From 8efbf15c97016f29fc007016f75ffe77050dd671 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marek=20Such=C3=A1nek?= Date: Thu, 8 Dec 2022 12:22:08 +0100 Subject: [PATCH 001/126] Use GitHub Actions for Jekyll and GitHub Pages --- .github/workflows/jekyll.yml | 78 +++++++++++++++++++++++--- .github/workflows/list_conversion.yml | 21 ++++++- .github/workflows/list_validation.yml | 13 ++++- Gemfile | 22 +++++++- Makefile | 15 +++++ _config.yml | 1 + _includes/dev-info.html | 3 + _plugins/jekyll-github-metadata-fix.rb | 13 +++++ index.html | 1 + 9 files changed, 153 insertions(+), 14 deletions(-) create mode 100644 Makefile create mode 100644 _includes/dev-info.html create mode 100644 _plugins/jekyll-github-metadata-fix.rb diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml index 5a4e76448..4ca216380 100644 --- a/.github/workflows/jekyll.yml +++ b/.github/workflows/jekyll.yml @@ -1,16 +1,78 @@ name: Jekyll site CI on: - pull_request: - branches: [ master ] + push: + workflow_dispatch: + +permissions: + contents: read + pages: write + id-token: write jobs: build: runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v3 + + - name: Setup Ruby + uses: ruby/setup-ruby@v1.127.0 + with: + ruby-version: '3.1' + bundler-cache: true + cache-version: 0 + + - name: Setup Pages + id: pages + uses: actions/configure-pages@v2 + + - name: Set Jekyll environment + id: name + run: | + if [ "$REPO_OWNER" == "elixir-europe" ]; then + echo "jekyll_env=production" >> $GITHUB_OUTPUT + else + echo "jekyll_env=development" >> $GITHUB_OUTPUT + fi + env: + REPO_OWNER: ${{ github.repository_owner }} + + - name: Install dependencies + run: | + bundle install + + - name: Build with Jekyll + # Outputs to the './_site' directory by default + run: | + bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" + env: + PAGES_REPO_NWO: ${{ github.repository }} + GITHUB_BRANCH: ${{ github.ref_name }} + JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }} + JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + - name: Upload artifact + uses: actions/upload-pages-artifact@v1 + + deploy: + runs-on: ubuntu-latest + needs: build + + if: | + github.event_name == 'workflow_dispatch' || + (github.event_name == 'push' && github.event.repository.default_branch == github.ref_name) + + concurrency: + group: "pages" + cancel-in-progress: true + + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: - - uses: actions/checkout@v2 - - name: Build the site in the jekyll/builder container - run: | - docker run \ - -v ${{ github.workspace }}:/srv/jekyll --env PAGES_REPO_NWO=${{github.repository}} -v ${{ github.workspace }}/_site:/srv/jekyll/_site \ - jekyll/builder:3.8.6 /bin/bash -c "gem install github-pages --no-document && chmod 777 /srv/jekyll && jekyll build" + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v1 diff --git a/.github/workflows/list_conversion.yml b/.github/workflows/list_conversion.yml index 0e8a3012e..b781b8ccc 100644 --- a/.github/workflows/list_conversion.yml +++ b/.github/workflows/list_conversion.yml @@ -4,45 +4,62 @@ on: schedule: - cron: '0 13 * * 1' workflow_dispatch: + jobs: build: runs-on: ubuntu-latest + + if: github.repository_owner == 'elixir-europe' + strategy: matrix: python-version: [3.8] + steps: - name: Checkout uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} + - name: Install dependencies run: | python -m pip install --upgrade pip pip install pyyaml requests python-frontmatter + - name: Run tool table 2 yaml run: | python var/conversions.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}" + - name: Fetch country names with corresponding iso run: | python var/country_list.py + - name: Update markdown pages with DSW links run: | python var/dsw_integration.py + - name: Get faircookbook-rdmkit repository uses: actions/checkout@v3 with: repository: elixir-europe/faircookbook-rdmkit path: faircookbook-rdmkit ref: main + - name: Update markdown pages with FAIR Cookbook links run: | python var/faircookbook_integration.py ${GITHUB_WORKSPACE}/faircookbook-rdmkit/faircookbook_rdmkit_mapping.yml + - name: Deleting faircookbook-rdmkit repository - run: rm -r faircookbook-rdmkit + run: | + rm -r faircookbook-rdmkit + - name: Show differences - run: 'git diff --stat' + run: | + git diff --stat + - name: Create Pull Request id: cpr uses: peter-evans/create-pull-request@v3 diff --git a/.github/workflows/list_validation.yml b/.github/workflows/list_validation.yml index 255946d2c..3d37bb45a 100644 --- a/.github/workflows/list_validation.yml +++ b/.github/workflows/list_validation.yml @@ -3,24 +3,33 @@ name: Validating the tool and resource table on: pull_request: branches: [ master ] + jobs: build: runs-on: ubuntu-latest + strategy: matrix: python-version: [3.8] + steps: - - uses: actions/checkout@v2 + - name: Checkout + uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} + - name: Install dependencies run: | python -m pip install --upgrade pip pip install pyyaml requests python-frontmatter + - name: Run tool table 2 yaml run: | python var/conversions.py + - name: Show differences - run: 'git diff --stat' + run: | + git diff --stat diff --git a/Gemfile b/Gemfile index 47909af85..44112daf6 100644 --- a/Gemfile +++ b/Gemfile @@ -1,5 +1,23 @@ source "https://rubygems.org" +gem "jekyll", "~> 3.9" +gem "jemoji", "~> 0.5.1" +gem "kramdown-parser-gfm", "~> 1.1" +gem "minima", "~> 2.5" +gem "webrick", "~> 1.7" + group :jekyll_plugins do - gem "github-pages" - end + gem "jekyll-feed", "~> 0.12" + gem "jekyll-github-metadata", "~> 2.15.0" + gem "jekyll-redirect-from", "~> 0.16.0" + gem "jekyll-remote-theme", "~> 0.4.3" + gem "jekyll-sitemap", "~> 1.4" +end + +platforms :mingw, :x64_mingw, :mswin, :jruby do + gem "tzinfo", ">= 1", "< 3" + gem "tzinfo-data" +end + +gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin] +gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby] diff --git a/Makefile b/Makefile new file mode 100644 index 000000000..ddac83d78 --- /dev/null +++ b/Makefile @@ -0,0 +1,15 @@ +.PHONY: install +install: + bundle install + +.PHONY: dev +dev: + JEKYLL_ENV=development bundle exec jekyll serve --livereload --incremental + +.PHONY: build +build: + JEKYLL_ENV=production bundle exec jekyll build + +.PHONY: clean +clean: + rm -rf _site .bundle .jekyll-cache .jekyll-metadata .sass-cache vendor diff --git a/_config.yml b/_config.yml index 3f0d3559d..b6474ec52 100644 --- a/_config.yml +++ b/_config.yml @@ -26,6 +26,7 @@ theme_variables: exclude: - README.md + - vendor defaults: - diff --git a/_includes/dev-info.html b/_includes/dev-info.html new file mode 100644 index 000000000..05854b96b --- /dev/null +++ b/_includes/dev-info.html @@ -0,0 +1,3 @@ +
+ Development build for {{ site.github.repository_nwo }}@{{ site.github.build_revision | slice: 0, 7 }} (branch: {{ site.github.source.branch }}) +
diff --git a/_plugins/jekyll-github-metadata-fix.rb b/_plugins/jekyll-github-metadata-fix.rb new file mode 100644 index 000000000..36ef0b4bd --- /dev/null +++ b/_plugins/jekyll-github-metadata-fix.rb @@ -0,0 +1,13 @@ +# As GitHub Actions are used for GitHub Pages, the branch must be set via environment variable +module Jekyll + module GitHubMetadata + class Repository + def source + { + "branch" => ENV["GITHUB_BRANCH"] || "?", + "path" => ENV["BASE_PATH"] || "/", + } + end + end + end +end diff --git a/index.html b/index.html index e4ebbaf4d..438649883 100644 --- a/index.html +++ b/index.html @@ -8,6 +8,7 @@ {% include head.html %} + {% if jekyll.environment == "development" %}{% include dev-info.html %}{% endif %} {% include topnav.html search=false %}
From ba7ed76f6f80d8ca66c92a7f2ce0a6e81e2f7ce4 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Thu, 8 Dec 2022 17:02:01 +0100 Subject: [PATCH 002/126] remote theme --- _config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_config.yml b/_config.yml index 3f0d3559d..7ebf6b392 100644 --- a/_config.yml +++ b/_config.yml @@ -4,7 +4,7 @@ title: RDMkit description: "Best practices and guidelines you can use for FAIR management of your research data." # Metadata description of the website -remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@1.21.0 +remote_theme: janslifka/elixir-toolkit-theme@tools-improvements sass: style: compressed From 8c53365f3f144c7561087adbd0f0f750dc1ea5d8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marek=20Such=C3=A1nek?= Date: Thu, 8 Dec 2022 12:22:08 +0100 Subject: [PATCH 003/126] Use GitHub Actions for Jekyll and GitHub Pages --- .github/workflows/jekyll.yml | 78 +++++++++++++++++++++++--- .github/workflows/list_conversion.yml | 21 ++++++- .github/workflows/list_validation.yml | 13 ++++- Gemfile | 22 +++++++- Makefile | 17 ++++++ _config.yml | 1 + _plugins/jekyll-github-metadata-fix.rb | 16 ++++++ index.html | 1 + 8 files changed, 155 insertions(+), 14 deletions(-) create mode 100644 Makefile create mode 100644 _plugins/jekyll-github-metadata-fix.rb diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml index 5a4e76448..4ca216380 100644 --- a/.github/workflows/jekyll.yml +++ b/.github/workflows/jekyll.yml @@ -1,16 +1,78 @@ name: Jekyll site CI on: - pull_request: - branches: [ master ] + push: + workflow_dispatch: + +permissions: + contents: read + pages: write + id-token: write jobs: build: runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v3 + + - name: Setup Ruby + uses: ruby/setup-ruby@v1.127.0 + with: + ruby-version: '3.1' + bundler-cache: true + cache-version: 0 + + - name: Setup Pages + id: pages + uses: actions/configure-pages@v2 + + - name: Set Jekyll environment + id: name + run: | + if [ "$REPO_OWNER" == "elixir-europe" ]; then + echo "jekyll_env=production" >> $GITHUB_OUTPUT + else + echo "jekyll_env=development" >> $GITHUB_OUTPUT + fi + env: + REPO_OWNER: ${{ github.repository_owner }} + + - name: Install dependencies + run: | + bundle install + + - name: Build with Jekyll + # Outputs to the './_site' directory by default + run: | + bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" + env: + PAGES_REPO_NWO: ${{ github.repository }} + GITHUB_BRANCH: ${{ github.ref_name }} + JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }} + JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + - name: Upload artifact + uses: actions/upload-pages-artifact@v1 + + deploy: + runs-on: ubuntu-latest + needs: build + + if: | + github.event_name == 'workflow_dispatch' || + (github.event_name == 'push' && github.event.repository.default_branch == github.ref_name) + + concurrency: + group: "pages" + cancel-in-progress: true + + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + steps: - - uses: actions/checkout@v2 - - name: Build the site in