diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..7e5cd09 --- /dev/null +++ b/.gitignore @@ -0,0 +1,7 @@ +_site +.sass-cache +.jekyll-cache +.jekyll-metadata +vendor + +.idea/ diff --git a/404.html b/404.html new file mode 100644 index 0000000..086a5c9 --- /dev/null +++ b/404.html @@ -0,0 +1,25 @@ +--- +permalink: /404.html +layout: default +--- + + + +
+

404

+ +

Page not found :(

+

The requested page could not be found.

+
diff --git a/Gemfile b/Gemfile new file mode 100644 index 0000000..9786586 --- /dev/null +++ b/Gemfile @@ -0,0 +1,7 @@ +source "https://rubygems.org" + +gem "github-pages", group: :jekyll_plugins +gem "jekyll-include-cache", group: :jekyll_plugins + +# TIMS custom +gem "webrick", "~> 1.8" \ No newline at end of file diff --git a/Gemfile.lock b/Gemfile.lock new file mode 100644 index 0000000..520cdf3 --- /dev/null +++ b/Gemfile.lock @@ -0,0 +1,273 @@ +GEM + remote: https://rubygems.org/ + specs: + activesupport (7.1.0) + base64 + bigdecimal + concurrent-ruby (~> 1.0, >= 1.0.2) + connection_pool (>= 2.2.5) + drb + i18n (>= 1.6, < 2) + minitest (>= 5.1) + mutex_m + tzinfo (~> 2.0) + addressable (2.8.5) + public_suffix (>= 2.0.2, < 6.0) + base64 (0.1.1) + bigdecimal (3.1.4) + coffee-script (2.4.1) + coffee-script-source + execjs + coffee-script-source (1.11.1) + colorator (1.1.0) + commonmarker (0.23.10) + concurrent-ruby (1.2.2) + connection_pool (2.4.1) + dnsruby (1.70.0) + simpleidn (~> 0.2.1) + drb (2.1.1) + ruby2_keywords + em-websocket (0.5.3) + eventmachine (>= 0.12.9) + http_parser.rb (~> 0) + ethon (0.16.0) + ffi (>= 1.15.0) + eventmachine (1.2.7) + execjs (2.9.1) + faraday (2.7.11) + base64 + faraday-net_http (>= 2.0, < 3.1) + ruby2_keywords (>= 0.0.4) + faraday-net_http (3.0.2) + ffi (1.16.3) + forwardable-extended (2.6.0) + gemoji (3.0.1) + github-pages (228) + github-pages-health-check (= 1.17.9) + jekyll (= 3.9.3) + jekyll-avatar (= 0.7.0) + jekyll-coffeescript (= 1.1.1) + jekyll-commonmark-ghpages (= 0.4.0) + jekyll-default-layout (= 0.1.4) + jekyll-feed (= 0.15.1) + jekyll-gist (= 1.5.0) + jekyll-github-metadata (= 2.13.0) + jekyll-include-cache (= 0.2.1) + jekyll-mentions (= 1.6.0) + jekyll-optional-front-matter (= 0.3.2) + jekyll-paginate (= 1.1.0) + jekyll-readme-index (= 0.3.0) + jekyll-redirect-from (= 0.16.0) + jekyll-relative-links (= 0.6.1) + jekyll-remote-theme (= 0.4.3) + jekyll-sass-converter (= 1.5.2) + jekyll-seo-tag (= 2.8.0) + jekyll-sitemap (= 1.4.0) + jekyll-swiss (= 1.0.0) + jekyll-theme-architect (= 0.2.0) + jekyll-theme-cayman (= 0.2.0) + jekyll-theme-dinky (= 0.2.0) + jekyll-theme-hacker (= 0.2.0) + jekyll-theme-leap-day (= 0.2.0) + jekyll-theme-merlot (= 0.2.0) + jekyll-theme-midnight (= 0.2.0) + jekyll-theme-minimal (= 0.2.0) + jekyll-theme-modernist (= 0.2.0) + jekyll-theme-primer (= 0.6.0) + jekyll-theme-slate (= 0.2.0) + jekyll-theme-tactile (= 0.2.0) + jekyll-theme-time-machine (= 0.2.0) + jekyll-titles-from-headings (= 0.5.3) + jemoji (= 0.12.0) + kramdown (= 2.3.2) + kramdown-parser-gfm (= 1.1.0) + liquid (= 4.0.4) + mercenary (~> 0.3) + minima (= 2.5.1) + nokogiri (>= 1.13.6, < 2.0) + rouge (= 3.26.0) + terminal-table (~> 1.4) + github-pages-health-check (1.17.9) + addressable (~> 2.3) + dnsruby (~> 1.60) + octokit (~> 4.0) + public_suffix (>= 3.0, < 5.0) + typhoeus (~> 1.3) + html-pipeline (2.14.3) + activesupport (>= 2) + nokogiri (>= 1.4) + http_parser.rb (0.8.0) + i18n (1.14.1) + concurrent-ruby (~> 1.0) + jekyll (3.9.3) + addressable (~> 2.4) + colorator (~> 1.0) + em-websocket (~> 0.5) + i18n (>= 0.7, < 2) + jekyll-sass-converter (~> 1.0) + jekyll-watch (~> 2.0) + kramdown (>= 1.17, < 3) + liquid (~> 4.0) + mercenary (~> 0.3.3) + pathutil (~> 0.9) + rouge (>= 1.7, < 4) + safe_yaml (~> 1.0) + jekyll-avatar (0.7.0) + jekyll (>= 3.0, < 5.0) + jekyll-coffeescript (1.1.1) + coffee-script (~> 2.2) + coffee-script-source (~> 1.11.1) + jekyll-commonmark (1.4.0) + commonmarker (~> 0.22) + jekyll-commonmark-ghpages (0.4.0) + commonmarker (~> 0.23.7) + jekyll (~> 3.9.0) + jekyll-commonmark (~> 1.4.0) + rouge (>= 2.0, < 5.0) + jekyll-default-layout (0.1.4) + jekyll (~> 3.0) + jekyll-feed (0.15.1) + jekyll (>= 3.7, < 5.0) + jekyll-gist (1.5.0) + octokit (~> 4.2) + jekyll-github-metadata (2.13.0) + jekyll (>= 3.4, < 5.0) + octokit (~> 4.0, != 4.4.0) + jekyll-include-cache (0.2.1) + jekyll (>= 3.7, < 5.0) + jekyll-mentions (1.6.0) + html-pipeline (~> 2.3) + jekyll (>= 3.7, < 5.0) + jekyll-optional-front-matter (0.3.2) + jekyll (>= 3.0, < 5.0) + jekyll-paginate (1.1.0) + jekyll-readme-index (0.3.0) + jekyll (>= 3.0, < 5.0) + jekyll-redirect-from (0.16.0) + jekyll (>= 3.3, < 5.0) + jekyll-relative-links (0.6.1) + jekyll (>= 3.3, < 5.0) + jekyll-remote-theme (0.4.3) + addressable (~> 2.0) + jekyll (>= 3.5, < 5.0) + jekyll-sass-converter (>= 1.0, <= 3.0.0, != 2.0.0) + rubyzip (>= 1.3.0, < 3.0) + jekyll-sass-converter (1.5.2) + sass (~> 3.4) + jekyll-seo-tag (2.8.0) + jekyll (>= 3.8, < 5.0) + jekyll-sitemap (1.4.0) + jekyll (>= 3.7, < 5.0) + jekyll-swiss (1.0.0) + jekyll-theme-architect (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-cayman (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-dinky (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-hacker (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-leap-day (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-merlot (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-midnight (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-minimal (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-modernist (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-primer (0.6.0) + jekyll (> 3.5, < 5.0) + jekyll-github-metadata (~> 2.9) + jekyll-seo-tag (~> 2.0) + jekyll-theme-slate (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-tactile (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-theme-time-machine (0.2.0) + jekyll (> 3.5, < 5.0) + jekyll-seo-tag (~> 2.0) + jekyll-titles-from-headings (0.5.3) + jekyll (>= 3.3, < 5.0) + jekyll-watch (2.2.1) + listen (~> 3.0) + jemoji (0.12.0) + gemoji (~> 3.0) + html-pipeline (~> 2.2) + jekyll (>= 3.0, < 5.0) + kramdown (2.3.2) + rexml + kramdown-parser-gfm (1.1.0) + kramdown (~> 2.0) + liquid (4.0.4) + listen (3.8.0) + rb-fsevent (~> 0.10, >= 0.10.3) + rb-inotify (~> 0.9, >= 0.9.10) + mercenary (0.3.6) + minima (2.5.1) + jekyll (>= 3.5, < 5.0) + jekyll-feed (~> 0.9) + jekyll-seo-tag (~> 2.1) + minitest (5.20.0) + mutex_m (0.1.2) + nokogiri (1.15.4-x86_64-linux) + racc (~> 1.4) + octokit (4.25.1) + faraday (>= 1, < 3) + sawyer (~> 0.9) + pathutil (0.16.2) + forwardable-extended (~> 2.6) + public_suffix (4.0.7) + racc (1.7.1) + rb-fsevent (0.11.2) + rb-inotify (0.10.1) + ffi (~> 1.0) + rexml (3.2.6) + rouge (3.26.0) + ruby2_keywords (0.0.5) + rubyzip (2.3.2) + safe_yaml (1.0.5) + sass (3.7.4) + sass-listen (~> 4.0.0) + sass-listen (4.0.0) + rb-fsevent (~> 0.9, >= 0.9.4) + rb-inotify (~> 0.9, >= 0.9.7) + sawyer (0.9.2) + addressable (>= 2.3.5) + faraday (>= 0.17.3, < 3) + simpleidn (0.2.1) + unf (~> 0.1.4) + terminal-table (1.8.0) + unicode-display_width (~> 1.1, >= 1.1.1) + typhoeus (1.4.0) + ethon (>= 0.9.0) + tzinfo (2.0.6) + concurrent-ruby (~> 1.0) + unf (0.1.4) + unf_ext + unf_ext (0.0.8.2) + unicode-display_width (1.8.0) + webrick (1.8.1) + +PLATFORMS + x86_64-linux-musl + +DEPENDENCIES + github-pages + jekyll-include-cache + webrick (~> 1.8) + +BUNDLED WITH + 2.3.25 diff --git a/README.md b/README.md index 12bc4e8..1246346 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,70 @@ -# Terminology Infrastructure and Management Systems Group (TIMS Group) -Please see [our website](https://hot-ecosystem.github.io/tims/) for additional information. +# 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/ + +## 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. + +## More information +
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. + +* Run `docker compose up` and wait until you see `Server running... press ctrl-c to stop.` +* Go to http://localhost:4000 in your browser. +* Open the page you want to edit in the browser and in your editor. +* Make changes, save, and you should see the results in your browser in a few seconds. +* The console where you ran `docker compse up` should show some logging. It might be useful if you're having issues. +* Commit your changes and push to GitHub +* Changes should be visible on the GitHub Pages side once they're built and deployed. You can watch and confirm if the build and deployment succeeded [here](https://github.com/HOT-Ecosystem/tims/actions) +* `CTRL+C` in the terminal should stop the Docker container. + * 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. + +

