diff --git a/.gitignore b/.gitignore index 94f467e26..b33f8c424 100644 --- a/.gitignore +++ b/.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/* diff --git a/docs/history.md b/docs/history.md index 3ca6ba3f3..a1d78ebbf 100644 --- a/docs/history.md +++ b/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). diff --git a/docs/onboarding.md b/docs/onboarding.md index 59a99ad13..5b9c4a6f3 100644 --- a/docs/onboarding.md +++ b/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?) diff --git a/docs/uberon-editor-sop.md b/docs/uberon-editor-sop.md index a9744f615..a103c1eca 100644 --- a/docs/uberon-editor-sop.md +++ b/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 diff --git a/mkdocs.yaml b/mkdocs.yaml index b63e320ce..06e5e0717 100644 --- a/mkdocs.yaml +++ b/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/mermaid@8.5.1/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