the jekyll/builder container - run: | - docker run \ - -v ${{ github.workspace }}:/srv/jekyll --env PAGES_REPO_NWO=${{github.repository}} -v ${{ github.workspace }}/_site:/srv/jekyll/_site \ - jekyll/builder:3.8.6 /bin/bash -c "gem install github-pages --no-document && chmod 777 /srv/jekyll && jekyll build" + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v1 diff --git a/.github/workflows/list_conversion.yml b/.github/workflows/list_conversion.yml index 0e8a3012e..b781b8ccc 100644 --- a/.github/workflows/list_conversion.yml +++ b/.github/workflows/list_conversion.yml @@ -4,45 +4,62 @@ on: schedule: - cron: '0 13 * * 1' workflow_dispatch: + jobs: build: runs-on: ubuntu-latest + + if: github.repository_owner == 'elixir-europe' + strategy: matrix: python-version: [3.8] + steps: - name: Checkout uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} + - name: Install dependencies run: | python -m pip install --upgrade pip pip install pyyaml requests python-frontmatter + - name: Run tool table 2 yaml run: | python var/conversions.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}" + - name: Fetch country names with corresponding iso run: | python var/country_list.py + - name: Update markdown pages with DSW links run: | python var/dsw_integration.py + - name: Get faircookbook-rdmkit repository uses: actions/checkout@v3 with: repository: elixir-europe/faircookbook-rdmkit path: faircookbook-rdmkit ref: main + - name: Update markdown pages with FAIR Cookbook links run: | python var/faircookbook_integration.py ${GITHUB_WORKSPACE}/faircookbook-rdmkit/faircookbook_rdmkit_mapping.yml + - name: Deleting faircookbook-rdmkit repository - run: rm -r faircookbook-rdmkit + run: | + rm -r faircookbook-rdmkit + - name: Show differences - run: 'git diff --stat' + run: | + git diff --stat + - name: Create Pull Request id: cpr uses: peter-evans/create-pull-request@v3 diff --git a/.github/workflows/list_validation.yml b/.github/workflows/list_validation.yml index 255946d2c..3d37bb45a 100644 --- a/.github/workflows/list_validation.yml +++ b/.github/workflows/list_validation.yml @@ -3,24 +3,33 @@ name: Validating the tool and resource table on: pull_request: branches: [ master ] + jobs: build: runs-on: ubuntu-latest + strategy: matrix: python-version: [3.8] + steps: - - uses: actions/checkout@v2 + - name: Checkout + uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} + - name: Install dependencies run: | python -m pip install --upgrade pip pip install pyyaml requests python-frontmatter + - name: Run tool table 2 yaml run: | python var/conversions.py + - name: Show differences - run: 'git diff --stat' + run: | + git diff --stat diff --git a/Gemfile b/Gemfile index 47909af85..44112daf6 100644 --- a/Gemfile +++ b/Gemfile @@ -1,5 +1,23 @@ source "https://rubygems.org" +gem "jekyll", "~> 3.9" +gem "jemoji", "~> 0.5.1" +gem "kramdown-parser-gfm", "~> 1.1" +gem "minima", "~> 2.5" +gem "webrick", "~> 1.7" + group :jekyll_plugins do - gem "github-pages" - end + gem "jekyll-feed", "~> 0.12" + gem "jekyll-github-metadata", "~> 2.15.0" + gem "jekyll-redirect-from", "~> 0.16.0" + gem "jekyll-remote-theme", "~> 0.4.3" + gem "jekyll-sitemap", "~> 1.4" +end + +platforms :mingw, :x64_mingw, :mswin, :jruby do + gem "tzinfo", ">= 1", "< 3" + gem "tzinfo-data" +end + +gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin] +gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby] diff --git a/Makefile b/Makefile new file mode 100644 index 000000000..5bfe941dd --- /dev/null +++ b/Makefile @@ -0,0 +1,17 @@ +.PHONY: install +install: + bundle install + +.PHONY: dev +dev: + GITHUB_BRANCH=$$(git rev-parse --abbrev-ref HEAD) \ + JEKYLL_ENV=development \ + bundle exec jekyll serve --livereload --incremental + +.PHONY: build +build: + JEKYLL_ENV=production bundle exec jekyll build + +.PHONY: clean +clean: + rm -rf _site .bundle .jekyll-cache .jekyll-metadata .sass-cache vendor diff --git a/_config.yml b/_config.yml index 3f0d3559d..b6474ec52 100644 --- a/_config.yml +++ b/_config.yml @@ -26,6 +26,7 @@ theme_variables: exclude: - README.md + - vendor defaults: - diff --git a/_plugins/jekyll-github-metadata-fix.rb b/_plugins/jekyll-github-metadata-fix.rb new file mode 100644 index 000000000..206efcc49 --- /dev/null +++ b/_plugins/jekyll-github-metadata-fix.rb @@ -0,0 +1,16 @@ +# As GitHub Actions are used for GitHub Pages, the branch must be set via environment variable +module Jekyll + module GitHubMetadata + module RepositoryFix + def source + { + "branch" => ENV["GITHUB_BRANCH"] || super["branch"], + "path" => ENV["BASE_PATH"] || super["path"], + } + end + end + class Repository + prepend RepositoryFix + end + end +end diff --git a/index.html b/index.html index e4ebbaf4d..438649883 100644 --- a/index.html +++ b/index.html @@ -8,6 +8,7 @@ {% include head.html %} + {% if jekyll.environment == "development" %}{% include dev-info.html %}{% endif %} {% include topnav.html search=false %}
