++ b/src/components/N4CFeatures.js @@ -84,6 +84,23 @@ const features = { "svg": "/img/nfdi4chem_Core_Facility_Manager.svg", "link": "/docs/core_facility_manager" } + ], + stakeholders_data_publishing: [ + { + "title": Authors, + "svg": "/img/nfdi4chem_Research_Group_Member.svg", + "link": "/docs/publishing_standards_authors" + }, + { + "title": Academic Publishers, + "svg": "/img/nfdi4chem_Data_Publication.svg", + "link": "/docs/publishing_standards_publishers" + }, + { + "title": Infrastructure Providers, + "svg": "/img/nfdi4chem_Core_Facility_Manager.svg", + "link": "/docs/publishing_standards_infrastructure" + } ] }; From f2c71242e18dbfe8096a94e5806a26594a1fa7b5 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Fri, 19 Jul 2024 11:06:11 +0200 Subject: [PATCH 37/44] feat: sorting section data publishing --- .../{10_repositories.mdx => 05_repositories.mdx} | 0 .../{25_best_practice.mdx => 15_best_practice.mdx} | 0 ...ilability_statement.mdx => 30_data_availability_statement.mdx} | 0 docs/50_data_publication/{30_licenses.mdx => 35_licenses.mdx} | 0 .../51_lbe/{00_lbe_intro.mdx => 20_lbe_intro.mdx} | 0 ...hing_standards_intro.mdx => 25_publishing_standards_intro.mdx} | 0 6 files changed, 0 insertions(+), 0 deletions(-) rename docs/50_data_publication/{10_repositories.mdx => 05_repositories.mdx} (100%) rename docs/50_data_publication/{25_best_practice.mdx => 15_best_practice.mdx} (100%) rename docs/50_data_publication/{50_data_availability_statement.mdx => 30_data_availability_statement.mdx} (100%) rename docs/50_data_publication/{30_licenses.mdx => 35_licenses.mdx} (100%) rename docs/50_data_publication/51_lbe/{00_lbe_intro.mdx => 20_lbe_intro.mdx} (100%) rename docs/50_data_publication/70_publishing_standards/{70_publishing_standards_intro.mdx => 25_publishing_standards_intro.mdx} (100%) diff --git a/docs/50_data_publication/10_repositories.mdx b/docs/50_data_publication/05_repositories.mdx similarity index 100% rename from docs/50_data_publication/10_repositories.mdx rename to docs/50_data_publication/05_repositories.mdx diff --git a/docs/50_data_publication/25_best_practice.mdx b/docs/50_data_publication/15_best_practice.mdx similarity index 100% rename from docs/50_data_publication/25_best_practice.mdx rename to docs/50_data_publication/15_best_practice.mdx diff --git a/docs/50_data_publication/50_data_availability_statement.mdx b/docs/50_data_publication/30_data_availability_statement.mdx similarity index 100% rename from docs/50_data_publication/50_data_availability_statement.mdx rename to docs/50_data_publication/30_data_availability_statement.mdx diff --git a/docs/50_data_publication/30_licenses.mdx b/docs/50_data_publication/35_licenses.mdx similarity index 100% rename from docs/50_data_publication/30_licenses.mdx rename to docs/50_data_publication/35_licenses.mdx diff --git a/docs/50_data_publication/51_lbe/00_lbe_intro.mdx b/docs/50_data_publication/51_lbe/20_lbe_intro.mdx similarity index 100% rename from docs/50_data_publication/51_lbe/00_lbe_intro.mdx rename to docs/50_data_publication/51_lbe/20_lbe_intro.mdx diff --git a/docs/50_data_publication/70_publishing_standards/70_publishing_standards_intro.mdx b/docs/50_data_publication/70_publishing_standards/25_publishing_standards_intro.mdx similarity index 100% rename from docs/50_data_publication/70_publishing_standards/70_publishing_standards_intro.mdx rename to docs/50_data_publication/70_publishing_standards/25_publishing_standards_intro.mdx From ad5bb1cc26b2275429e1f62a2e16ce6e0f6dbdd3 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Fri, 19 Jul 2024 11:16:30 +0200 Subject: [PATCH 38/44] fix: git fail. added Nikkis edits --- .../70_publication_standards.mdx | 302 ------------------ .../10_publishing_standards_authors.mdx | 10 +- .../20_publishing_standards_publishers.mdx | 22 +- .../25_publishing_standards_intro.mdx | 2 +- ...30_publishing_standards_infrastructure.mdx | 26 +- 5 files changed, 30 insertions(+), 332 deletions(-) delete mode 100644 docs/50_data_publication/70_publication_standards.mdx diff --git a/docs/50_data_publication/70_publication_standards.mdx b/docs/50_data_publication/70_publication_standards.mdx deleted file mode 100644 index fc3b3d11..00000000 --- a/docs/50_data_publication/70_publication_standards.mdx +++ /dev/null @@ -1,302 +0,0 @@ ---- -title: "Publishing Standards" -slug: "/publishing_standards" ---- - -On this page we collect a non-exhaustive list of data publication standards, formulated as principles, that have been developed within the NFDI4Chem Publication Standards project. These standards are intended to improve the quality of metadata and streamline publication workflows, including the manuscript review process with corresponding datasets published in research data repositories. - -For more generic information for authors on publishing in field-specific and generic, multidisciplinary repositories such as publishing data in open formats or providing machine-readable chemical structures alongside the analytical data, please have a look to our page on [Best-Practices](/docs/best_practice/). - -:::info Applies to: -Authors, publishers and infrastructure operators are the target audiences for these standards. -::: - -## For Authors - -### Use ORCID iD to Identifiy Authors and ROR to Identifiy Institutions - -:::tip Standard -*Authors should provide their ORCID iD to identify the authors/creators and contributors, and their ROR identifier to identify the institution to which they are affiliated.* -::: - -ORCID iDs allow authors to be uniquely identified, whereas author names may not be unique, may change, or may have different ordering conventions depending on cultural differences. Similarly, affiliations can vary according to style and granularity. In order to uniquely identify the institutions to which authors are affiliated, the ROR identifier should be provided. Please note that the ROR identifier is not intended to resolve down to the departmental level. Nevertheless, both identifiers improve findability. - -### How to use Dataset PIDs in Scientific Articles - -During deposition of research data, a [persistent identifier (PID)](/docs/pid) is assigned to the data. Authors should use PIDs in their scientific article for interlinking and referencing in **two main ways**: - -#### How to use Dataset PIDs of own Datasets in Scientific Articles - - -:::tip Standard -*Authors should add the PID of their corresponding dataset(s) to the data availability statement and should add PIDs of dataset(s) to the reference section in order to specifically cite dataset(s).