From 037c8a2dbc4eeec1a58ba3ab0beab148f5659cfe Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 11:29:50 +0200 Subject: [PATCH 01/12] link to arc website --- src/content/articles/arc-development.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/content/articles/arc-development.md b/src/content/articles/arc-development.md index 74285760..72dc2962 100644 --- a/src/content/articles/arc-development.md +++ b/src/content/articles/arc-development.md @@ -2,7 +2,7 @@ title: Contribute to ARC development description: You want to contribute to our Annotated Research Context (ARC) concept or tools? Find out more. --- -The [**A**nnotated **R**esearch **C**ontext (ARC)](https://nfdi4plants.github.io/arc-website/) is DataPLANT's central concept for organizing and documenting research data, focal point of collaboration, data exchange, and overall FAIR Digital Object of choice. +The [**A**nnotated **R**esearch **C**ontext (ARC)](https://arc-rdm.org) is DataPLANT's central concept for organizing and documenting research data, focal point of collaboration, data exchange, and overall FAIR Digital Object of choice. When using the DataPLANT tools (e.g. [ARCitect](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/ARCitect-Manual/index.html]) and [guides](https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html) to create ARCs, the majority of ARC guidelines will be followed automatically. @@ -11,5 +11,5 @@ However, the **ARC is not a top-down mandated concept**, but rather a community- The ARC specification is a living document that is continuously improved and extended upon. It is [hosted on GitHub](https://github.com/nfdi4plants/ARC-specification) and open for contributions from the community, as well as [general discussions](https://github.com/nfdi4plants/ARC-specification/discussions). -The same is true for all ARC-related tooling developed by DataPLANT: development is done out in the open on our [GitHub organization](https://github.com/nfdi4plants), which also has an [top-level discussion forum](https://github.com/orgs/nfdi4plants/discussions). +The same is true for all ARC-related tooling developed by DataPLANT: development is done out in the open on our [GitHub organization](https://github.com/nfdi4plants), which also has a [top-level discussion forum](https://github.com/orgs/nfdi4plants/discussions). For the core ARC tools, we even have an [open development board](https://github.com/orgs/nfdi4plants/projects/10/views/2), which gives an overview on the entire development process of our core developer team. \ No newline at end of file From 0b4ff0c8f538f6d006201522abe6962c7944b6a1 Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:18:46 +0200 Subject: [PATCH 02/12] typo --- src/content/articles/arc-general.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/content/articles/arc-general.md b/src/content/articles/arc-general.md index 6a53029f..fa3074b3 100644 --- a/src/content/articles/arc-general.md +++ b/src/content/articles/arc-general.md @@ -13,6 +13,6 @@ It is important to mention, since it is is often misunderstood, that the ‘A’ The [ARC (**A**nnotated **R**esearch **C**ontext)](https://arc-rdm.org) is an implementation of the FDO concept. It is a framework for organizing and documenting research data, as well as a container that continuously supports collaboration, data exchange, and adherence to FAIR principles among various researchers. -It is developed under the umbrella of DataPLANT for for plant research, but is applicable to many other research domains. +While being developed under the umbrella of DataPLANT for plant research, the ARC is applicable to many other research domains. DataPLANT develops and maintains [tools for the ARC ecosystem](/resources/#toolbox), hosts [services to collaborate on ARCs](https://nfdi4plants.github.io/arc-data-hub/), and provides [training and support](https://nfdi4plants.github.io/support/) for ARC users. From 4b40f760e568a05114365942a3f97f776f3851ff Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:22:04 +0200 Subject: [PATCH 03/12] unify ARC Commander --- src/content/articles/arc-how-to-start.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/content/articles/arc-how-to-start.md b/src/content/articles/arc-how-to-start.md index e597e2eb..0eff8bf3 100644 --- a/src/content/articles/arc-how-to-start.md +++ b/src/content/articles/arc-how-to-start.md @@ -3,14 +3,14 @@ title: Start your own ARC description: You want to make your scientific data FAIR (Findable, Accessible, Interoperable, and Reusable)? Start now with our Annotated Research Context (ARC). --- -The ARC is the central framework for research data management in DataPLANT. -ARCs are fair digital objects, that follow the RO Crate and ISA standard and package all research data and metadata related to your investigation. +The ARC is the central framework for research data management (RDM) in DataPLANT. +ARCs are fair digital objects (FDOs), that follow