From 2c3e3d0355e4285d7b4bef18bdbde937ced7bae5 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Wed, 14 Dec 2022 16:51:49 +0100 Subject: [PATCH 004/126] using gems --- Gemfile | 25 +- Makefile | 17 - _config.yml | 5 +- _data/main_tool_and_resource_list.csv | 342 ----- _data/tool_and_resource_list.yml | 1756 +++++------------------- _includes/dev-info.html | 3 - _plugins/jekyll-github-metadata-fix.rb | 16 - index.html | 1 - pages/your_tasks/data_publication.md | 6 +- 9 files changed, 372 insertions(+), 1799 deletions(-) delete mode 100644 Makefile delete mode 100644 _data/main_tool_and_resource_list.csv delete mode 100644 _includes/dev-info.html delete mode 100644 _plugins/jekyll-github-metadata-fix.rb diff --git a/Gemfile b/Gemfile index 44112daf6..3bb8d8f10 100644 --- a/Gemfile +++ b/Gemfile @@ -1,23 +1,16 @@ source "https://rubygems.org" -gem "jekyll", "~> 3.9" -gem "jemoji", "~> 0.5.1" -gem "kramdown-parser-gfm", "~> 1.1" -gem "minima", "~> 2.5" +gem "elixir-toolkit-theme-plugins", ">= 0.1.0" gem "webrick", "~> 1.7" +gem "jekyll", "~> 4.3.1" +gem "jemoji", "~> 0.13.0" +gem "kramdown-parser-gfm", "~> 1.1" group :jekyll_plugins do - gem "jekyll-feed", "~> 0.12" - gem "jekyll-github-metadata", "~> 2.15.0" gem "jekyll-redirect-from", "~> 0.16.0" - gem "jekyll-remote-theme", "~> 0.4.3" gem "jekyll-sitemap", "~> 1.4" -end - -platforms :mingw, :x64_mingw, :mswin, :jruby do - gem "tzinfo", ">= 1", "< 3" - gem "tzinfo-data" -end - -gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin] -gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby] + gem "jekyll-github-metadata", "~> 2.15" + gem "jekyll-relative-links", "~> 0.6" + gem "jekyll-seo-tag", "~> 2.8" + gem "jekyll-remote-theme" +end \ No newline at end of file diff --git a/Makefile b/Makefile deleted file mode 100644 index 5bfe941dd..000000000 --- a/Makefile +++ /dev/null @@ -1,17 +0,0 @@ -.PHONY: install -install: - bundle install - -.PHONY: dev -dev: - GITHUB_BRANCH=$$(git rev-parse --abbrev-ref HEAD) \ - JEKYLL_ENV=development \ - bundle exec jekyll serve --livereload --incremental - -.PHONY: build -build: - JEKYLL_ENV=production bundle exec jekyll build - -.PHONY: clean -clean: - rm -rf _site .bundle .jekyll-cache .jekyll-metadata .sass-cache vendor diff --git a/_config.yml b/_config.yml index e765c0d79..0d7ed1cc8 100644 --- a/_config.yml +++ b/_config.yml @@ -4,7 +4,7 @@ title: RDMkit description: "Best practices and guidelines you can use for FAIR management of your research data." # Metadata description of the website -remote_theme: janslifka/elixir-toolkit-theme@tools-improvements +remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@dev sass: style: compressed @@ -27,7 +27,7 @@ theme_variables: exclude: - README.md - vendor - + defaults: - scope: @@ -129,6 +129,7 @@ defaults: sidebar: about plugins: + - elixir-toolkit-theme-plugins - jemoji - jekyll-redirect-from - jekyll-sitemap diff --git a/_data/main_tool_and_resource_list.csv b/_data/main_tool_and_resource_list.csv deleted file mode 100644 index d29c1a84a..000000000 --- a/_data/main_tool_and_resource_list.csv +++ /dev/null @@ -1,342 +0,0 @@ -name,url,description,registry,related_pages -3D-Beacons,https://3d-beacons.org,Network providing unified programmatic access to experimentally determined and predicted structure models,,struct_bioinfo -Access to Biological Collection Data Schema (ABCD),https://www.tdwg.org/standards/abcd/,A standard schema for primary biodiversity data,biotools:NA,micro_biotech -Ada Discovery Analytics (Ada),https://ada-discovery.github.io/,"Ada is a performant and highly configurable system for secured integration, visualization, and collaborative analysis of heterogeneous data sets, primarily targeting clinical and experimental sources.",,"data_analysis, transmed" -Addgene,https://www.addgene.org/browse/,A searchable repository with a focus on plasmids,,micro_biotech -AgroPortal,http://agroportal.lirmm.fr/,Browser for ontologies for agricultural science based on NBCO BioPortal.,biotools:AgroPortal,plant_pheno_assembly -Amazon Web Services,https://aws.amazon.com/,Amazon Web Services,,"storage, data_analysis, transfer" -Amnesia,https://amnesia.openaire.eu/,Amnesia is a GDPR compliant high accuracy data anonymization tool,,sensitive -AOP4EUpest,http://www.biomedicale.parisdescartes.fr/aop4EUpest/home.php,AOP4EUpest web server is devoted to the identification of pesticides involved in an Adverse Outcome Pathway via text mining approaches.,biotools:aop4eupest,toxicology_data -APID Interactomes,http://apid.dep.usal.es/,APID (Agile Protein Interactomes DataServer) is a server that provides a comprehensive collection of protein interactomes for more than 400 organisms based in the integration of known experimentally validated protein-protein physical interactions (PPIs),biotools:apid,idp -Argos,https://argos.openaire.eu/splash/,"Plan and follow your data. Bring your Data Management Plans closer to where data are generated, analysed and stored.",,"dmp, researcher, data_manager" -ArrayExpress,https://www.ebi.ac.uk/arrayexpress/,A repository of array based genomics data,,"micro_biotech, data_publication" -Arvados,https://arvados.org,"With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources.",,"it_support, policy_officer, researcher, data_analysis" -Aspera Fasp,https://www.ibm.com/products/aspera,"With fast file transfer and streaming solutions built on the award-winning IBM FASP protocol, IBM Aspera software moves data of any size across any distance",,"transfer, it_support" -ATCC,https://www.lgcstandards-atcc.org/en.aspx#,"Biological materials resource including cell-lines, strains and genomics tools",,micro_biotech -Atlas,https://github.com/OHDSI/Atlas/wiki,"Free, publicly