* -::: - -For corresponding data, i.e. directly underlying the results reported in the article, add the PID to the article's [data availability statement](/docs/data_availability_statement), or a similarly termed section. In order to specifically reference and cite your data within the text, add your dataset to the references as well. - -:::danger Notice: -This distinction is important, because **the link** to the dataset in CrossRef's DOI metadata of scientific articles **is differently set**, depending on whether the dataset is a directly related source of information or a specifically referenced resource. -::: - -#### How to use Dataset PIDs for Datasets by other Researchers in Scientific Articles - - -:::tip Standard -*Authors should include PIDs for datasets published by other researchers that have been reused in the references, rather than citing the corresponding article.* -::: - -For datasets published by other researchers and reused in a study, include the dataset PID in the reference section of the manuscript and cite within the text accordingly. - -### How to Link Datasets to their Corresponding Scientific Article - -:::tip Standard -*Researchers should link their datasets to be published to their corresponding articles by adding the article DOI to the dataset's DataCite metadata as a related identifier.* -::: - -Research data repositories offer the option to add a related identifier to link datasets to related resources, such as a corresponding article. This considerably enhances the [FAIRness](/docs/fair/) of datasets, mainly the findability ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) as well as the interoperability ([I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). - -### Usage of Relation Type for Linking Datasets with Scientific Articles - -:::tip Standard -*Researchers should link their datasets to be published to their corresponding articles using the relation type `IsSupplementTo`.* -::: - -According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. For published articles, [CrossRef's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmenetTo` should be used to link datasets generated as part of research results. - -### Usage of Collection DOIs - -:::tip Standard -*Researchers should use the Collection DOI provided by a repository in the data availability statements of their corresponding manuscript to wrap research data objects that are relevant to that of an article to be published.* -::: - -Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. - -To facilitate the process of manuscript submission and article publication, researchers should add the **Collection DOI** provided by the repository to the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. - -If individual reactions, molecules, or analytical data should be referenced, add the DOIs of these individual research objects to the reference section and cite within the text accordingly. - - - -## For Publishers and Journals - -### Recommendations for Trusted, Chemistry-friendly Repositories - -:::tip Standard -*Journals should recommend trusted, chemistry-friendly research data repositories.* -::: - -To assist authors in selecting **well-established and community-specific [repositories](/docs/repositories/)** for their research data, [trusted chemistry friendly repositories](/docs/choose_repository/) should be recommended by journals. These should be included within the author guidelines or the data policies. - -### Recommendations to Include Data Availability Statements - -:::tip Standard -*Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.* -::: - -[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should be made available to authors in the journal's author guidelines. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned whether templates are selectable and information should be provided via the manuscript submission system. - -### Data Availability Statements and Manuscript Submission Systems - -:::tip Standard -*Journals should add a data availability statement to published articles and collect the necessary information through their submission systems.* -::: - -[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g. `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used. - -### Link Datasets to Articles in CrossRef DOI Metadata - -:::tip Standard -*Journals should use the information available in data availability statements to enhance CrossRef DOI metadata by linking articles to datasets.* -::: - -With the DOI and repository name in hand, journals should enrich CrossRef DOI metadata of articles published following the [FAIR](/docs/fair/) principles (e.g [F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below), [I3](/docs/fair/#i3-metadata-include-qualified-references-to-other-metadata)). This establishes a structured **link** between the DOI of the article and the DOI of the dataset and ensures humans and machines alike can interpret the relationship between the published objects. For CrossRef metadata, a `related_item` should be added to mention the name of the repository (equal to `publisher` in the corresponding dataset DataCite DOI metadata). - -In XML: -```xml - - - - Dataset in . - - 10.prefix/suffix - - - -``` - -In agreement with [Crossref's documentation on **linking datasets** to published items](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/), the relationship type `isSupplementedBy` should be used. - -### Add Data Publications to Prior Publication Policy - -:::tip Standard -*Journal author guidelines should explicitly encourage pre-submission of datasets.* -::: - -Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is also already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of datasets are registered. DOIs can therefore be validated and datasets can be included in the review process. - -:::danger Danger -A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset must then be manually updated by the authors after the article has been published. Datasets with status *under review* are one way to overcome this disadvantage (see below). -::: - -### Recommendations to Include Research Data in the Review Process - -:::tip Standard -*Journal author guidelines should explicitly encourage research data to be included in the review process.* -::: - -Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not yet published, i.e. it does not have a DOI registered. Therefore, the DOI cannot be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers. - -### Encourage Authors to Publish Datasets prior Publishing Articles - -:::tip Standard -*Journal author guidelines should require that datasets under review to be published prior to the publication of the associated article.