Knowledgebase

src/components/Navbar.astro

@@ -22,12 +22,13 @@ export const MainNav: RecursiveMenu[] = [
     title: 'Tools',
     slug: '/toolbox',
     children: [
-      { title: 'ARCitect', slug: 'https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/ARCitect-Manual/index.html' },
+      { title: 'ARCitect', slug: 'https://nfdi4plants.github.io/nfdi4plants.knowledgebase/arcitect/' },
       { title: 'Swate', slug: 'https://swate-alpha.nfdi4plants.org/' },
       { title: 'DataPLAN', slug: 'https://dmpg.nfdi4plants.org/' },
       { title: 'ARCManager', slug: 'https://www.nfdi4plants.de/nfdi4plants.knowledgebase/docs/ARCmanager-manual/00_index.html' },
     ]
   },
+  { title: 'Knowledge Base', slug: 'https://www.nfdi4plants.de/nfdi4plants.knowledgebase/' },
 ]
 
 ---

src/content/articles/arc-development.md

@@ -4,7 +4,7 @@ description: You want to contribute to our Annotated Research Context (ARC) conc
 ---
 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.
+When using the DataPLANT tools (e.g. [ARCitect](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/arcitect/) and [guides](https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html) to create ARCs, the majority of ARC guidelines will be followed automatically.
 
 The detailed description of these technical requirements are captured in the **ARC specification**.
 However, the **ARC is not a top-down mandated concept**, but rather a community-driven effort.

src/content/articles/arc-how-to-start.md

@@ -13,4 +13,4 @@ ARC Commander and ARCitect also allow you to track all commits and push your ARC
 
 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 [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.
+If you want to start creating your ARC, you can find a detailed [getting started guide](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/start-here/) in the knowledge base.

src/content/articles/broker-ontology.md

@@ -15,5 +15,5 @@ Our ontology curators will check whether the term already exists in external ont
 
 If the term did not previously exist in an ontology, our ontology curators will suggest the term to be added to a suitable external ontology.
 This way, little by little, missing terms for data annotation should become available in commonly used ontologies.
-To read more about DataPLANT’s ontology service landscape, you can read our [Knowledge Base article](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/implementation/OntologyServiceLandscape.html).
+To read more about DataPLANT’s ontology service landscape, you can read our [Knowledge Base article](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/fundamentals/ontology-service-landscape/).
 To directly contribute to our DPBO, visit our [GitHub repository](https://github.com/nfdi4plants/nfdi4plants_ontology/issues/new/choose).

src/content/articles/collect-and-structure.md

@@ -13,6 +13,6 @@ ARCitect and ARC Commander initialize your ARC as a git repository, allowing you
 The tools can also be used to back-up and synchronize your ARC with the DataHUB as well as to download and modify ARCs from the DataHUB.
 Managing data throughout the research lifecycle is thus simplified.
 
-[Try ARCitect](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/ARCitect-Manual/index.html)
+[Try ARCitect](https://nfdi4plants.org/nfdi4plants.knowledgebase/arcitect)
 
-[Try ARC Commander](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/ArcCommanderManual/index.html)
+[Try ARC Commander](https://nfdi4plants.org/nfdi4plants.knowledgebase/arc-commander)

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 [Knowledge Base](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/fundamentals/index.html).
+You can find these articles in our [Knowledge Base](https://nfdi4plants.org/nfdi4plants.knowledgebase/fundamentals/index.html).

src/content/articles/open-educational-resources.md

@@ -5,4 +5,4 @@ description: "Videos, slides, GitHub repositories and more: Explore our free sel
 
 Whether you already participated in a personal DataPLANT training or not, you can become more familiar with DataPLANT’s tools and RDM concept by browsing our open educational resources.
 
-These include training slides in the [knowledge base](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/teaching-materials/index.html), [YouTube videos](https://www.youtube.com/@nfdi4plants816) and detailed information in our [GitHub repositories](https://github.com/nfdi4plants).
+These include training materials in the [knowledge base](https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html), [YouTube videos](https://www.youtube.com/@nfdi4plants816) and detailed information in our [GitHub repositories](https://github.com/nfdi4plants).

src/content/articles/swate-templates.md

@@ -12,5 +12,5 @@ If there is no template representing your metadata requirements, you can contrib
 You can create the template using the online version of [Swate](https://swate-alpha.nfdi4plants.org/) and add tags for it to be easily findable.
 The addition to our Swate database that makes it available in the tool occurs via a pull request on GitHub.
 
-A detailed guide for creating and contributing templates you can find in the [Knowledge Base](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/guides/swate_template-contribution.html).
+A detailed guide for creating and contributing templates you can find in the [Knowledge Base](https://nfdi4plants.org/nfdi4plants.knowledgebase/swate/swate-template-contribution/).
 You can find here the respective [GitHub repo here](https://github.com/nfdi4plants/Swate-templates).

src/content/articles/teaching-materials.md

@@ -6,4 +6,4 @@ description: "Data management, annotation or publication: Have a look at our tra
 We offer frequent trainings by our Data Stewards to bring different scientific groups on board with DataPLANT’s concepts and tools as well as keep them up to date.
 The materials used for teaching are openly shared in our knowledge base and can be useful whether you participated in a training or are looking for an introduction to our tools independently.
 
-You can explore them [here](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/teaching-materials/index.html).
+You can explore them [here](https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html).

src/content/articles/training-knowledgebase.md

@@ -12,4 +12,4 @@ For community support, DataPLANT provides a helpdesk and a Git-based project exc
 This platform enables project planning and offers a space for researchers to share experiences, seek advice, and collaborate. 
 DataPLANT also organizes community events, including onboarding sessions, consortium meetings, summer schools, lectures, practical courses, and hackathons together with Data Stewards to encourage knowledge sharing and engagement. 
 
-[DataPLANT Teaching material](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/teaching-materials/index.html)
+[DataPLANT Teaching material](https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html)

src/content/subpageContent/toolbox/arcitect.md

@@ -2,7 +2,7 @@
 title: ARCitect
 summary: An end-to-end GUI application to manage ARCs.
 icon: tabler:layout-grid-add
-href: https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/ARCitect-Manual/index.html
+href: https://nfdi4plants.org/nfdi4plants.knowledgebase/arcitect
 ---
 
 The ARCitect bundles many of the individual tools from DataPLANT into a single GUI application.
@@ -12,5 +12,5 @@ Use [Swate](#swate) to enrich Assays and Studies with metadata from ontologies.
 Edit any metadata directly. Select validation packages to use in ARC Data Hub CQC pipelines.
 
 **Read more:**
-- [ARCitect manual](https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/ARCitect-Manual/index.html)
+- [ARCitect manual](https://nfdi4plants.org/nfdi4plants.knowledgebase/arcitect)
 - [ARCitect source code on GitHub](https://github.com/nfdi4plants/ARCitect)

src/content/subpageContent/toolbox/swate.md

@@ -9,6 +9,5 @@ Swate provides a familiar, spreadsheet-like work environment that makes it easy
 Swate is integrated into the [ARCitect](#arcitect), but can also be used as a [standalone-web based tool](https://swate-alpha.nfdi4plants.org/).
 
 **Read more:**
-- [Swate intro](https://www.nfdi4plants.de/nfdi4plants.knowledgebase/docs/implementation/Swate.html)
-- [Swate manual](https://www.nfdi4plants.de/nfdi4plants.knowledgebase/docs/SwateManual/index.html)
+- [Swate intro and manual](https://www.nfdi4plants.de/nfdi4plants.knowledgebase/swate/)
 - [Swate source code on GitHub](https://github.com/nfdi4plants/Swate)