Merge pull request #5 from HOT-Ecosystem/gh-pages-2023-11-06

Joe's edits for 2023/11/06

README.md

@@ -1,10 +1,15 @@
-# Terminology Infrastructure and Management Systems Group (TIMS Group)
+# Terminology Infrastructure and Management Services Group (TIMS Group) - website
+TIMS is using Jekyll and GitHub Pages for its static site: https://hot-ecosystem.github.io/tims/
 
-## TIMS GitHub pages setup
+## How to update the site
+1. **Edit files**: [What files to edit](_docs/site.md)
+2. **Depoy updates**: Push/make a commit to the `gh-pages` branch, and the update will automatmically be deployed.
 
-TIMS is using Jekyll and GitHub Pages for [its static site](https://hot-ecosystem.github.io/tims/)
+## More information
+<details><summary>Using on your local machine</summary>
+<p>
 
-## Using on your local machine
+### Using on your local machine
 
 The Docker Compose setup should allow you to run the Jekyll server locally (in Docker), edit files, and see the results with live reload.
 
@@ -19,10 +24,29 @@ The Docker Compose setup should allow you to run the Jekyll server locally (in D
   * No need to do a `docker compsoe down` unless you need to start with a clean container, which takes time to do the initial setu.
   * Running `docker compse up` the next time to continue with the live reload should be much faster the next time.
 
-## Contributing
+</p>
+</details> 
 
-Content can be added by following Jekyll's documentation and using the required markdown.
+<details><summary>Initial setup</summary>
+<p>
+
+## Initial Setup
+
+* Jekyll based: https://jekyllrb.com/docs/
+  * Server sepecific settings, which you can use in the docker-compose-yaml file, are here: https://jekyllrb.com/docs/configuration/options/#serve-command-options
+  * 
+* GitHub specifics: https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll
+* Custom theme: https://mmistakes.github.io/minimal-mistakes/
+
+</p>
+</details>
+
+<details><summary>Jekyll static site resources</summary>
+<p>
 
+## Jekyll static site resources
+
+Content can be added by following Jekyll's documentation and using the required markdown.
 * Pages: https://jekyllrb.com/docs/pages/
 * Posts: https://jekyllrb.com/docs/posts/
 
@@ -31,10 +55,16 @@ Jekyll uses [Kramdown](https://kramdown.gettalong.org/index.html) for markdown.
 * [Quick reference](https://kramdown.gettalong.org/quickref.html)
 * [Documentation](https://kramdown.gettalong.org/documentation.html)
 
-## Initial Setup
+</p>
+</details>
 
-* Jekyll based: https://jekyllrb.com/docs/
-  * Server sepecific settings, which you can use in the docker-compose-yaml file, are here: https://jekyllrb.com/docs/configuration/options/#serve-command-options
-  * 
-* GitHub specifics: https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll
-* Custom theme: https://mmistakes.github.io/minimal-mistakes/
+<details><summary>Additional devops resources</summary>
+<p>
+
+### Additional devops resources
+* [Deployment action logs](https://github.com/HOT-Ecosystem/tims/actions/workflows/pages/pages-build-deployment)
+* [Alternate page for: Deployment action logs](https://github.com/HOT-Ecosystem/tims/deployments)
+* [GitHub pages site settings](https://github.com/HOT-Ecosystem/tims/settings/pages)
+
+</p>
+</details>

_config.yml

@@ -19,10 +19,10 @@
 # in the templates via {{ site.myvariable }}.
 
 title: TIMS Group
-subtitle: Terminology Infrastructure Management Systems Group
+subtitle: Terminology Infrastructure Management Services Group
 email: [email protected]
 description: >- # this means to ignore newlines until "baseurl:"
-  Terminology Infrastructure Management Systems Group
+  Terminology Infrastructure Management Services Group
 baseurl: "/tims" # the subpath of your site, e.g. /blog
 url: "https://hot-ecosystem.github.io/" # the base hostname & protocol for your site, e.g. http://example.com
 #twitter_username: jekyllrb

_data/navigation.yml

@@ -1,19 +1,19 @@
 main:
-  - title: Home
-    url: /
-  - title: Blog
-    url: /blog/
   - title: About
-    url: /about/
-  - title: Contact
-    url: /contact/
-  - title: Documentation
-    url: /docs/
+    url: /
+#  - title: Blog
+#    url: /blog/
+  - title: Team
+    url: /team/
+  - title: Projects
+    url: /projects/
+  - title: Terminology Server
+    url: /terminology-server/
 