* -::: - -To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published prior to the publication of the article**. Once a manuscript has been accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journals can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet, can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article is published, and its DOI is registered. - -### Scholix.org - -:::tip Standard -*Journals and publishers should use Scholix.org.* -::: - -[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above). - -## For Research Data Infrastructure and Resource Providers - -### Metadata Should be Part of a Dataset - -:::tip Standard -*Research data repositories should include the metadata in datasets downloaded by researchers.* -::: - -While researchers upload their data, metadata is attached. For generic, multidisciplinary repositories, additional metadata is provided via a metadata editor. For field-specific repositories, the metadata is extracted from the analytical data files and provided by researchers along their lab workflows, as this is the case for Chemotion ELN. Once data is retrieved from a repository, this metadata should not be lost but should be included in the downloaded package. The minimum to include is the descriptive DataCite metadata. - -[BagIt](https://www.rfc-editor.org/rfc/rfc8493.html), a set of hierarchical file system conventions, is one solution for including metadata in downloaded dataset. - -### Structured Domain-Specific Metadata Should be Part of a Dataset - -:::tip Standard -*Research data repositories should include structured, domain-specific metadata in datasets downloaded by researchers.* -::: - -Beside of metadata following generic schemes such as DataCite's metadata scheme, domain-specific metadata should be part of each dataset. This metadata should also be provided in datasets downloaded by researchers for reuse. - -One solution to this is to include Schema.org metadata by [combining RO-Crate and BagIt](https://www.researchobject.org/ro-crate/specification/1.1/appendix/implementation-notes.html#adding-ro-crate-to-bagit). - -### Collection DOIs - -:::tip Standard -*Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to a single article that is to be published.* -::: - -Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. - -### Embargo Period and Metadata Accessibility - -:::tip Standard -*Datasets published with an embargo period should have inaccessible data but accessible metadata.* -::: - -While an **embargo** period restricts access to a published dataset, the **metadata should be accessible**—*publish* with embargo. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accessible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. - -### Scholix.org - -:::tip Standard -*Research data repositories should contribute to Scholix.org.* -::: - -[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information is used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset. - -### Datasets under Review - -:::tip Standard -*Research data repositories should provide access to datasets under review.* -::: - -In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* in addition to the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via a URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset has not yet been published. - -### Reviewer Access to Datasets under Review - -:::tip Standard -*URLs to access datasets under review should have the access credentials encoded within the URL.* -::: - -**Review links** for datasets *under review* should have the **access credentials** encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. - -### Publisher and PublisherIdentifier in DataCite Metadata - -:::tip Standard -*Research data repositories should provide the repository name as 'publisher' as well as a 'publisherIdentifier' in a dataset's DataCite metadata.* -::: - -DOI prefixes are specific to each registrant. As each registrant may host more than one repository, the prefix is not necessarily specific to an individual repository. As stated by [**DataCite's documentation on the publisher field**](https://datacite-metadata-schema.readthedocs.io/en/4.5/properties/publisher/#publisher), the required `publisher` field is used to formulate the citation of the data and should therefore be the repository name. In addition, a repository identifier such as the re3data identifier should be provided to unambiguously identify the repository. Both fields should be automatically populated by the repository and should not be editable by the submitter. - -In the case of RADAR4Chem the relationship would be described as follows: - ->Publisher: RADAR4Chem -> ->publisherIdentifier: http://doi.org/10.17616/R31NJNAY -> ->publisherIdentifierScheme: re3data -> ->schemeURI: https://re3data.org/ - -In XML: -```xml -RADAR4Chem -``` - -This ensures humans as well as machines can trace and interpret where the data has been published. - -### Metadata Corrections and Updates - -:::tip Standard -*Research data repositories should allow researchers to correct and update the metadata of datasets.* -::: - -As the process of adding metadata via a metadata editor can be error-prone, creators should be allowed to **correct and update** the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. Updating metadata contributes to [FAIR](/docs/fair) ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) by enhancing the richness of metadata, and also allows creators to add additional related identifiers for recently published related datasets and articles. - -### Legal Issues on Dataset Abstract - -:::tip Standard -*Research data repositories should inform authors and data curators about possible rights conflicts for the abstract field in the datasets DataCite metadata.* -::: - -Dataset's should have their **own description as an abstract**. Copying the related article abstract can result in a **rights conflict** with the respective academic publisher. This is particularly the case in German law. Authors and data curators should be informed of this conflict, e.g. via a **tooltip** when adding metadata using a metadata editor. - -### Group Licences - -:::tip Standard -*In research data repositories, licences should be grouped into research data licences and software licences.* -::: - -Repositories often tend to provide confusingly long lists of licences. Furthermore, **licences** differ for datasets and software. Providing a **grouping** will greatly assist authors in selecting from the correct set. - -### Encourage Creative Commons Licences - -:::tip Standard -*Research data repositories should encourage researchers to choose a Creative Commons licence to simplify the landscape of licences and their choice.