available web-based, open-source software application developed by the OHDSI community to support the design and execution of observational analyses to generate real world evidence from patient level observational data.",fairsharing:NA,"data_manager, researcher, transmed" -b2share,https://b2share.eudat.eu/,Store and publish your research data. Can be used to bridge between domains,,"storage, data_publication, bioimaging_data" -BacDive,https://bacdive.dsmz.de,A searchable database for bacteria specific information,,micro_biotech -Bacillus Genetic Stock Center (BGSC),http://www.bgsc.org/,A repository specific to Bacillus strains,biotools:NA,micro_biotech -BASE,https://www.base-search.net/,A search engine for academic web resources,,existing_data -BBMRI-ERIC's ELSI Knowledge Base,https://www.bbmri-eric.eu/elsi/knowledge-base/,The ELSI Knowledge Base is an open-access resource platform that aims at providing practical know-how for responsible research.,,"data_protection, sensitive, policy_officer, data_manager, human_data" -Beacon,https://beacon-project.io/,The Beacon protocol defines an open standard for genomics data discovery.,,"researcher, data_manager, it_support, human_data" -Benchling,https://www.benchling.com,R&D Platform for Life Sciences,,micro_biotech -BIAFLOWS,https://biaflows.neubias.org/,BIAFLOWS is an open-soure web framework to reproducibly deploy and benchmark bioimage analysis workflows,biotools:biaflows,data_analysis -BigNASim,https://mmb.irbbarcelona.org/BigNASim/,Repository for Nucleic Acids MD simulations,biotools:bignasim,"biomol_sim, data_publication" -BIII,https://biii.eu/,"The BioImage Informatics Index is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis",biotools:BISE,"it_support, data_analysis" -BindingDB,https://www.bindingdb.org/,"Public, web-accessible database of measured binding affinities","fairsharing:3b36hk, biotools:bindingdb",biomol_sim -Bio-Formats,https://www.openmicroscopy.org/bio-formats/,"Bio-Formats is a software tool for reading and writing image data using standardized, open formats",biotools:bio-formats,"ome, bioimaging_data" -Bioactive Conformational Ensemble,https://mmb.irbbarcelona.org/BCE/,Platform designed to efficiently generate bioactive conformers and speed up the drug discovery process.,biotools:bce,biomol_sim -Bioconda,https://bioconda.github.io/,Bioconda is a bioinformatics channel for the Conda package manager,biotools:bioconda,"it_support, data_analysis" -Biodiversity Information Standards (TDWG),https://www.tdwg.org,"Biodiversity Information Standards (TDWG), historically the Taxonomic Databases Working Group, work to develop biodiversity information standards",,micro_biotech -BioExcel COVID-19,https://bioexcel-cv19.bsc.es/#/,Platform designed to provide web-access to atomistic-MD trajectories for macromolecules involved in the COVID-19 disease.,,biomol_sim -BioImageArchive,https://www.ebi.ac.uk/bioimage-archive/,The BioImage Archive stores and distributes biological images that are useful to life-science researchers.,fairsharing:x38D2k,"data_publication, bioimaging_data" -BioModels,https://www.ebi.ac.uk/biomodels/,A repository of mathematical models for application in biological sciences,fairsharing:paz6mh,"micro_biotech, data_publication" -BIONDA,http://bionda.mpc.ruhr-uni-bochum.de/start.php,"BIONDA is a free and open-access biomarker database, which employs various text mining methods to extract structured information on biomarkers from abstracts of scientific publications",biotools:bionda,"storage, researcher, human_data, proteomics" -BioSamples,https://www.ebi.ac.uk/biosamples/,BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry.,fairsharing:ewjdq6,"plants, plant_geno_assembly" -Bioschemas,https://bioschemas.org,"Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials",,"machine_actionability, it_support" -BioStudies,https://www.ebi.ac.uk/biostudies/,A database hosting datasets from biological studies. Useful for storing or accessing data that is not compliant for mainstream repositories.,,"micro_biotech, plants, data_publication" -BisQue,https://bioimage.ucsb.edu/bisque,Resource for management and analysis of 5D biological images,,"data_organisation, data_manager, data_analysis, bioimaging_data" -Bitbucket,https://bitbucket.org/,"Git based code hosting and collaboration tool, built for teams.",,"data_organisation, data_manager, it_support" -BMRB,https://bmrb.io/,Biological Magnetic Resonance Data Bank,,"idp, researcher" -BoostDM,https://www.intogen.org/boostdm/search,BoostDM is a method to score all possible point mutations (single base substitutions) in cancer genes for their potential to be involved in tumorigenesis.,biotools:boostdm,"data_analysis, human_data" -Box,https://www.box.com,Cloud storage and file sharing service,,"storage, it_support, transfer" -BrAPI,https://www.brapi.org,"Specification for a standard API for plant data: plant material, plant phenotyping data",,"it_support, plants, plant_pheno_assembly" -BRENDA,https://www.brenda-enzymes.org/,"Database of enzyme and enzyme-ligand information, across all taxonomic groups, manually extracted from primary literature and extended by text mining procedures",fairsharing:etp533,micro_biotech -Bulk Rename Utility,https://www.bulkrenameutility.co.uk/,File renaming software