the RO Crate and ISA standard and package all research data and metadata related to your investigation. Their folder structure comprises studies, assays, workflows and runs, as well as subfolders for protocols and raw data. By default, ARCs also contain metadata files that follow the ISA standard. -To facilitate and partly automate the creation of ARCs two tools were developed: The ARCCommander is a command line-based tool for ARC creation, whereas ARCitect employs a graphical user interface for ARC creation and also integrates the annotation tool Swate. +To facilitate and partly automate the creation of ARCs two tools were developed: The ARC Commander is a command line-based tool for ARC creation, whereas ARCitect employs a graphical user interface for ARC creation and also integrates the annotation tool Swate. -ARCCommander and ARCitect also allow you to track all commits and push your ARC to the PLANTdataHUB for versioning, storage and sharing with collaborators or the whole scientific community. +ARC Commander and ARCitect also allow you to track all commits and push your ARC to the PLANTdataHUB for versioning, storage and sharing with collaborators or the whole scientific community. To read more about ARCs, check out our [ARC website](arc-rdm.org). -If you want to start creating your ARC, you can find detailed guides for the [ARCCommander](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/ArcCommanderManual/index.html) and [ARCitect](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/ARCitect-Manual/index.html) in the knowledgebase. \ No newline at end of file +If you want to start creating your ARC, you can find detailed guides for the [ARC Commander](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/ArcCommanderManual/index.html) and [ARCitect](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/ARCitect-Manual/index.html) in the knowledge base. \ No newline at end of file From 97f8017649a69b4b796059199c92bc349b534dff Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:22:22 +0200 Subject: [PATCH 04/12] simplify registration link --- src/content/articles/become-a-member.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/content/articles/become-a-member.md b/src/content/articles/become-a-member.md index 4a294cdd..d4985676 100644 --- a/src/content/articles/become-a-member.md +++ b/src/content/articles/become-a-member.md @@ -8,4 +8,4 @@ All tools can be downloaded on [GitHub](https://github.com/nfdi4plants) or are a To use all functionalities related to your FAIR digital research object, the Annotated Research Context (ARC), creating a free DataPLANT account will be useful. This will allow you to upload and continuously synchronize your ARC with the PLANTdataHUB, share it with collaborators and access or contribute to ARCs of collaborators that are not public. -To create a DataPLANT account you can follow [this link](https://auth.nfdi4plants.org/realms/dataplant/protocol/openid-connect/auth?client_id=account&redirect_uri=https%3A%2F%2Fauth.nfdi4plants.org%2Frealms%2Fdataplant%2Faccount%2Flogin-redirect&state=0%2F2083ce25-95bf-4a38-ba82-0502f7060042&response_type=code&scope=openid). \ No newline at end of file +To create a DataPLANT account you can follow [this link](https://register.nfdi4plants.org). \ No newline at end of file From 89eb17c1ff52da044506c921b0f7746c957ec9b5 Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:30:37 +0200 Subject: [PATCH 05/12] typo --- src/content/articles/collect-and-structure.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/content/articles/collect-and-structure.md b/src/content/articles/collect-and-structure.md index 96b64f9c..383aa1d0 100644 --- a/src/content/articles/collect-and-structure.md +++ b/src/content/articles/collect-and-structure.md @@ -6,7 +6,7 @@ description: Our tools ARCitect and ARCCommander simplify the creation, structur The ARCitect and ARCCommander are two essential tools developed by DataPLANT that assist users with the creation and management of ARCs. ARCitect employs a graphical user interface to guide researchers in creating, organizing, and annotating research data, ensuring adherence to FAIR principles. ARCCommander complements ARCitect by offering robust management capabilities via the command line. -By initializing a new ARC using ARCitect or ARCCommander, the ARC folder structure, including studies, assays, workflows and runs as well as subfolders is contructed. +By initializing a new ARC using ARCitect or ARCCommander, the ARC folder structure, including studies, assays, workflows and runs as well as subfolders is constructed. ISA metadata files are automatically added to each study and assay and can be easily filled using the same tools. The tools provide structured assistance and automation with processes following the ARC specification. ARCitect and ARCCommander initialize your ARC as a git repository, allowing you to track changes of your ARC. From dcf777d72b5932a65368d4ff648102989124e716 Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:34:29 +0200 Subject: [PATCH 06/12] obfuscate email --- src/content/articles/custom-training.