* -::: - -In line with grouping licences between software and datasets, pointing authors towards the selection of a [**Creative Commons (CC)**](https://creativecommons.org/) licence alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. - -### Promote the least Restrictive Creative Commons Licences - -:::tip Standard -*Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can inhibit reuse.* -::: - -Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licences/by/4.0/)** as opposed to more restrictive licences such as [CC BY-SA](https://creativecommons.org/licences/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licences/by-nc-nd/4.0/). Such restrictive licenses can make data reuse difficult. - -### Creators and Contributors - -:::tip Standard -*Research data repositories should label fields for creators in their (DataCite) metadata editor as* Authors/Creators. -::: - -Researchers are used to talking about authors when it comes to the publication of results with one of the scientific publishers. On the other hand, DataCite distinguishes between authors and contributors, with the latter also being assigned a role. To avoid confusion for researchers who want to publish their data, repositories should guide researchers when adding metadata by labelling the field for creators in their (DataCite) metadata editors as *Authors/Creators*. - ----- -Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) diff --git a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx index 3a93cb0e..a97b1550 100644 --- a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx +++ b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx @@ -30,7 +30,7 @@ For corresponding data, i.e. directly underlying the results reported in the art This distinction is important, because **the link** to the dataset in CrossRef's DOI metadata of scientific articles **is differently set**, depending on whether the dataset is a directly related source of information or a specifically referenced resource. ::: -#### How to use Dataset PIDs of Datasets of other Researchers in Scientific Articles +#### How to use Dataset PIDs for Datasets by other Researchers in Scientific Articles :::tip Standard @@ -50,22 +50,22 @@ Research data repositories offer the option to add a related identifier to link ### Usage of Relation Type for Linking Datasets with Scientific Articles :::tip Standard -*Researchers should link their datasets to be published to their corresponding articles using the relation type `IsSupplementTo` .* +*Researchers should link their datasets to be published to their corresponding articles using the relation type `IsSupplementTo`.* ::: -According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. On the other side of the pond, [CrossRef's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmenetTo` should be used to link datasets generated as part of research results. +According to the [DataCite Metadata Schema](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/), [`IsCitedBy`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#iscitedby) and [`IsSupplementTo`](https://datacite-metadata-schema.readthedocs.io/en/4.5/appendices/appendix-1/relationType/#issupplementto) are both recommended for discovery. For published articles, [CrossRef's documentation on relationships](https://www.crossref.org/documentation/schema-library/markup-guide-metadata-segments/relationships/) recommends that `isSupplmenetTo` should be used to link datasets generated as part of research results. ### Usage of Collection DOIs :::tip Standard -*Researchers should use the Collection DOI provided by a repository in the data availability statements of their corresponding manuscript to wrap research data objects that are relevant to that an article to be published.* +*Researchers should use the Collection DOI provided by a repository in the data availability statements of their corresponding manuscript to wrap research data objects that are relevant to that of an article to be published.* ::: Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, researchers should add the **Collection DOI** provided by the repository to the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. -If individual reactions, molecules or analytical data should be referenced, add the DOIs of these individual research objects to the reference section and cite within the text accordingly. +If individual reactions, molecules, or analytical data should be referenced, add the DOIs of these individual research objects to the reference section and cite within the text accordingly. diff --git a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx index fe7583ae..e9bcf97f 100644 --- a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx +++ b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx @@ -16,10 +16,10 @@ To assist authors in selecting **well-established and community-specific [reposi ### Recommendations to Include Data Availability Statements :::tip Standard -Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.* +*Journals should recommend that authors provide a data availability statement. Author guidelines should also provide templates for illustration.* ::: -[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or similarly termed section should be made available to authors in author guidelines of journals. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned if templates are selectable and information should be provided via the manuscript submission system. +[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should be made available to authors in the journal's author guidelines. This guides authors in correctly submitting underlying data with their manuscript and effectively communicating how to find and access the data by including the DOI or other PID, enabling the FAIR principles (e.g. [A1](docs/fair#a1-metadata-are-retrievable-by-their-identifier-using-a-standardized-communications-protocol), [I3](/docs/fair#i3-metadata-include-qualified-references-to-other-metadata)). It should also be mentioned whether templates are selectable and information should be provided via the manuscript submission system. ### Data Availability Statements and Manuscript Submission Systems @@ -27,7 +27,7 @@ Journals should recommend that authors provide a data availability statement. Au *Journals should add a data availability statement to published articles and collect the necessary information through their submission systems.