for Windows,,"data_organisation, data_manager, researcher" -CalibraCurve,https://github.com/mpc-bioinformatics/CalibraCurve,A highly useful and flexible tool for calibration of targeted MS?based measurements. CalibraCurve enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays. The software uses a variety of measures to assess the accuracy of the calibration and provides intuitive visualizations.,biotools:calibracurve,"data_analysis, proteomics" -CAMEO,https://cameo3d.org,Continuous evaluation of the accuracy and reliability of protein structure prediction methods in a fully automated manner,"biotools:cameo, fairsharing:dq34p2",struct_bioinfo -Cancer Genome Interpreter,https://www.cancergenomeinterpreter.org/home,Cancer Genome Interpreter (CGI) is designed to support the identification of tumor alterations that drive the disease and detect those that may be therapeutically actionable.,biotools:cgi,"data_analysis, human_data" -CAPRI,https://www.ebi.ac.uk/pdbe/complex-pred/capri/,Critical assessment of structure prediction methods for protein-protein interactions,,struct_bioinfo -CAS Registry,https://www.cas.org/cas-data/cas-registry,"The CAS Registry (Chemical Abstracts Service Registry) includes more than 188 million unique chemicals. CAS Registry Numbers are broadly used as a unique identifier for chemical substances. The Registry is maintained by CAS, a subdivision of the American Chemical Society.",,toxicology_data -CASP,https://predictioncenter.org,Biennial critical assessment of techniques for protein structure prediction,,struct_bioinfo -Castor,https://www.castoredc.com,"Castor is an EDC system for researchers and institutions. With Castor, you can create and customize your own database in no time. Without any prior technical knowledge, you can build a study in just a few clicks using our intuitive Form Builder. Simply define your data points and start collecting high quality data, all you need is a web browser.",fairsharing:NA,"identifiers, it_support, data_manager" -CATH,http://www.cathdb.info/,A hierarchical domain classification of protein structures in the Protein Data Bank.,fairsharing:xgcyyn, -CEDAR,https://metadatacenter.org,"CEDAR is making data submission smarter and faster, so that scientific researchers and analysts can create and use better metadata.",,"metadata, machine_actionability, researcher, data_manager" -CellRepo,https://cellrepo.herokuapp.com/,A version management tool for modifying strains,,micro_biotech -Cellular Microscopy Phenotype Ontology (CMPO),https://www.ebi.ac.uk/cmpo/,An ontology for expressing cellular (or multi-cellular) terms with applications in microscopy,,micro_biotech -CERNBox,https://cernbox.web.cern.ch/cernbox/,"CERNBox cloud data storage, sharing and synchronization",,storage -ChEBI,https://www.ebi.ac.uk/chebi/,Dictionary of molecular entities focused on 'small' chemical compounds,fairsharing:62qk8w,micro_biotech -ChEMBL,https://www.ebi.ac.uk/chembl/,"Database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties and abstracted bioactivities.","biotools:chembl, fairsharing:m3jtpg","data_analysis, researcher, toxicology_data" -ChIPSummitDB,http://summit.med.unideb.hu/summitdb/,ChIPSummitDB is a database of transcription factor binding sites and the distances of the binding sites relative to the peak summits.,biotools:chipsummitdb,human_data -Choose a license,https://choosealicense.com,Choose an open source license,,"licensing, researcher, data_manager, policy_officer" -ClinicalTrials.gov,https://clinicaltrials.gov/,ClinicalTrials.gov is a resource depending on the National Library of medicine which makes available private and public-funded clinical trials.,,toxicology_data -Common Data Elements (CDE) in a box ,https://github.com/ejp-rd-vp/cde-in-box,"A collection of software applications which enables creation, storing and publishing of ""Common Data Elements"" according to the CDE semantic model.",,rare_disease -Common Workflow Language (CWL),https://www.commonwl.org,An open standard for describing workflows that are build from command line tools,fairsharing:8y5ayx,"it_support, researcher, data_analysis" -Comptox,https://comptox.epa.gov/dashboard,The CompTox Chemicals Dashboard provides toxicological information for over 800.000 chemical compounds. It is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks.,biotools:comptox_chemistry_dashboard,toxicology_data -COmputational Modeling in BIology NEtwork (COMBINE),http://co.mbine.org,An initiative to bring together various formats and standard for computational models in biology,,micro_biotech -Conda,https://docs.conda.io/en/latest/,Open source package management system,,"it_support, data_analysis" -Consent Clauses for Genomic Research,https://drive.google.com/file/d/1O5Ti7g7QJqS3h0ABm-LyTe02Gtq8wlKM/view?usp=sharing,A resource for researchers when drafting consent forms so they can use language matching cutting-edge GA4GH international standards,,human_data -Cookiecutter,https://github.com/cookiecutter/cookiecutter,"A command-line utility that creates projects from cookiecutters (project templates), e.g. creating a Python package project from a Python package project template.",,"data_organisation, it_support, data_manager" -COPO,https://copo-project.org/,Portal for scientists to broker more easily rich metadata