NanoCommons · egonw · Jan 11, 2024 · Sep 15, 2023 · Sep 15, 2023 · Sep 18, 2023
diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
@@ -0,0 +1,94 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# Note: added step to capitalize the ERMs
+# Note: if deploy fails, remove deployment branches and tags restrictions for the environment github-pages from /erm-database/settings/environments
+
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Custom Deploy Jekyll site to Pages
+
+on:
+  push:
+    branches: ["data-setup"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@8575951200e472d5f2d95c625da0c7bec8217c42 # v1.161.0
+        with:
+          ruby-version: '3.1' # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+          cache-version: 0 # Increment this number if you need to re-download cached gems
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v4
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          JEKYLL_ENV: production
+      - name: fix capitalization for ERM* pages
+        env:
+            JEKYLL_ENV: production
+        run: |
+            # Navigate to the directory containing the erm
+            cd _site/substance/erm
+            echo before:
+            ls
+
+            # Loop through all files containing 'erm*'
+            for file in erm*; do
+                # Check if the file exists
+                if [ -e "$file" ]; then
+                    # Create the new file name with 'ERM'
+                    new_name=$(echo "$file" | sed 's/erm/ERM/')
+
+                    # Rename the file
+                    mv "$file" "$new_name"
+
+                    echo "Renamed: $file to $new_name"
+                fi
+            done 
+            echo after:
+            ls
+      - name: Upload artifact
+        # Automatically uploads an artifact from the './_site' directory by default
+        uses: actions/upload-pages-artifact@v3
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+    permissions:
+     contents: read
+     pages: write
+     id-token: write
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,4 @@ _site/
 # Ignore folders generated by Bundler
 .bundle/
 vendor/
+_data/nanomiles/data.tsv
diff --git a/Gemfile b/Gemfile
@@ -20,6 +20,7 @@ group :jekyll_plugins do
   gem 'jekyll-seo-tag'
   gem 'jekyll-sitemap'
   gem 'jekyll-paginate'
+  gem 'jekyll-datapage-generator'
 end
 
 # Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -31,6 +31,7 @@ GEM
       safe_yaml (~> 1.0)
       terminal-table (>= 1.8, < 4.0)
       webrick (~> 1.7)
+    jekyll-datapage-generator (1.4.0)
     jekyll-feed (0.17.0)
       jekyll (>= 3.7, < 5.0)
     jekyll-mastodon_webfinger (1.0.2)
@@ -81,6 +82,7 @@ PLATFORMS
 DEPENDENCIES
   http_parser.rb (~> 0.6.0)
   jekyll (~> 4.3.2)
+  jekyll-datapage-generator
   jekyll-feed (~> 0.12)
   jekyll-mastodon_webfinger (~> 1.0)
   jekyll-paginate

diff --git a/_config.yml b/_config.yml
@@ -13,8 +13,18 @@ plugins:
   - jekyll-seo-tag
   - jekyll/mastodon_webfinger
   - jekyll-paginate
+  - jekyll-datapage-generator
 