* ::: -[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for data [**availability statements**](/docs/data_availability_statement) or similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used. +[Templates](/docs/data_availability_statement/#templates-for-data-availability-statements) for [**data availability statements**](/docs/data_availability_statement) or a similarly termed section should also be added to the manuscript submission system. Once a template has been selected by the submitter, the data availability statement should be editable to allow authors to add additional information, such as what data are included in the dataset, similar to what is currently often mentioned in the section on supporting information PDF files. The submission system should then require the submitter to provide the necessary information, such as the DOI (specified as [DOI name](https://www.doi.org/doi-handbook/HTML/doi-name-syntax2.html) e.g. `10.1000/182` or as a URL i.e. including a resolver e.g. `https://doi.org/10.1000/182` ), repository name, third party name and contact information, or reasons for restricted access and information on how to access a dataset, depending on the template used. ### Link Datasets to Articles in CrossRef DOI Metadata @@ -59,27 +59,27 @@ In agreement with [Crossref's documentation on **linking datasets** to published *Journal author guidelines should explicitly encourage pre-submission of datasets.* ::: -Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is also already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of dataset are registered, DOIs can be validated and datasets can be included in the review process. +Similar to the publication of preprints, journal author guidelines should allow for the pre-submission of datasets, as this is also already the case for many journals for crystallographic data published in CSD with CCDC. Datasets published prior to manuscript submission facilitate manuscript submission workflows as DOIs of datasets are registered. DOIs can therefore be validated and datasets can be included in the review process. :::danger Danger -A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset need to be manually updated by the authors after the article got published. Datasets with status *under review* are one way to overcome this disadvantage (see below). +A disadvantage of pre-submission is that researchers cannot link the dataset to the manuscript, as the manuscript has not yet been published and no DOI has been registered. The metadata of the dataset must then be manually updated by the authors after the article has been published. Datasets with status *under review* are one way to overcome this disadvantage (see below). ::: ### Recommendations to Include Research Data in the Review Process :::tip Standard -*Journal author guidelines should explicitly encourage to include research data in the review process.* +*Journal author guidelines should explicitly encourage research data to be included in the review process.* ::: -Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not published, i.e. it does not have a DOI registered, which can be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers. +Some repositories have an *under review* status alongside the *draft* and *published* statuses. A dataset *under review* is not editable and not yet published, i.e. it does not have a DOI registered. Therefore, the DOI cannot be validated. Nonetheless, the dataset has an internally reserved DOI and is accessible via a URL to provide access to editors and reviewers. This allows research data to be included in the review process. The URL to access the dataset should be requested by the submission system so that it can be forwarded to editors and reviewers. -### Encourage to Publish Datasets prio Publishing Articles +### Encourage Authors to Publish Datasets prior Publishing Articles :::tip Standard -*Journal author guidelines should require that datasets under review get published prior an article gets published.* +*Journal author guidelines should require that datasets under review to be published prior to the publication of the associated article.* ::: -To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published prior to the publication of the article**. Once a manuscript is accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journal can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article gets published, and its DOI gets registered. +To assist in automated workflows, such as linking the datasets to the published article through their respective PIDs, **datasets *under review* should be published prior to the publication of the article**. Once a manuscript has been accepted, the authors should be informed to publish their dataset *under review*. This ensures that the data has a registered DOI when the article gets published. Consequently, journals can run quality control checks on the provided DOI such as validation. This process must be explicitly communicated with authors through the author guidelines, yet, can also be included within other communication upon acceptance. Contemporaneous, the DOI for the article should be provided so that authors can include this information in their dataset's metadata prior to the publication of the dataset. Finally, the article is published, and its DOI is registered. ### Scholix.org @@ -87,7 +87,7 @@ To assist in automated workflows, such as linking the datasets to the published *Journals and publishers should use Scholix.org.* ::: -[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above). +[**Scholix**](https://doi.org/10.1045/january2017-burton) provides the framework for improving the links between scientific literature and research data as well as between data and data with the goal of providing a **high-level interoperability framework for exchanging information about these links**. Thus, Scholix hubs, such as [DataCite](https://datacite.org/) or [OpenAire](https://www.openaire.eu/), contribute information on their metadata records, which contain information on connected digital objects. This information should be used by academic publishers to discover datasets that correspond to an article but were published after the article was published, which allows the metadata of the article to be updated with links to the dataset (see above). ---- Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) \ No newline at end of file diff --git a/docs/50_data_publication/70_publishing_standards/25_publishing_standards_intro.mdx b/docs/50_data_publication/70_publishing_standards/25_publishing_standards_intro.mdx index a8f06ee1..3143eeeb 100644 --- a/docs/50_data_publication/70_publishing_standards/25_publishing_standards_intro.mdx +++ b/docs/50_data_publication/70_publishing_standards/25_publishing_standards_intro.mdx @@ -10,7 +10,7 @@ import N4CFeatures from '/src/components/N4CFeatures.js'; Authors, academic publishers and research data infrastructure and resource providers are the target audiences for these standards. ::: -On this page we collect a non-exhaustive list of data publication