diff --git a/.github/workflows/placeholder_create_erm_datasets b/.github/workflows/placeholder_create_erm_datasets new file mode 100644 index 0000000..e69de29 diff --git a/.github/workflows/placeholder_create_erm_literature b/.github/workflows/placeholder_create_erm_literature new file mode 100644 index 0000000..e69de29 diff --git a/.gitignore b/.gitignore index 74a9223..1059128 100644 --- 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 index 317d89c..4cd6edd 100644 --- 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 index 438c75f..ed43e83 100644 --- 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 index 4b23f56..544cb3f 100644 --- 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'].sub('ERM', '')" + title_expr: "record['title']" \ No newline at end of file diff --git a/_data/enmo/CHEBI:23367.yml b/_data/enmo/CHEBI:23367.yml new file mode 100644 index 0000000..48f46bb --- /dev/null +++ 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 \ No newline at end of file diff --git a/_data/enmo/npo:NPO_1486.yml b/_data/enmo/npo:NPO_1486.yml new file mode 100644 index 0000000..fae26f0 --- /dev/null +++ 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 \ No newline at end of file diff --git a/_data/enmo/npo:NPO_1542.yml b/_data/enmo/npo:NPO_1542.yml new file mode 100644 index 0000000..ca382ad --- /dev/null +++ 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 \ No newline at end of file diff --git a/_data/enmo/npo:NPO_707.yml b/_data/enmo/npo:NPO_707.yml new file mode 100644 index 0000000..f84e240 --- /dev/null +++ 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 \ No newline at end of file diff --git a/_data/enmo/obo:BFO_0000040.yml b/_data/enmo/obo:BFO_0000040.yml new file mode 100644 index 0000000..5e8b30e --- /dev/null +++ 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 \ No newline at end of file diff --git a/_data/erm/ERM00000063.yml b/_data/erm/ERM00000063.yml new file mode 100644 index 0000000..4a19e9b --- /dev/null +++ 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 \ No newline at end of file diff --git a/_data/erm/ERM00000064.yml b/_data/erm/ERM00000064.yml new file mode 100644 index 0000000..7b35300 --- /dev/null +++ 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] \ No newline at end of file diff --git a/substance/ERM00000397.markdown b/_data/erm/ERM00000397.yml similarity index 56% rename from substance/ERM00000397.markdown rename to _data/erm/ERM00000397.yml index b43acb6..b47078f 100644 --- a/substance/ERM00000397.markdown +++ b/_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 \ No newline at end of file diff --git a/substance/ERM00000400.markdown b/_data/erm/ERM00000400.yml similarity index 65% rename from substance/ERM00000400.markdown rename to _data/erm/ERM00000400.yml index ae5c555..2f6f784 100644 --- a/substance/ERM00000400.markdown +++ b/_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 \ No newline at end of file diff --git a/substance/ERM00000403.markdown b/_data/erm/ERM00000403.yml similarity index 64% rename from substance/ERM00000403.markdown rename to _data/erm/ERM00000403.yml index 1f814a7..dcf8b0b 100644 --- a/substance/ERM00000403.markdown +++ b/_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 \ No newline at end of file diff --git a/substance/ERM00000409.markdown b/_data/erm/ERM00000409.yml similarity index 62% rename from substance/ERM00000409.markdown rename to _data/erm/ERM00000409.yml index 0d6b85f..edcd0e7 100644 --- a/substance/ERM00000409.markdown +++ b/_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 \ No newline at end of file diff --git a/_data/erm/ERM00000416.yml b/_data/erm/ERM00000416.yml new file mode 100644 index 0000000..51b049f --- /dev/null +++ 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 \ No newline at end of file diff --git a/substance/ERM00000421.markdown b/_data/erm/ERM00000421.yml similarity index 65% rename from substance/ERM00000421.markdown rename to _data/erm/ERM00000421.yml index af92a1d..45628c3 100644 --- a/substance/ERM00000421.markdown +++ b/_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 \ No newline at end of file diff --git a/substance/ERM00000424.markdown b/_data/erm/ERM00000424.yml similarity index 63% rename from substance/ERM00000424.markdown rename to _data/erm/ERM00000424.yml index baa7e2a..c42f1a9 100644 --- a/substance/ERM00000424.markdown +++ b/_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 \ No newline at end of file diff --git a/substance/ERM00000442.markdown b/_data/erm/ERM00000442.yml similarity index 68% rename from substance/ERM00000442.markdown rename to _data/erm/ERM00000442.yml index 36e73f7..f0d5dd9 100644 --- a/substance/ERM00000442.markdown +++ b/_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 \ No newline at end of file diff --git a/substance/ERM00000445.markdown b/_data/erm/ERM00000445.yml similarity index 63% rename from substance/ERM00000445.markdown rename to _data/erm/ERM00000445.yml index 033eda7..43836f2 100644 --- a/substance/ERM00000445.markdown +++ b/_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 \ No newline at end of file