 feed:
   tags: true
 
 tags:
+
+### Page generator from _data files
+
+page_gen:
+- data: "erm"
+  template: "substance"
+  dir: "substance/erm/"
+  name_expr: "record['id']"
+  title_expr: "record['title']"
diff --git a/_data/enmo/CHEBI:23367.yml b/_data/enmo/CHEBI:23367.yml
@@ -0,0 +1,4 @@
+label: molecular entity
+URI: http://purl.obolibrary.org/obo/CHEBI_23367
+curie: CHEBI:23367
+a: obo:BFO_0000040
diff --git a/_data/enmo/npo:NPO_1486.yml b/_data/enmo/npo:NPO_1486.yml
@@ -0,0 +1,4 @@
+label: titanium oxide nanoparticle
+URI: http://purl.bioontology.org/ontology/npo#NPO_1486
+curie: npo:NPO_1486
+a: npo:NPO_707
diff --git a/_data/enmo/npo:NPO_1542.yml b/_data/enmo/npo:NPO_1542.yml
@@ -0,0 +1,4 @@
+label: zinc oxide nanoparticle
+URI: http://purl.bioontology.org/ontology/npo#NPO_1542
+curie: npo:NPO_1542
+a: npo:NPO_707
diff --git a/_data/enmo/npo:NPO_707.yml b/_data/enmo/npo:NPO_707.yml
@@ -0,0 +1,4 @@
+label: nanoparticle
+URI: http://purl.bioontology.org/ontology/npo#NPO_707
+curie: npo:NPO_707
+a: CHEBI_23367
diff --git a/_data/enmo/obo:BFO_0000040.yml b/_data/enmo/obo:BFO_0000040.yml
@@ -0,0 +1,3 @@
+label: material entity
+URI: http://purl.obolibrary.org/obo/BFO_0000040
+curie: obo:BFO_0000040
diff --git a/_data/erm/ERM00000063.yml b/_data/erm/ERM00000063.yml
@@ -0,0 +1,14 @@
+title: "Material: ERM00000063"
+type: ChemicalSubstance
+id: ERM00000063
+tag: erm:ERM00000063
+chemicalComposition: ZnO
+tags: doi:10.3389/FTOX.2022.981701 erm:ERM00000063
+scholarlyArticleDOI: [10.3389/ftox.2022.981701]
+datasetDOI:
+a: npo:NPO_1542 # TODO It is not technically a nanoparticle but a nanoparticle 
+otherLinks: 
+  - name:
+    url: https://www.sigmaaldrich.com/NL/en/sds/aldrich/721077
+    title: SAFETY DATA SHEET - Sigma-Aldrich
+    type: pdf
diff --git a/_data/erm/ERM00000064.yml b/_data/erm/ERM00000064.yml
@@ -0,0 +1,15 @@
+title: "Material: ERM00000064"
+type: ChemicalSubstance
+id: ERM00000064
+tag: erm:ERM00000064
+tags: erm:ERM00000064 10.3389/ftox.2022.981701
+chemicalComposition: TiO2
+scholarlyArticleDOI: [10.3389/ftox.2022.981701]
+datasetDOI: 
+a: npo:NPO_1486
+otherLinks: 
+ - url: https://joint-research-centre.ec.europa.eu/system/files/2016-06/JRC%2520Nanomaterials%2520Repository-List%2520of%2520Representative%2520Nanomaterials-201606.pdf
+   title: EUROPEAN COMMISSION JOINT RESEARCH CENTRE JRC NANOMATERIALS REPOSITORY - List of Representative Nanomaterials
+   type: pdf
+cas: 13463-67-7
+sameAs: [JRCNM01005a]
diff --git a/substance/ERM00000397.markdown → _data/erm/ERM00000397.yml b/substance/ERM00000397.markdown → _data/erm/ERM00000397.yml
@@ -1,7 +1,5 @@
----
-layout: substance
 title: "Material: ERM00000397"
 type: ChemicalSubstance
+id: ERM00000397
 tag: erm:ERM00000397
-chemicalComposition: CeO2/Co3O4
----
+a: CHEBI:23367
diff --git a/substance/ERM00000400.markdown → _data/erm/ERM00000400.yml b/substance/ERM00000400.markdown → _data/erm/ERM00000400.yml
@@ -1,7 +1,6 @@
----
-layout: substance
 title: "Material: ERM00000400"
 type: ChemicalSubstance
-tag: erm:ERM00000400