+
+ +
Initial setup +

+ +## 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/ + +

+
+ +
Jekyll static site resources +

+ +## 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/ + +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) + +

+
+ +
Additional devops resources +

+ +### 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) + +

+
\ No newline at end of file diff --git a/_config.yml b/_config.yml new file mode 100644 index 0000000..e373bd2 --- /dev/null +++ b/_config.yml @@ -0,0 +1,80 @@ +# Welcome to Jekyll! +# +# This config file is meant for settings that affect your whole blog, values +# which you are expected to set up once and rarely edit after that. If you find +# yourself editing this file very often, consider using Jekyll's data files +# feature for the data you need to update frequently. +# +# For technical reasons, this file is *NOT* reloaded automatically when you use +# 'bundle exec jekyll serve'. If you change this file, please restart the server process. +# +# If you need help with YAML syntax, here are some quick references for you: +# https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml +# https://learnxinyminutes.com/docs/yaml/ +# +# Site settings +# These are used to personalize your new site. If you look in the HTML files, +# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on. +# You can create any custom variable you would like, and they will be accessible +# in the templates via {{ site.myvariable }}. + +title: TIMS +subtitle: Terminology Infrastructure Management Services Group +email: shahim@essaid.com +description: >- # this means to ignore newlines until "baseurl:" + Terminology Infrastructure Management Services Group +baseurl: "/tims-website" # 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 +github_username: HOT-Ecosystem + +# Build settings +remote_theme: "mmistakes/minimal-mistakes@4.24.0" +plugins: + - jekyll-feed + - jekyll-include-cache + +include: + - _pages + +defaults: + - scope: + path: "" + type: pages + values: + layout: single + author_profile: true + - scope: + path: "" + type: docs + values: + layout: single + author_profile: true + share: false + sidebar: + nav: docs + +collections: + docs: + output: true + permalink: /:collection/:path/ + +# Exclude from processing. +# The following items will not be processed, by default. +# Any item listed under the `exclude:` key here will be automatically added to +# the internal "default list". +# +# Excluded items can be processed by explicitly listing the directories or +# their entries' file path in the `include:` list. +# +# exclude: +# - .sass-cache/ +# - .jekyll-cache/ +# - gemfiles/ +# - Gemfile +# - Gemfile.lock +# - node_modules/ +# - vendor/bundle/ +# - vendor/cache/ +# - vendor/gems/ +# - vendor/ruby/ diff --git a/_config_local.yml b/_config_local.yml new file mode 100644 index 0000000..18cdff1 --- /dev/null +++ b/_config_local.yml @@ -0,0 +1,2 @@ +baseurl: "" # the subpath of your site, e.g. /blog +url: "https://localhost" # the base hostname & protocol for your site, e.g. http://example.com diff --git a/_data/navigation.yml b/_data/navigation.yml new file mode 100644 index 0000000..7984213 --- /dev/null +++ b/_data/navigation.yml @@ -0,0 +1,19 @@ +main: + - title: About + 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/ diff --git a/_docs/hapi.md b/_docs/hapi.md new file mode 100644 index 0000000..f7561ce --- /dev/null +++ b/_docs/hapi.md @@ -0,0 +1,5 @@ +--- +title: TIMS HAPI Server +--- + +TIMS HAPI Server page documentation. \ No newline at end of file diff --git a/_docs/site.md b/_docs/site.md new file mode 100644 index 0000000..6378007 --- /dev/null +++ b/_docs/site.md @@ -0,0 +1,10 @@ +--- +title: Contributing to this site and the blog +--- + +You can contribute to this site by editing various files [here](https://github.com/HOT-Ecosystem/tims/tree/gh-pages) + +* The top menu is configurable [here](https://github.com/HOT-Ecosystem/tims/tree/gh-pages/_data/navigation.yml) +* Additional pages get added [here](https://github.com/HOT-Ecosystem/tims/tree/gh-pages/_pages/) but will not show up unless they are linked from somewhere. There is a way to list all pages, as you can see for the `Documentation` section. This is even more configurable as we develop more pages. +* Posts can be added [here](https://github.com/HOT-Ecosystem/tims/tree/gh-pages/_posts/) by following the welcome example, and they will show up on the Blog page. +* You can add additional documentation pages [here](https://github.com/HOT-Ecosystem/tims/tree/gh-pages/_docs/) and then add them to the sidebar by editing the `docs` entry [here](https://github.com/HOT-Ecosystem/tims/tree/gh-pages/_data/navigation.yml) \ No newline at end of file diff --git a/_pages/about.md b/_pages/about.md new file mode 100644 index 0000000..c4b84df --- /dev/null +++ b/_pages/about.md @@ -0,0 +1,12 @@ +--- +title: About +permalink: / +--- + +### 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 +tims-team@tislab.org diff --git a/_pages/blog.md b/_pages/blog.md new file mode 100644 index 0000000..183adc4 --- /dev/null +++ b/_pages/blog.md @@ -0,0 +1,7 @@ +--- +title: Blog +permalink: /blog/ +layout: posts +--- + +Blog page content. \ No newline at end of file diff --git a/_pages/projects.md b/_pages/projects.md new file mode 100644 index 0000000..3ccaba2 --- /dev/null +++ b/_pages/projects.md @@ -0,0 +1,40 @@ +--- +title: Projects +permalink: /projects/ +--- + +All our projects are open source and can be found [on GitHub](https://github.com/HOT-Ecosystem). + +### 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://fhir.terminology-services.com]) +- [http://20.3.198.176:8080/](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/](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](https://github.com/HOT-Ecosystem/owl-on-fhir) + +### OMOP2OWL-vocab +Convert OMOP vocab into OWL and SemanticSQL. + +[https://github.com/HOT-Ecosystem/omop2owl-vocab](https://github.com/HOT-Ecosystem/omop2owl-vocab) + +### OMOP2FHIR-vocab +Convert OMOP vocab to FHIR. + +[https://github.com/HOT-Ecosystem/omop2fhir-vocab](https://github.com/HOT-Ecosystem/omop2fhir-vocab) + +### TimsUI +A minimalistic web UI for the TIMS terminology server. + +[https://github.com/HOT-Ecosystem/TimsUI](https://github.com/HOT-Ecosystem/TimsUI) diff --git a/_pages/team.md b/_pages/team.md new file mode 100644 index 0000000..297b83a --- /dev/null +++ b/_pages/team.md @@ -0,0 +1,16 @@ +--- +title: Team +permalink: /team/ +--- + + +Director: Melissa Haendel +Director: Chris Chute +Project Management: Lisa Eskenazi +Development: Shahim Essaid +Development: Joe Flack +Contributor: Davera Gabriel +Contributor: Sigfried Gold +Contributor: Stephanie Hong +Contributor: Tim Putman +Contributor: Chris Roeder diff --git a/_pages/terminology-server.md b/_pages/terminology-server.md new file mode 100644 index 0000000..2da9e98 --- /dev/null +++ b/_pages/terminology-server.md @@ -0,0 +1,51 @@ +--- +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://fhir.terminology-services.com) +- [http://20.3.198.176:8080/](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 +[//]: # (TODO: need to clarify this list) +**CodeSystems** +TIMS hosts several popular biomedical terminologies, but is unique in that it offers several biomedical ontologies in +the FHIR CodeSystem format, including: +* ICD10CM +* RxNorm +* SNOMED-CT +* Mondo +* HPO +* CompLoinc +* OMOP vocabularies + +A real-time listing of everything currently loaded can be found: [here](http://20.3.198.176:8080/fhir/CodeSystem?_summary=true) + +A list of next the code systems currently in the works can be found: [here](https://github.com/HOT-Ecosystem/hapi-issues/issues/4) + +**ConceptMap** +Many of the terminologies and ontologies also contain mappings to other terminologies/ontologies, and are represented +as FHIR ConceptMap resources. TIMS uniquely includes additional fields from the [SSSOM]( +https://mapping-commons.github.io/sssom/home/) extensions (Simple Standard fo Sharing Ontology Mappings) standard, +embedded as FHIR extensions. + +[//]: # (#### ValueSet) + +[//]: # (In development.) \ No newline at end of file diff --git a/_posts/2023-10-12-welcome-to-tims.markdown b/_posts/2023-10-12-welcome-to-tims.markdown new file mode 100644 index 0000000..7abe082 --- /dev/null +++ b/_posts/2023-10-12-welcome-to-tims.markdown @@ -0,0 +1,8 @@ +--- +layout: single +title: "Welcome to TIMS!" +date: 2023-10-12 10:30:00 -0700 +categories: [tims] +--- + +Welcome to TIMS Blog post. diff --git a/about.markdown.off b/about.markdown.off new file mode 100644 index 0000000..5c4b7d0 --- /dev/null +++ b/about.markdown.off @@ -0,0 +1,18 @@ +--- +layout: single +title: About +permalink: /about/ +--- + +This is the base Jekyll theme. You can find out more info about customizing your Jekyll theme, as well as basic Jekyll usage documentation at [jekyllrb.com](https://jekyllrb.com/) + +You can find the source code for Minima at GitHub: +[jekyll][jekyll-organization] / +[minima](https://github.com/jekyll/minima) + +You can find the source code for Jekyll at GitHub: +[jekyll][jekyll-organization] / +[jekyll](https://github.com/jekyll/jekyll) + + +[jekyll-organization]: https://github.com/jekyll diff --git a/docker-compose.yaml b/docker-compose.yaml new file mode 100644 index 0000000..90b5486 --- /dev/null +++ b/docker-compose.yaml @@ -0,0 +1,25 @@ +services: + jekyll: + build: + context: ./docker + + volumes: + - type: bind + source: ./ + target: /srv/jekyll + + ports: + - target: 4000 + published: 4000 + - target: 35729 + published: 35729 + # command: ["jekyll", "serve", "-l"] + environment: + - JEKYLL_LOG_LEVEL=debug + command: [ "jekyll", "serve", "-l", "--config", "_config.yml,_config_local.yml" ] + + +# stdin_open: true +# tty: true +# entrypoint: ["bash"] + diff --git a/docker/Dockerfile b/docker/Dockerfile new file mode 100644 index 0000000..7a16997 --- /dev/null +++ b/docker/Dockerfile @@ -0,0 +1 @@ +FROM jekyll/jekyll:4 diff --git a/index.markdown.off b/index.markdown.off new file mode 100644 index 0000000..cf94508 --- /dev/null +++ b/index.markdown.off @@ -0,0 +1,9 @@ +--- +layout: home +author_profile: true +--- + +TIMS home page. + +See the [Minimal Mistakes](https://mmistakes.github.io/minimal-mistakes/) for how this site can look out of the box. See +the [README.md](https://github.com/HOT-Ecosystem/tims/tree/gh-pages) for getting started with using this setup.