alongside data to public repos.,"biotools:copo, fairsharing-coll:bsg-d001247","metadata, researcher, plants, machine_actionability, plant_pheno_assembly" -COVID-19 Molecular Structure and Therapeutics Hub,https://covid.bioexcel.eu/,COVID-19 Molecular Structure and Therapeutics Hub,,biomol_sim -Create a Codebook,https://ddialliance.org/training/getting-started-new-content/create-a-codebook,Examples and tools to create a codebook by the Data Documentation Initiative (DDI),,"metadata, researcher, data_manager" -Creative Commons License Chooser,https://creativecommons.org/choose/,It helps you choose the right Creative Commons license for your needs.,,"licensing, researcher, data_manager, policy_officer" -Crop Ontology,https://www.cropontology.org,"The Crop Ontology compiles concepts to curate phenotyping assays on crop plants, including anatomy, structure and phenotype.",fairsharing:wgfrmg,"researcher, data_manager, it_support, plants" -Crypt4GH,https://crypt4gh.readthedocs.io/en/latest/,"A Python tool to encrypt, decrypt or re-encrypt files, according to the GA4GH encryption file format.",,human_data -CS3,https://www.cs3community.org/,Cloud Storage Services for Synchronization and Sharing (CS3),,storage -CTD,http://ctdbase.org/,A database that aims to advance understanding about how environmental exposures affect human health.,biotools:ctd,toxicology_data -cURL,https://curl.se,command line tool and library for transferring data with URLs,,"transfer, it_support" -Cytomine-IMS,https://github.com/cytomine/Cytomine-IMS,Image Data management,,"data_manager, bioimaging_data" -DAISY,https://daisy-demo.elixir-luxembourg.org,Data Information System to keep sensitive data inventory and meet GDPR accountability requirement.,biotools:Data_Information_System_DAISY,"it_support, policy_officer, human_data, data_protection, transmed" -Data Catalog,https://datacatalog.elixir-luxembourg.org/,"Unique collection of project-level metadata from large research initiatives in a diverse range of fields, including clinical, molecular and observational studies. Its aim is to improve the findability of these projects following FAIR data principles.",fairsharing:NA,"metadata, transmed" -Data Catalog Vocabulary (DCAT),https://www.w3.org/TR/vocab-dcat-2/,DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.,,"machine_actionability, it_support, rare_disease" -Data Curation Centre Metadata list,https://www.dcc.ac.uk/guidance/standards/metadata/list,List of metadata standards,,"metadata, researcher, data_manager" -Data INRAE,https://data.inrae.fr/,Dataverse for life sciences and agronomic related data,fairsharing:178BmT,"plants, plant_geno_assembly, researcher, data_manager, plant_pheno_assembly" -Data Stewardship Wizard,https://ds-wizard.org/,Publicly available online tool for composing smart data management plans,biotools:Data_Stewardship_Wizard,"dmp, researcher, data_manager, it_support, nels, tsd, plant_pheno_assembly" -Data Use Ontology,https://github.com/EBISPOT/DUO,DUO allows to semantically tag datasets with restriction about their usage.,fairsharing:5dnjs2,"data_manager, researcher, human_data" -data.world Data License list,https://help.data.world/hc/en-us/articles/115006114287-Common-license-types-for-datasets,Overview of typical licenses used for data resources,,"licensing, biomol_sim" -DataCite,https://search.datacite.org/,A search engine for the complete collection of publicly available DataCite DOIs,fairsharing:yknezb,existing_data -DATAVERSE,https://dataverse.org/,Open source research data respository software.,fairsharing:NA,"storage, researcher, data_manager, it_support, ifb" -DAWID,https://dawid.elixir-luxembourg.org/,The Data Agreement Wizard is a tool developed by ELIXIR-Luxembourg to facilitate data sharing agreements.,,"data_protection, policy_officer, human_data" -dbGAP,https://www.ncbi.nlm.nih.gov/gap/,The database of Genotypes and Phenotypes (dbGaP) archives and distributes data from studies investigating the interaction of genotype and phenotype in Humans,fairsharing:88v2k0,"data_publication, researcher, it_support, human_data" -DisGeNET,https://www.disgenet.org/,A discovery platform containing collections of genes and variants associated to human diseases.,biotools:disgenet,"data_analysis, human_data, researcher, toxicology_data" -DisProt,https://disprot.org/,A database of intrinsically disordered proteins,biotools:disprot,"idp, researcher" -DMP Canvas Generator,https://dmp.vital-it.ch,"Questionnaire, which generates a pre-filled a DMP",,"dmp, researcher, data_manager" -DMPlanner,https://dmplanner.athenarc.gr/,"Semi-automatically generated, searchable catalogue of resources that are relevant to data management plans.",,"dmp, researcher, data_manager" -DMPRoadmap,https://github.com/DMPRoadmap/roadmap,DMP Roadmap is a Data Management Planning tool.,,"dmp, researcher, data_manager" -DMPTool,https://dmptool.org,Build your Data Management Plan,,"dmp, researcher, data_manager" -DNA Data Bank of Japan (DDBJ),https://www.ddbj.nig.ac.jp/index-e.html,A database of DNA sequences,,micro_biotech -Docker,https://www.docker.com/,"Docker is a software for the execution of applications in virtualized environments called containers. It is linked to DockerHub, a library for sharing container images",fairsharing-coll:bsg-d001254,"it_support, data_analysis" -DropBox,https://www.dropbox.com/?landing=dbv2,Cloud