+id: ERM00000400
 chemicalComposition: Ce0.75Zr0.25O2
----
+a: owl:Thing
+tag: erm:ERM00000400
diff --git a/substance/ERM00000403.markdown → _data/erm/ERM00000403.yml b/substance/ERM00000403.markdown → _data/erm/ERM00000403.yml
@@ -1,7 +1,6 @@
----
-layout: substance
 title: "Material: ERM00000403"
 type: ChemicalSubstance
-tag: erm:ERM00000403
+id: ERM00000403
 chemicalComposition: Ce0.1Zr0.9O2
----
+a: owl:Thing
+tag: erm:ERM00000403
diff --git a/substance/ERM00000409.markdown → _data/erm/ERM00000409.yml b/substance/ERM00000409.markdown → _data/erm/ERM00000409.yml
@@ -1,7 +1,6 @@
----
-layout: substance
 title: "Material: ERM00000409"
 type: ChemicalSubstance
-tag: erm:ERM00000409
+id: ERM00000409
 chemicalComposition: Fe3O4
----
+a: owl:Thing
+tag: erm:ERM00000409
diff --git a/_data/erm/ERM00000416.yml b/_data/erm/ERM00000416.yml
@@ -0,0 +1,8 @@
+layout: substance
+title: "Material: ERM00000416"
+id: ERM00000416
+tags: doi:10.5281/ZENODO.7940162 ERM00000416
+chemicalComposition: ZnO
+datasetDOI: 10.5281/ZENODO.7940162
+a: npo:NPO_1542
+tag: erm:ERM00000416
diff --git a/substance/ERM00000421.markdown → _data/erm/ERM00000421.yml b/substance/ERM00000421.markdown → _data/erm/ERM00000421.yml
@@ -1,7 +1,6 @@
----
-layout: substance
 title: "Material: ERM00000421"
 type: ChemicalSubstance
-tag: erm:ERM00000421
+id: ERM00000421
 chemicalComposition: Ce0.75Zr0.25O2
----
+a: owl:Thing
+tag: erm:ERM00000421
diff --git a/substance/ERM00000424.markdown → _data/erm/ERM00000424.yml b/substance/ERM00000424.markdown → _data/erm/ERM00000424.yml
@@ -1,7 +1,6 @@
----
-layout: substance
 title: "Material: ERM00000424"
 type: ChemicalSubstance
-tag: erm:ERM00000424
+id: ERM00000424
 chemicalComposition: Ce0.1Zr0.9O2
----
+a: CHEBI:23367
+tag: erm:ERM00000424
diff --git a/substance/ERM00000442.markdown → _data/erm/ERM00000442.yml b/substance/ERM00000442.markdown → _data/erm/ERM00000442.yml
@@ -1,7 +1,7 @@
----
 layout: substance
 title: "Material: ERM00000442"
 type: ChemicalSubstance
-tag: erm:ERM00000442
+id: ERM00000442
 chemicalComposition: Ce0.75Zr0.25O2
----
+a: owl:Thing
+tag: erm:ERM00000442
diff --git a/substance/ERM00000445.markdown → _data/erm/ERM00000445.yml b/substance/ERM00000445.markdown → _data/erm/ERM00000445.yml
@@ -1,7 +1,6 @@
----
-layout: substance
 title: "Material: ERM00000445"
 type: ChemicalSubstance
-tag: erm:ERM00000445
+id: ERM00000445
 chemicalComposition: Ce0.1Zr0.9O2
----
+a: CHEBI:23367
+tag: erm:ERM00000445
diff --git a/substance/ERM00000582.markdown → _data/erm/ERM00000582.yml b/substance/ERM00000582.markdown → _data/erm/ERM00000582.yml
@@ -1,8 +1,8 @@
----
-layout: substance
 title: "Material: ERM00000582"
 type: ChemicalSubstance
-tag: erm:ERM00000582
-tags: doi:10.5281/ZENODO.7990251
+id: ERM00000582
 chemicalSubstance: Au
----
+datasetDOI: [10.5281/ZENODO.7990251]
+a: CHEBI:23367
+tag: erm:ERM00000582
+sameAs: [RiskGONE NM 18]
diff --git a/_data/erm/ERM00000583.yml b/_data/erm/ERM00000583.yml
@@ -0,0 +1,7 @@
+title: "Material: ERM00000583"
+id: ERM00000583
+chemicalComposition: Fe3O4