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/content/articles/custom-training.md b/src/content/articles/custom-training.md index cec8cdce..c1bbd656 100644 --- a/src/content/articles/custom-training.md +++ b/src/content/articles/custom-training.md @@ -5,4 +5,4 @@ description: You want to learn how you can use the Annotated Research Context to In addition to offering educational material on DataPLANT’s concepts and tools online, DataPLANT’s Data Stewards offer custom support for your RDM. -If you are interested in arranging a 1-2 day custom training with our Data Stewards you can reach out to us via our email address info@nfdi4plants.org. \ No newline at end of file +If you are interested in arranging a 1-2 day custom training with our Data Stewards you can reach out to us via email. \ No newline at end of file From 19962e6e962682c54c3faa24261abe00cacf28cd Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:39:03 +0200 Subject: [PATCH 07/12] typos --- src/content/articles/discover-and-explore-arcsearch.md | 2 +- src/content/articles/fundamentals-rdm.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/content/articles/discover-and-explore-arcsearch.md b/src/content/articles/discover-and-explore-arcsearch.md index d5d5069a..f86993c7 100644 --- a/src/content/articles/discover-and-explore-arcsearch.md +++ b/src/content/articles/discover-and-explore-arcsearch.md @@ -7,6 +7,6 @@ The ARCSearch is a tool for integrated search and analysis of individual ARCs an The web-based user interface provides a consolidated real-time view of the public ARCs within the DataPLANT community as well as of a user's private ARCs after log-in. The search functions of the ARC Registry application enable users to explore the ARCs and their assay data based on keywords and metadata. The users can look up the ARCs by specific keywords, such as the working group they are interested in, the ARC creator or by the title of the ARC. -Most importantly, the users can also search and explore the experimental metadata from various ARCs simultaneously, thus, paving the way toward crossomics metadata exploration within the community. +Most importantly, the users can also search and explore the experimental metadata from various ARCs simultaneously, thus, paving the way toward cross-omics metadata exploration within the community. [Try ARCSearch](https://arcregistry.nfdi4plants.org/isasearch) \ No newline at end of file diff --git a/src/content/articles/fundamentals-rdm.md b/src/content/articles/fundamentals-rdm.md index d4e899b5..01cf4ece 100644 --- a/src/content/articles/fundamentals-rdm.md +++ b/src/content/articles/fundamentals-rdm.md @@ -5,4 +5,4 @@ description: Learn more about research data management and why it is important ( Whether you are new to RDM or simply want to increase your knowledge and skills, we have compiled several articles on the fundamentals of RDM, including the FAIR principles, metadata and ontologies, data sharing and publications and more. -You can find these articles in our [knowledgebase](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/fundamentals/index.html). \ No newline at end of file +You can find these articles in our [Knowledge Base](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/fundamentals/index.html). \ No newline at end of file From 759325ad93311e1db0838e76fa5173b1e6287f4a Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:39:30 +0200 Subject: [PATCH 08/12] delete knowledge-base article, that is duplicate of task-areas --- src/content/articles/knowledge-base.md | 43 -------------------------- 1 file changed, 43 deletions(-) delete mode 100644 src/content/articles/knowledge-base.md diff --git a/src/content/articles/knowledge-base.md b/src/content/articles/knowledge-base.md deleted file mode 100644 index 36d931ef..00000000 --- a/src/content/articles/knowledge-base.md +++ /dev/null @@ -1,43 +0,0 @@ ---- -title: DataPLANT Task Areas -description: Overview of the DataPLANT Task Areas ---- - -## Task Area 1 - -_Data Quality, Standardization, Interoperability_ - -Will provide support, including AI-based approaches, to facilitate the collection of vocabularies and ontologies, encouraging broader community participation. -TA1 will enhance ontologies embedded within international consortia, which are essential for improving data and workflow interoperability and ensuring AI-readiness through machine actionability. -This will connect user documentation, technical endpoints, workflow engines, and domain-specific requirements. -To guarantee high-quality (meta)data, TA1 will implement automated validation processes, supplemented by a community-driven data publication review system. -Furthermore, TA1 will promote RDM practices through the involvement of data stewards, fostering a