standards, formulated as principles, that have been developed within the NFDI4Chem Publication Standards project. These standards are intended to implement the [FAIR Data Principles](/docs/fair/) with repect to data publication workflows. The main objective of these standards is to improve the quality of metadata and streamline publication workflows, including the peer-review process for manuscripts with corresponding datasets published in research data repositories. +On this page we collect a non-exhaustive list of data publication standards, formulated as principles, that have been developed within the NFDI4Chem Publication Standards project. These standards are intended to implement the [FAIR Data Principles](/docs/fair/) with repect to data publication workflows. The main objective of these standards is to improve the quality of metadata and streamline publication workflows, including the manuscript peer-review process with corresponding datasets published in research data repositories. Click on a button below to get started with with standards for authors, academic publishers and infrastructure providers. These standards will be continously updated. diff --git a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx index ba68d470..40a4cd37 100644 --- a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx +++ b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx @@ -11,9 +11,9 @@ slug: "/publishing_standards_infrastructure" *Research data repositories should include the metadata in datasets downloaded by researchers.* ::: -While researchers upload their data, metadata is attached. For generic, multidisciplinary repositories, additional metadata is provided via a metadata editor. For field-specific repositories, the metadata is extracted from the analytical data files and provided by researcher along their lab workflows, as this is the case for Chemotion ELN. Once data is retrieved from a repository, this metadata should not be lost but should be included in the downloaded package. The minimum to include is the descriptive DataCite metadata. +While researchers upload their data, metadata is attached. For generic, multidisciplinary repositories, additional metadata is provided via a metadata editor. For field-specific repositories, the metadata is extracted from the analytical data files and provided by researchers along their lab workflows, as this is the case for Chemotion ELN. Once data is retrieved from a repository, this metadata should not be lost but should be included in the downloaded package. The minimum to include is the descriptive DataCite metadata. -[BagIt](https://www.rfc-editor.org/rfc/rfc8493.html), a set of hierarchical file system conventions, is one solution for including metadata in downloaded dataset. +[BagIt](https://www.rfc-editor.org/rfc/rfc8493.html), a set of hierarchical file system conventions, is one solution for including metadata in downloaded dataset. ### Structured Domain-Specific Metadata Should be Part of a Dataset @@ -28,10 +28,10 @@ One solution to this is to include Schema.org metadata by [combining RO-Crate an ### Collection DOIs :::tip Standard -*Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to an article to be published.* +*Research data repositories should provide a Collection DOI to wrap research data objects that are relevant to a single article that is to be published.* ::: -Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for a whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. +Field-specific research data repositories may provide DOIs to reference individual chemical reactions, molecules, and their analytical data. Generic, multidisciplinary research data repositories provide DOIs for whole published datasets, while more than one published dataset may be relevant to study results published via an article. In other words, many DOIs may be relevant to a published article, whereas **a data availability statement may provide some DOIs but not many DOIs**. To facilitate the process of manuscript submission and article publication, each repository should provide a **Collection DOI** that wraps relevant data that should be referenced in the data availability statement. This will ensure that all data underlying a published manuscript can be linked to an article in the data availability statement and the CrossRef metadata of that article. ### Embargo Period and Metadata Accessibility @@ -39,7 +39,7 @@ Field-specific research data repositories may provide DOIs to reference individu *Datasets published with an embargo period should have inaccessible data but accessible metadata.* ::: -While an **embargo** period restricts access to a published dataset, the **metadata should be accessible** – *publish* with embargo. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accessible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. +While an **embargo** period restricts access to a published dataset, the **metadata should be accessible**—*publish* with embargo. This allows relevant information on the dataset to be retrieved and enables [FAIR](/docs/fair) ([A2](/docs/fair/#a2-metadata-are-accessible-even-when-the-data-are-no-longer-available)), while guaranteeing first rights to the data to the authors. Findable and accessible metadata is required to link articles and datasets, as DOIs to datasets need to be **validated** before the metadata record of articles gets updated. ### Scholix.org @@ -55,12 +55,12 @@ While an **embargo** period restricts access to a published dataset, the **metad *Research data repositories should provide access to datasets under review.* ::: -In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* beside of the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via a URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset is not yet published. +In order to include datasets in the review process of manuscripts, repositories should provide access to reviewers. It is strongly encouraged that repositories provide a status *in review* in addition to the statuses *draft* and *published*. **A dataset under review should not be editable but should be accessible** via a URL, while the DOI is not yet discoverable and the DOI metadata is not yet accessible as the dataset has not yet been published. ### Reviewer Access to Datasets under Review :::tip Standard -*URLs to access datasets under review should have the access credentials encoded in the URL.* +*URLs to access datasets under review should have the access credentials encoded within the URL.