+datasetDOI: [10.5281/ZENODO.7990302]
+a: CHEBI:23367
+tag: erm:ERM00000583
+sameAs: [RiskGONE NM 19]
diff --git a/substance/ERM00000584.markdown → _data/erm/ERM00000584.yml b/substance/ERM00000584.markdown → _data/erm/ERM00000584.yml
@@ -1,12 +1,9 @@
----
-layout: substance
 title: "Material: ERM00000584"
 type: ChemicalSubstance
-tag: erm:ERM00000584
+id: ERM00000584
 chemicalComposition: ZnO
 tags: doi:10.5281/ZENODO.7990214
----
-
-### Datasets
-
-* [10.5281/ZENODO.7990214](https://doi.org/10.5281/ZENODO.7990214)
+datasetDOI: [10.5281/ZENODO.7990214]
+a: npo:NPO_1542
+tag: erm:ERM00000584
+sameAs: [RiskGONE NM 20]
diff --git a/_data/work/10.1186/S13321-022-00614-7.yml b/_data/work/10.1186/S13321-022-00614-7.yml
@@ -0,0 +1,5 @@
+title: "Work: European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials"
+type:  ScholarlyArticle
+tag:  doi:10.1186/S13321-022-00614-7
+doi:  doi:10.1186/S13321-022-00614-7
+uri: https://doi.org/doi:10.1186/S13321-022-00614-7
diff --git a/_data/work/10.3389/FTOX.2022.981701.yml b/_data/work/10.3389/FTOX.2022.981701.yml
@@ -0,0 +1,5 @@
+title: "Work: The alamar blue assay in the context of safety testing of nanomaterials"
+type:  ScholarlyArticle
+tag:  doi:10.3389/FTOX.2022.981701
+doi:  doi:10.3389/FTOX.2022.981701
+uri: https://doi.org/doi:10.3389/FTOX.2022.981701
diff --git a/_data/work/10.5281/ZENODO.7940162.yml b/_data/work/10.5281/ZENODO.7940162.yml
@@ -0,0 +1,5 @@
+title: "Work: Physico-chemical characterization of sterilized ZnO nanoparticles by XPS / HAXPES / SEM"
+type:  Dataset
+tag:  doi:10.5281/ZENODO.7940162
+doi:  10.5281/ZENODO.7940162
+uri: https://doi.org/10.5281/ZENODO.7940162
diff --git a/_data/work/10.5281/ZENODO.7965603.yml b/_data/work/10.5281/ZENODO.7965603.yml
@@ -0,0 +1,5 @@
+title: "Work: Physico-chemical characterization of sterilized Ce0.1Zr0.9O2 nanoparticles by XPS / HAXPES / SEM"
+type:  Dataset
+tag:  doi:10.5281/ZENODO.7965603
+doi:  doi:10.5281/ZENODO.7965603
+uri: https://doi.org/doi:10.5281/ZENODO.7965603
diff --git a/_data/work/10.5281/ZENODO.7966134.yml b/_data/work/10.5281/ZENODO.7966134.yml
@@ -0,0 +1,5 @@
+title: "Work: Physico-chemical characterization of sterilized Ce0.75Zr0.25O2 nanoparticles by XPS / HAXPES / SEM"
+type:  Dataset
+tag:  doi:10.5281/ZENODO.7966134
+doi:  doi:10.5281/ZENODO.7966134
+uri: https://doi.org/doi:10.5281/ZENODO.7966134
diff --git a/_data/work/10.5281/ZENODO.7989699.yml b/_data/work/10.5281/ZENODO.7989699.yml
@@ -0,0 +1,5 @@
+title: "Work: Physico-chemical characterization of CeO2/Co3O4 nanoparticles by XPS / HAXPES / SEM"
+type:  Dataset
+tag:  doi:10.5281/ZENODO.7989699
+doi:  doi:10.5281/ZENODO.7989699
+uri: https://doi.org/doi:10.5281/ZENODO.7989699
diff --git a/_data/work/10.5281/ZENODO.7990086.yml b/_data/work/10.5281/ZENODO.7990086.yml
@@ -0,0 +1,5 @@
+title: "Work: Physico-chemical characterization of Fe3O4 nanoparticles by XPS / HAXPES / SEM"
+type:  Dataset
+tag:  doi:10.5281/ZENODO.7990086
+doi:  doi:10.5281/ZENODO.7990086
+uri: https://doi.org/doi:10.5281/ZENODO.7990086