culture of traceability within the community. - -## Task Area 2 -_Infrastructure, Service, and Workflow Platform_ - -Will enhance the DataPLANT DataHUB and associated services to ensure deep integration with both national and international infrastructures. -This includes platforms such as the NFDI Research Data Commons, OpenAIRE, EOSC, and EBI. -These efforts aim to improve the visibility and recognition of DataPLANT by journals, the NFDI, the EU, and key international RDM initiatives and stakeholders. -Task Area 2 supports efficient data management and analysis, enabling the execution of actionable FAIR Digital Objects (FDOs) within established workflow environments. -It will leverage consortium cloud environments and the NFDI FAIR data spaces to implement an infrastructure-as-a-service model for distribution and maintenance. - -## Task Area 3 - -_Software, Application, and Transfer_ - -Will promote an open-source culture, encouraging participation and skill development in research data projects and software. -TA3 will foster community engagement by offering personalized support through tailored digital assistance. -It will also refine and consolidate the plant FAIR Digital Object (FDO) software stack to enhance interoperability with other NFDI and international RDM services. -TA3 will provide open educational resources and implement a "train the trainer" model to support the embedded data steward approach. -This will include the development of improved documentation, tutorials, and teaching materials, empowering active community participation through transparent, community-driven feedback and development processes. -Additionally, TA3 will establish a support framework for embedded and geo-distributed data stewards. - -## Task Area 4 - -_Coordination and Management_ - -Will focus on efficiently managing the consortium and ensuring alignment with community-driven objectives. -TA4 will coordinate the dissemination of project information and outcomes from all task areas, ensuring that all stakeholders, both within and outside the consortium, are well-informed. -It will also establish bidirectional advocacy structures and create low-barrier participation opportunities for the broader community and beyond. -Additionally, TA4 will form special interest groups for the life sciences (LS), address legal matters, represent the consortium in dealings with the DFG, and foster collaboration among state-level initiatives, compute centers, faculty IT, research institutions, libraries, and NFDI liaison efforts to drive consolidation. \ No newline at end of file From f8cea63bd5bc86da6bea32f8e77658d749af66ed Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:53:58 +0200 Subject: [PATCH 09/12] unify names --- src/content/articles/manuals.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/content/articles/manuals.md b/src/content/articles/manuals.md index c73e08db..6177c64b 100644 --- a/src/content/articles/manuals.md +++ b/src/content/articles/manuals.md @@ -4,7 +4,7 @@ description: Browse our guides to learn more about DataPLANTs tools and services --- DataPLANT offers several tools to facilitate RDM. -To help you make the most of these tools we offer detailed, step by step guides and examples in our knowledgebase. -Here you can find guides for creating and managing ARCs with the ARCCommander, ARCitect or ARCmanager, creating metadata annotation tables with Swate and sharing your data on the DataHUB. +To help you make the most of these tools we offer detailed, step by step guides and examples in our knowledge base. +Here you can find guides for creating and managing ARCs with the ARC Commander, ARCitect or ARCmanager, creating metadata annotation tables with Swate and sharing your data on the DataHUB. Explore our [knowledge base](https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html) to find manuals for tools but also guides for e.g. contributing to ontologies and applying metadata standards. \ No newline at end of file From 1093ff8e9c97bf352f3903ccbc7a95ca6def7fdb Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:54:24 +0200 Subject: [PATCH 10/12] typo! --- src/content/subpageContent/about/rdm-concept.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/content/subpageContent/about/rdm-concept.md b/src/content/subpageContent/about/rdm-concept.md index 17fc75b7..c6c41a3b 100644 --- a/src/content/subpageContent/about/rdm-concept.md +++ b/src/content/subpageContent/about/rdm-concept.md @@ -6,7 +6,7 @@ summary: "DataPLANT’s Research Data Management (RDM) concept focusses on FAIR --- DataPLANT’s research data management (RDM) concept focusses on FAIR compliance, data and service interoperability, community participation, knowledge transfer, and long-term sustainability. -It is tailored to the plant community and aims to establish sustainable RDM processes and habits. DatapPLANT sees RDM as a collaborative and continuous process. +It is tailored to the plant