Update Uberon docs to better (obook) design

And fix some build warnings while I was at it.

.gitignore

@@ -220,3 +220,4 @@ src/ontology/subsets/*.owl
 src/ontology/subsets/*.tsv
 src/ontology/imports/*_import.owl
 !src/ontology/imports/orcidio_import.owl
+/site/*

docs/history.md

@@ -1,3 +1,5 @@
 # A brief history of UBERON
 
 The following page gives an overview of the history of UBERON.
+
+See Monarch Seminar Series: The Uberon Anatomy Ontology (2024) [slides](https://docs.google.com/presentation/d/15JyOunBw6R_xcs7wBWdZZPvmcQsPLKUDa6ycEqa5NE4/edit#slide=id.g2445be87c8e_0_0).

docs/onboarding.md

@@ -6,8 +6,8 @@ informations and the access that they need in order to start working
 with Uberon.
 
 1. Invite them to the [Anatomy and Cell
-   Ontologies](anatomy-and-cell-onto.slack.com) Slack workspace.
-2. Invite them to the [OBO Community](obo-communitygroup.slack.com)
+   Ontologies](https://anatomy-and-cell-onto.slack.com) Slack workspace.
+2. Invite them to the [OBO Community](https://obo-communitygroup.slack.com)
    Slack workspace and point them to the `#uberon` channel.
 3. Add them to the meeting invites on the Monarch Calendar (FIXME: How
    to do that? Who is the person to contact?)

docs/uberon-editor-sop.md

@@ -14,7 +14,7 @@ Uberon is a cross-species ontology, and editors should be careful when adding ta
 
 ## Relations Guide
 
-The following is a guide for relations to use with some notes and examples. This is not a comprehensive list and will be continually worked on, however, it contains some of the more common relations used in Uberon. Do familiarise yourself with them and use this section as a reference when you are adding relations. (Should we add something here to direct to DOSDP patterns that Chris generated with the patterniser? It is a bit more complicated to explain that but [here's the folder](../patterns/generated))
+The following is a guide for relations to use with some notes and examples. This is not a comprehensive list and will be continually worked on, however, it contains some of the more common relations used in Uberon. Do familiarise yourself with them and use this section as a reference when you are adding relations. (Should we add something here to direct to DOSDP patterns that Chris generated with the patterniser? It is a bit more complicated to explain that but [here's the folder](https://github.com/obophenotype/uberon/tree/master/patterns/generated))
 
 #### overlaps
 
@@ -43,7 +43,7 @@ means that
 2. All parts of the brain endothelium are part of the brain (e.g. all cells that are part_of the brain endothelium are also cells that are part_of the brain) 
 3. Brain endothelium are part_of some brain at all times. (Makes more of a difference for cells being part of anatomical structure, e.g. a blood cell is not part_of the brain endothelium because it moves out of the brain endothelium.)
 
-Related Equivalence Pattern: [X_part_of_X](../patterns/generated/X_part_of_X.yaml)
+Related Equivalence Pattern: [X_part_of_X](https://github.com/obophenotype/uberon/blob/master/patterns/generated/X_part_of_X.yaml)
 
 #### has part
 

mkdocs.yaml

@@ -1,5 +1,58 @@
-site_name: Uberon multi-species anatomy ontology
-theme: readthedocs
+site_name: Uberon Multi-species Anatomy Ontology
+theme:
+  name: material
+  icon:
+    edit: material/pencil 
+  features:
+    - content.action.edit
+    #- navigation.tabs
+    #- toc.integrate
+    #- navigation.sections
+    #- navigation.top
+    - search.suggest
+    - search.highlight
+    #- content.tabs.link
+    - content.code.annotation
+    - content.code.copy
+    - content.code.select
+plugins:
+  - search
+markdown_extensions:
+  - toc:
+      permalink: true
+  - pymdownx.superfences:
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_div_format
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.tabbed
+  - pymdownx.critic
+  - pymdownx.caret
+  - pymdownx.details
+  - pymdownx.keys
+  - pymdownx.mark
+  - pymdownx.tilde
+  - attr_list
+  - md_in_html
+  - pymdownx.highlight:
+      anchor_linenums: true
+  - admonition
+  - pymdownx.arithmatex:
+      generic: true
+  - footnotes
+  - attr_list
+  - md_in_html
+  - tables
+
+extra_javascript:
+  - https://unpkg.com/[email protected]/dist/mermaid.min.js
+
+repo_url: https://github.com/obophenotype/uberon/
+site_url: https://obophenotype.github.io/uberon/
+edit_uri: edit/master/docs/
+
 nav:
   - Home: index.md
   - About:
@@ -8,6 +61,7 @@ nav:
       - Uberon on GitHub: https://github.com/obophenotype/uberon
       - Issue Tracker: https://github.com/obophenotype/uberon
       - Adopters: adopters.md
+      - History: history.md
       - Acknowledgements: acknowledgements.md
       - Cite: cite.md
   - Browse:
@@ -31,6 +85,8 @@ nav:
           - Imports management: odk-workflows/UpdateImports.md
           - Managing the documentation: odk-workflows/ManageDocumentation.md
           - Continuous Integration: odk-workflows/ContinuousIntegration.md
+          - Manage automated checks: odk-workflows/ManageAutomatedTest.md
+          - Manage components: odk-workflows/components.md
           - Your ODK Repository Overview: odk-workflows/RepositoryFileStructure.md
   - Uberon Internal Docs: 
       - Uberon Release: uberon-release.md