* ::: **Review links** for datasets *under review* should have the **access credentials** encoded in the URL, rather than having separate login and password. This avoids having to forward these details to the reviewer via the submission system. @@ -96,7 +96,7 @@ This ensures humans as well as machines can trace and interpret where the data h *Research data repositories should allow researchers to correct and update the metadata of datasets.* ::: -As the process of adding metadata via a metadata editor can be error-prone, creators should be allowed to **correct and update** the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. Updating of metadata contributes to [FAIR](/docs/fair) ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) by enhancing the richness of metadata, and also allows creators to add additional related identifiers for recently published related datasets and articles. +As the process of adding metadata via a metadata editor can be error-prone, creators should be allowed to **correct and update** the PID metadata as well as any other metadata. For full transparency, metadata may be **versioned**. The record may indicate to viewers that changes were made. Updating metadata contributes to [FAIR](/docs/fair) ([F2](/docs/fair/#f2-data-are-described-with-rich-metadata-defined-by-r1-below)) by enhancing the richness of metadata, and also allows creators to add additional related identifiers for recently published related datasets and articles. ### Legal Issues on Dataset Abstract @@ -120,23 +120,23 @@ Repositories often tend to provide confusingly long lists of licences. Furthermo *Research data repositories should encourage researchers to choose a Creative Commons licence to simplify the landscape of licences and their choice.* ::: -In line with grouping licences between software and datasets, pointing authors towards the selection of [**Creative Commons (CC)**](https://creativecommons.org/) licence alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. +In line with grouping licences between software and datasets, pointing authors towards the selection of a [**Creative Commons (CC)**](https://creativecommons.org/) licence alleviates the selection process. When publishing research data, Creative Commons licences that are no more restrictive than CC BY are strongly recommended. ### Promote the least Restrictive Creative Commons Licences :::tip Standard -*Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can make reuse very difficult.* +*Research data repositories should suggest licences such as CC0 or CC BY by pre-selecting such a licence rather than more restrictive licences such as CC BY-SA or even CC BY-NC-ND, which can inhibit reuse.* ::: -Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licences/by/4.0/)** as opposed to more restrictive licences such as [CC BY-SA](https://creativecommons.org/licences/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licences/by-nc-nd/4.0/). +Shared data should be as **open as possible, as closed as necessary** with the intent of allowing and enabling others to reuse and build upon the work. Thus, encouraging rather open licences such as **[CC0](https://creativecommons.org/public-domain/cc0/)** and **[CC BY](https://creativecommons.org/licences/by/4.0/)** as opposed to more restrictive licences such as [CC BY-SA](https://creativecommons.org/licences/by-sa/4.0/) or even [CC BY-NC-ND](https://creativecommons.org/licences/by-nc-nd/4.0/). Such restrictive licenses can make data reuse difficult. ### Creators and Contributors :::tip Standard -*Research data repositories should label fields for creators in their (DataCite) metadata editor as authors/creators.* +*Research data repositories should label fields for creators in their (DataCite) metadata editor as* Authors/Creators. ::: -Researchers are used to talking about authors when it comes to the publication of results with one of the scientific publishers. On the other hand, DataCite distinguishes between authors and contributors, with the latter also being assigned a role. To avoid confusion for researchers who want to publish their data, metadata editors of repositories should guide researchers when adding metadata by labelling the field for creators in their (DataCite) metadata editors as authors/creators. +Researchers are used to talking about authors when it comes to the publication of results with one of the scientific publishers. On the other hand, DataCite distinguishes between authors and contributors, with the latter also being assigned a role. To avoid confusion for researchers who want to publish their data, repositories should guide researchers when adding metadata by labelling the field for creators in their (DataCite) metadata editors as *Authors/Creators*. ---- Main authors: [ORCID:0000-0003-4480-8661](https://orcid.org/0000-0003-4480-8661), [ORCID: 0000-0002-6243-2840](https://orcid.org/0000-0002-6243-2840) \ No newline at end of file From 6d4b839f51817c7c787429903292c6eefa297a66 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Fri, 19 Jul 2024 11:20:47 +0200 Subject: [PATCH 39/44] fix: clean up sorting within data pub section --- .../{05_repositories.mdx => 10_repositories.mdx} | 0 .../{10_choose_repository.mdx => 20_choose_repository.mdx} | 0 .../{15_best_practice.mdx => 30_best_practice.mdx} | 0 .../51_lbe/{20_lbe_intro.mdx => 40_lbe_intro.mdx} | 0 ...ilability_statement.mdx => 60_data_availability_statement.mdx} | 0 docs/50_data_publication/{35_licenses.mdx => 70_licenses.mdx} | 0 ...hing_standards_intro.mdx => 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docs/50_data_publication/70_publishing_standards/70_publishing_standards_publishers.mdx rename to docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx diff --git a/docs/50_data_publication/70_publishing_standards/50_publishing_standards_intro.mdx b/docs/50_data_publication/70_publishing_standards/25_publishing_standards_intro.mdx similarity index 100% rename from docs/50_data_publication/70_publishing_standards/50_publishing_standards_intro.mdx rename to docs/50_data_publication/70_publishing_standards/25_publishing_standards_intro.mdx diff --git a/docs/50_data_publication/70_publishing_standards/80_publishing_standards_infrastructure.mdx b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx similarity index 100% rename from docs/50_data_publication/70_publishing_standards/80_publishing_standards_infrastructure.mdx rename to docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx diff --git a/docs/50_data_publication/90_data_articles.mdx b/docs/50_data_publication/80_data_articles.mdx similarity index 100% rename from docs/50_data_publication/90_data_articles.mdx rename to docs/50_data_publication/80_data_articles.mdx From ddd59985ba18174a99cd802c963d7a8d9a0cae71 Mon Sep 17 00:00:00 2001 From: Johannes Liermann Date: Mon, 22 Jul 2024 18:57:11 +0200 Subject: [PATCH 41/44] Revert "feat: sorting