community and aims to establish sustainable RDM processes and habits. DataPLANT sees RDM as a collaborative and continuous process. The goal is to transform static research artifacts into dynamic, growing research objects that are continuously extended, annotated, processed, analyzed, and managed alongside ongoing research activities, ensuring that research artifacts are produced in a FAIR manner. The core technology for DataPLANT’s strategy is the ARC. ARCs provide a set of guidelines for combining data, metadata, and workflows in a file system layout that is easy to understand and ensures that changes to data, metadata, or workflows are well-defined and consistent. From 298afc1f51d413a5f850d60a482a4b573fe10e1f Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:56:23 +0200 Subject: [PATCH 11/12] typos --- src/content/articles/planning-dataplan.md | 2 +- src/content/subpageContent/participation/github.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/content/articles/planning-dataplan.md b/src/content/articles/planning-dataplan.md index 37cb6e75..75a45c27 100644 --- a/src/content/articles/planning-dataplan.md +++ b/src/content/articles/planning-dataplan.md @@ -8,7 +8,7 @@ Data management plans (DMPs) describe the handling of research data throughout i To streamline the creation of DMPs for plant scientists, DataPLANT developed the DMP Generator DataPLAN as a web-based tool. Tailored to the needs of researchers in plant science, DataPLAN provides a user-friendly interface that guides scientists through the process of creating comprehensive, FAIR-compliant DMPs. It provides templates fitting the DMP requirements of different funders, like DFG, Horizon Europe, or BMBF, making it easier for researchers to meet compliance obligations. -In addition to presenting the respective questions to be answered, DataPLAN also comprises prewritten text blocks as answers. +In addition to presenting the respective questions to be answered, DataPLAN also comprises pre-written text blocks as answers. These answers in part depend on the selections, e.g. of data types to be generated, made by the users. Any required free text information is asked for in the form of simple questions and automatically integrated into the text at the necessary positions. diff --git a/src/content/subpageContent/participation/github.md b/src/content/subpageContent/participation/github.md index 19a15268..b6649f4b 100644 --- a/src/content/subpageContent/participation/github.md +++ b/src/content/subpageContent/participation/github.md @@ -1,6 +1,6 @@ --- title: Contribute to our GitHub repositories -summary: DataPLANT's work is openly accesible on GitHub. Contributions to our repositories are welcome. +summary: DataPLANT's work is openly accessible on GitHub. Contributions to our repositories are welcome. icon: tabler:brand-github href: "/articles/github" --- \ No newline at end of file From b2e6ca889c9167f72e231da095cc549a74461fbb Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Wed, 16 Oct 2024 12:58:45 +0200 Subject: [PATCH 12/12] rename template-repo to swate-templates --- src/content/articles/{template-repo.md => swate-templates.md} | 0 src/content/subpage/participation.md | 2 +- .../participation/{template-repo.md => swate-templates.md} | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename src/content/articles/{template-repo.md => swate-templates.md} (100%) rename src/content/subpageContent/participation/{template-repo.md => swate-templates.md} (86%) diff --git a/src/content/articles/template-repo.md b/src/content/articles/swate-templates.md similarity index 100% rename from src/content/articles/template-repo.md rename to src/content/articles/swate-templates.md diff --git a/src/content/subpage/participation.md b/src/content/subpage/participation.md index a63f6cbe..abb4e5b1 100644 --- a/src/content/subpage/participation.md +++ b/src/content/subpage/participation.md @@ -7,7 +7,7 @@ content: - participation/arc-how-to-start - participation/github - participation/broker-ontology - - participation/template-repo + - participation/swate-templates - participation/arc-development image: /src/assets/images/subpage/participation/participation-mainpage.svg styling: diff --git a/src/content/subpageContent/participation/template-repo.md b/src/content/subpageContent/participation/swate-templates.md similarity index 86% rename from src/content/subpageContent/participation/template-repo.md rename to src/content/subpageContent/participation/swate-templates.md index ba7306d0..6760df55 100644 --- a/src/content/subpageContent/participation/template-repo.md +++ b/src/content/subpageContent/participation/swate-templates.md @@ -2,5 +2,5 @@ title: Contribute to our templates summary: Our annotation tool Swate simplifies adding standardized metadata for your experimental workflows. You would like to contribute a template? icon: tabler:table-share -href: "/articles/template-repo" +href: "/articles/swate-templates" ---