diff --git a/substance/ERM00000582.markdown b/_data/erm/ERM00000582.yml similarity index 51% rename from substance/ERM00000582.markdown rename to _data/erm/ERM00000582.yml index f464566..7338b18 100644 --- a/substance/ERM00000582.markdown +++ b/_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] \ No newline at end of file diff --git a/_data/erm/ERM00000583.yml b/_data/erm/ERM00000583.yml new file mode 100644 index 0000000..ea6150a --- /dev/null +++ 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] \ No newline at end of file diff --git a/substance/ERM00000584.markdown b/_data/erm/ERM00000584.yml similarity index 55% rename from substance/ERM00000584.markdown rename to _data/erm/ERM00000584.yml index 9cf4318..703ff72 100644 --- a/substance/ERM00000584.markdown +++ b/_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] \ No newline at end of file diff --git a/_data/work/10.1186/S13321-022-00614-7.yml b/_data/work/10.1186/S13321-022-00614-7.yml new file mode 100644 index 0000000..ae0fe5b --- /dev/null +++ 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 new file mode 100644 index 0000000..e6292bb --- /dev/null +++ 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 new file mode 100644 index 0000000..a0ce393 --- /dev/null +++ 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 new file mode 100644 index 0000000..6198792 --- /dev/null +++ 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 new file mode 100644 index 0000000..5092b69 --- /dev/null +++ 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 new file mode 100644 index 0000000..a1be2f5 --- /dev/null +++ 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 new file mode 100644 index 0000000..9137ce2 --- /dev/null +++ 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 diff --git a/_data/work/10.5281/ZENODO.7990214.yml b/_data/work/10.5281/ZENODO.7990214.yml new file mode 100644 index 0000000..d686cc3 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7990214.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of sterile ZnO nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990214 +doi: doi:10.5281/ZENODO.7990214 +uri: https://doi.org/doi:10.5281/ZENODO.7990214 diff --git a/_data/work/10.5281/ZENODO.7990251.yml b/_data/work/10.5281/ZENODO.7990251.yml new file mode 100644 index 0000000..903a273 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7990251.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of sterile citrated stabilized Au nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990251 +doi: doi:10.5281/ZENODO.7990251 +uri: https://doi.org/doi:10.5281/ZENODO.7990251 diff --git a/_data/work/10.5281/ZENODO.7990302.yml b/_data/work/10.5281/ZENODO.7990302.yml new file mode 100644 index 0000000..daea4c4 --- /dev/null +++ b/_data/work/10.5281/ZENODO.7990302.yml @@ -0,0 +1,5 @@ +title: "Work: Physico-chemical characterization of sterile Fe3O4 nanoparticles by XPS / HAXPES / SEM" +type: Dataset +tag: doi:10.5281/ZENODO.7990302 +doi: 10.5281/ZENODO.7990302 +uri: https://doi.org/10.5281/ZENODO.7990302 diff --git a/_data/work/10.5281/ZENODO.8015080.yml b/_data/work/10.5281/ZENODO.8015080.yml new file mode 100644 index 0000000..3d3a5f2 --- /dev/null +++ b/_data/work/10.5281/ZENODO.8015080.yml @@ -0,0 +1,5 @@ +title: "Work: Ontology IRIs for the JRC representative industrial nanomaterials" +type: Report +tag: doi:10.5281/ZENODO.8015080 +doi: doi:10.5281/ZENODO.8015080 +uri: https://doi.org/doi:10.5281/ZENODO.8015080 diff --git a/_includes/collecttags.html b/_includes/collecttags.html deleted file mode 100644 index 7a3092e..0000000 --- a/_includes/collecttags.html +++ /dev/null @@ -1,19 +0,0 @@ - -{% assign rawtags = "" %} -{% for post in site.posts %} - {% assign ttags = post.tags | join:'|' | append:'|' %} - {% assign rawtags = rawtags | append:ttags %} -{% endfor %} -{% assign rawtags = rawtags | split:'|' | sort %} - -{% assign site.tags = "" %} -{% for tag in rawtags %} - {% if tag != "" %} - {% if tags == "" %} - {% assign tags = tag | split:'|' %} - {% endif %} - {% unless tags contains tag %} - {% assign tags = tags | join:'|' | append:'|' | append:tag | split:'|' %} - {% endunless %} - {% endif %} -{% endfor %} diff --git a/_includes/head.html b/_includes/head.html index 1a62f76..e22765f 100644 --- a/_includes/head.html +++ b/_includes/head.html @@ -5,11 +5,6 @@ {%- seo -%} - {%- feed_meta -%} - - {% if site.tags != "" %} - {% include collecttags.html %} - {% endif %} diff --git a/_includes/header.html b/_includes/header.html index 81bdfcc..8ebd3fe 100644 --- a/_includes/header.html +++ b/_includes/header.html @@ -24,6 +24,7 @@ {% elsif my_page.title contains "Molecule:" %} {% elsif my_page.title contains "Material:" %} {% elsif my_page.title contains "Work:" %} + {% elsif my_page.title contains "class" %} {% elsif my_page.title %} {{ my_page.title | escape }} {% endif %} diff --git a/_layouts/substance.html b/_layouts/substance.html index eabcb81..6fbd964 100644 --- a/_layouts/substance.html +++ b/_layouts/substance.html @@ -17,6 +17,17 @@
| ERM ID | +Ontology class | +CURIE | +Chemical Composition | +In Dataset | +Same As | +
|---|