section data publishing" This reverts commit f2c71242e18dbfe8096a94e5806a26594a1fa7b5. --- .../{05_repositories.mdx => 10_repositories.mdx} | 0 .../{15_best_practice.mdx => 25_best_practice.mdx} | 0 docs/50_data_publication/{35_licenses.mdx => 30_licenses.mdx} | 0 ...ilability_statement.mdx => 50_data_availability_statement.mdx} | 0 .../51_lbe/{20_lbe_intro.mdx => 00_lbe_intro.mdx} | 0 ...hing_standards_intro.mdx => 70_publishing_standards_intro.mdx} | 0 6 files changed, 0 insertions(+), 0 deletions(-) rename docs/50_data_publication/{05_repositories.mdx => 10_repositories.mdx} (100%) rename docs/50_data_publication/{15_best_practice.mdx => 25_best_practice.mdx} (100%) rename docs/50_data_publication/{35_licenses.mdx => 30_licenses.mdx} (100%) rename docs/50_data_publication/{30_data_availability_statement.mdx => 50_data_availability_statement.mdx} (100%) rename docs/50_data_publication/51_lbe/{20_lbe_intro.mdx => 00_lbe_intro.mdx} (100%) rename docs/50_data_publication/70_publishing_standards/{25_publishing_standards_intro.mdx => 70_publishing_standards_intro.mdx} (100%) diff --git a/docs/50_data_publication/05_repositories.mdx b/docs/50_data_publication/10_repositories.mdx similarity index 100% rename from docs/50_data_publication/05_repositories.mdx rename to docs/50_data_publication/10_repositories.mdx diff --git a/docs/50_data_publication/15_best_practice.mdx b/docs/50_data_publication/25_best_practice.mdx similarity index 100% rename from docs/50_data_publication/15_best_practice.mdx rename to docs/50_data_publication/25_best_practice.mdx diff --git a/docs/50_data_publication/35_licenses.mdx b/docs/50_data_publication/30_licenses.mdx similarity index 100% rename from docs/50_data_publication/35_licenses.mdx rename to docs/50_data_publication/30_licenses.mdx diff --git a/docs/50_data_publication/30_data_availability_statement.mdx b/docs/50_data_publication/50_data_availability_statement.mdx similarity index 100% rename from docs/50_data_publication/30_data_availability_statement.mdx rename to docs/50_data_publication/50_data_availability_statement.mdx diff --git a/docs/50_data_publication/51_lbe/20_lbe_intro.mdx b/docs/50_data_publication/51_lbe/00_lbe_intro.mdx similarity index 100% rename from docs/50_data_publication/51_lbe/20_lbe_intro.mdx rename to docs/50_data_publication/51_lbe/00_lbe_intro.mdx diff --git a/docs/50_data_publication/70_publishing_standards/25_publishing_standards_intro.mdx b/docs/50_data_publication/70_publishing_standards/70_publishing_standards_intro.mdx similarity index 100% rename from docs/50_data_publication/70_publishing_standards/25_publishing_standards_intro.mdx rename to docs/50_data_publication/70_publishing_standards/70_publishing_standards_intro.mdx From e02f10131879057f3762ecd395d96971ac276688 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Tue, 23 Jul 2024 12:54:27 +0200 Subject: [PATCH 42/44] fix: removed double main headlines pub standards --- .../70_publishing_standards/10_publishing_standards_authors.mdx | 2 -- .../20_publishing_standards_publishers.mdx | 2 -- .../30_publishing_standards_infrastructure.mdx | 2 -- 3 files changed, 6 deletions(-) diff --git a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx index a97b1550..8a236d90 100644 --- a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx +++ b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx @@ -3,8 +3,6 @@ title: "Authors" slug: "/publishing_standards_authors" --- -## For Authors - ### Use ORCID iD to Identifiy Authors and ROR to Identifiy Institutions :::tip Standard diff --git a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx index e9bcf97f..3691adb1 100644 --- a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx +++ b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx @@ -3,8 +3,6 @@ title: "Academic Publishers" slug: "/publishing_standards_publishers" --- -## For Publishers and Journals - ### Recommendations for Trusted, Chemistry-friendly Repositories :::tip Standard diff --git a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx index 40a4cd37..87321d15 100644 --- a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx +++ b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx @@ -3,8 +3,6 @@ title: "Infrastructure Providers" slug: "/publishing_standards_infrastructure" --- -## For Research Data Infrastructure and Resource Providers - ### Metadata Should be Part of a Dataset :::tip Standard From cbb91f3f98795ea2bfcccab132e4456689e67754 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Tue, 23 Jul 2024 12:56:55 +0200 Subject: [PATCH 43/44] fix: added "For" from dublicate headling pub std --- .../70_publishing_standards/10_publishing_standards_authors.mdx | 2 +- .../20_publishing_standards_publishers.mdx | 2 +- .../30_publishing_standards_infrastructure.mdx | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx index 8a236d90..4d61d1f8 100644 --- a/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx +++ b/docs/50_data_publication/70_publishing_standards/10_publishing_standards_authors.mdx @@ -1,5 +1,5 @@ --- -title: "Authors" +title: "For Authors" slug: "/publishing_standards_authors" --- diff --git a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx index 3691adb1..e2743bc9 100644 --- a/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx +++ b/docs/50_data_publication/70_publishing_standards/20_publishing_standards_publishers.mdx @@ -1,5 +1,5 @@ --- -title: "Academic Publishers" +title: "For Academic Publishers" slug: "/publishing_standards_publishers" --- diff --git a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx index 87321d15..fb72d19e 100644 --- a/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx +++ b/docs/50_data_publication/70_publishing_standards/30_publishing_standards_infrastructure.mdx @@ -1,5 +1,5 @@ --- -title: "Infrastructure Providers" +title: "For Infrastructure Providers" slug: "/publishing_standards_infrastructure" --- From 7ab93d24f55798d817013358de734aa03b5a1f63 Mon Sep 17 00:00:00 2001 From: tilfischer Date: Tue, 23 Jul 2024 12:58:21 +0200 Subject: [PATCH 44/44] feat: move up pub std in nav bar --- ...hing_standards_intro.mdx => 28_publishing_standards_intro.mdx} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/50_data_publication/70_publishing_standards/{70_publishing_standards_intro.mdx => 28_publishing_standards_intro.mdx} (100%) diff --git a/docs/50_data_publication/70_publishing_standards/70_publishing_standards_intro.mdx b/docs/50_data_publication/70_publishing_standards/28_publishing_standards_intro.mdx similarity index 100% rename from docs/50_data_publication/70_publishing_standards/70_publishing_standards_intro.mdx rename to docs/50_data_publication/70_publishing_standards/28_publishing_standards_intro.mdx