-docs:
-  - title: Getting Started
-    children:
-      - title: "TIMS HAPI Server"
-        url: /docs/hapi/
-      - title: "Web and blog contribution"
-        url: /docs/site/
+#docs:
+#  - title: Getting Started
+#    children:
+#      - title: "TIMS HAPI Server"
+#        url: /docs/hapi/
+#      - title: "Web and blog contribution"
+#        url: /docs/site/

_pages/about.md

@@ -1,6 +1,12 @@
 ---
 title: About
-permalink: /about/
+permalink: /
 ---
 
-About page content.
+### The TIMS Group
+Terminology Infrastructure Management Services (TIMS) promotes parity and interoperability across different contexts for
+the ontology community and basic clinical research bioinformatics. We do this mainly through our [open source tools](
+/projects/) and [FHIR-based terminology server](/terminology-server/).
+
+### Contact
+[email protected]

_pages/projects.md

@@ -0,0 +1,38 @@
+---
+title: Projects
+permalink: /projects/
+---
+
+### FHIR Terminology Server
+TIMS hosts a FHIR server that provides a unique set of ontologies, terminologies, with unique features such as text 
+search and  SSSOM-formatted mappings.
+
+- http://fhir.terminology-services.com
+- http://20.3.198.176:8080/ (mirror)
+- [More information](/terminology-server/)
+
+### SSSOM
+SSSOM is a non-TIMS project, but TIMS contributes to this project by enabling it to export FHIR ConceptMap JSON 
+resources with SSSOM extensions. 
+
+https://github.com/mapping-commons/sssom-py/
+
+### OWL-on-FHIR
+Python-based non-minimalistic OWL to FHIR converter.
+
+https://github.com/HOT-Ecosystem/owl-on-fhir
+
+### OMOP2OWL-vocab
+Convert OMOP vocab into OWL and SemanticSQL.
+
+https://github.com/HOT-Ecosystem/omop2owl-vocab
+
+### OMOP2FHIR-vocab
+Convert OMOP vocab to FHIR.
+
+https://github.com/HOT-Ecosystem/omop2fhir-vocab
+
+### TimsUI
+A minimalistic web UI for the TIMS terminology server.
+
+https://github.com/HOT-Ecosystem/TimsUI

_pages/team.md

@@ -0,0 +1,12 @@
+---
+title: Team
+permalink: /team/
+---
+
+Director: Melissa Haendel  
+Director: Chris Chute  
+Project Management: Lisa Eskenazi  
+Development: Shahim Essaid
+Development: Joe Flack
+Development: Sigfried Gold
+Development: Stephanie Hong

_pages/terminology-server.md

@@ -0,0 +1,45 @@
+---
+title: Terminology Server
+permalink: /terminology-server/
+---
+
+TIMS hosts a FHIR server that provides a unique set of ontologies, terminologies, with unique features such as text 
+search and  SSSOM-formatted mappings.
+
+- http://fhir.terminology-services.com
+- http://20.3.198.176:8080/ (mirror)
+
+### Notable features
+[//]: # (TODO: need to clarify this list)
+- Content: CodeSystem and ConceptMap resources (see more below), and ValueSets (in development).
+- CodeSystem operations: [$subsumes](https://build.fhir.org/codesystem-operations.html#subsumes), [$lookup](https://build.fhir.org/codesystem-operations.html#lookup)
+- ConceptMap operations: [$closure](https://build.fhir.org/conceptmap-operations.html#closure) (in development)
+- ValueSet operations: [$expand](https://build.fhir.org/valueset-operations.html#expand), [$validate-code](https://build.fhir.org/valueset-operations.html#validate-code) (in development)
+
+#### Unique offerings
+[//]: # (TODO: need to clarify this list)
+The TIMS server has a few unique features, some of which are not available on any other terminology server:
+- Text search of concepts (in development)
+- Biomedical ontologies as CodeSystems
+- [SSSOM](https://mapping-commons.github.io/sssom/home/) extensions for ConceptMap resources
+
+### Terminology content
+#### CodeSystems
+[//]: # (TODO: need to clarify this list)
+TIMS hosts several popular biomedical terminologies, but is unique in that it offers several biomedical ontologies in 
+the FHIR CodeSystem format.
+* ICD10CM
+* RxNorm
+* SNOMED-CT 
+* Mondo 
+* HPO
+* CompLoinc
+* OMOP vocabularies
+* And more on the way
+
+#### ConceptMap
+Many of the terminologies and ontologies for which CodeSystems are available also  
+
+[//]: # (#### ValueSet)
+
+[//]: # (In development.)