storage and file sharing service,,"storage, it_support, transfer" -Drug Matrix,https://ntp.niehs.nih.gov/data/drugmatrix/,A toxicogenomic resource that provides access to the gene expression profiles of over 600 different compounds in several cell types from rats and primary rat hepatocytes.,,toxicology_data -Dryad,https://datadryad.org/,"Open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data",fairsharing:wkggtx,"data_publication, biomol_sim, bioimaging_data" -Dynameomics,http://www.dynameomics.org/,Database of folding / unfolding pathway of representatives from all known protein folds by MD simulation,,biomol_sim -e!DAL,https://edal.ipk-gatersleben.de/,Electronic data archive library is a framework for publishing and sharing research data,biotools:edal,"storage, it_support" -e!DAL-PGP,https://edal-pgp.ipk-gatersleben.de/,Plant Genomics and Phenomics Research Data Repository,fairsharing:rf3m4g,"plants, plant_geno_assembly, researcher, data_manager, it_support, data_publication, metadata, plant_pheno_assembly" -ECOTOX,https://cfpub.epa.gov/ecotox/,"The ECOTOXicology Knowledgebase (ECOTOX) is a comprehensive, publicly available Knowledgebase providing single chemical environmental toxicity data on aquatic life, terrestrial plants, and wildlife.",,toxicology_data -ECPGR,https://www.ecpgr.cgiar.org/,Hub for the identification of plant genetic resources in Europe,,"plants, researcher, data_manager" -EDKB,https://www.fda.gov/science-research/bioinformatics-tools/endocrine-disruptor-knowledge-base,"Endocrine Disruptor Knowledge Base is a platform designed to foster the development of computational predictive toxicology. This platform allows direct access to ten libraries containing the following resources: a biological activity database, QSAR training sets, in vitro and in vivo experimental data for more than 3,000 chemicals, literature citations, chemical-structure search capabilities.",,toxicology_data -ELIXIR Core Data Resources,https://elixir-europe.org/platforms/data/core-data-resources,Set of European data resources of fundamental importance to the wider life-science community and the long-term preservation of biological data,fairsharing-coll:bsg-c000039,"existing_data, covid-19" -ELIXIR Deposition Databases for Biomolecular Data,https://elixir-europe.org/platforms/data/elixir-deposition-databases,List of discipline-specific deposition databases recommended by ELIXIR.,fairsharing-coll:bsg-c000039,"data_publication, researcher, data_manager, it_support, covid-19, nels, ifb, csc" -ELIXIR-AAI,https://elixir-europe.org/services/compute/aai,The ELIXIR Authentication and Authorisation Infrastructure (AAI),,"sensitive, nels, tsd, transmed" -EMBL-EBI Ontology Lookup Service,https://www.ebi.ac.uk/ols/index,EMBL-EBI’s web portal for finding ontologies,,"metadata, data_manager, researcher" -EMBL-EBI's data submission wizard,https://www.ebi.ac.uk/submission/,EMBL-EBI's wizard for finding the right EMBL-EBI repository for your data.,,"data_publication, researcher, data_manager" -EMPIAR,https://www.ebi.ac.uk/pdbe/emdb/empiar/,"Electron Microscopy Public Image Archive is a public resource for raw, 2D electron microscopy images. You can browse, upload and download the raw images used to build a 3D structure",,"data_publication, ome, bioimaging_data" -ENA COMPARE Data Hubs,https://github.com/nadimm-rahman/ena-datahub-setup,This tool carries out data hub set up at the European Nucleotide Archive (ENA).,,"dm_coordination, it_support, data_manager" -ENA upload tool,https://github.com/usegalaxy-eu/ena-upload-cli,The program submits experimental data and respective metadata to the European Nucleotide Archive (ENA).,,"it_support, data_manager, researcher, data_brokering" -Ensembl,https://www.ensembl.org/index.html,"Genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.",fairsharing:fx0mw7, -Ensembl Genomes,https://ensemblgenomes.org/,"Comparative analysis, data mining and visualisation for the genomes of non-vertebrate species",fairsharing:923a0p, -Ensembl Plants,https://plants.ensembl.org/,Open-access database of full genomes of plant species.,fairsharing:j8g2cv,plant_geno_assembly -ERPA,https://gitlab.sib.swiss/clinbio/erpa-app,Web-based tool allowing users to create and manage a register of personal data processing activities (ROPA).,,"policy_officer, human_data, data_protection" -EU General Data Protection Regulation,https://eur-lex.europa.eu/legal-content/EN/TXT/HTML/?uri=CELEX:32016R0679&from=EN,"Regulation (eu) 2016/679 of the european parliament and of the council on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing directive 95/46/ec (general data protection regulation).",,"data_protection, policy_officer, human_data, tsd" -EUDAT licence selector wizard,https://ufal.github.io/public-license-selector/,EUDAT's wizard for finding the right licence for your data or code.,,"licensing, researcher, data_manager, policy_officer" -EudraVigilance,https://www.ema.europa.eu/en/human-regulatory/research-development/pharmacovigilance/eudravigilance,The European database of suspected adverse drug reaction reports is a public resource aimed to provide access to reported suspected side-effects of drugs. Side-effects are defined according to the MedDRA ontology.,,toxicology_data -EUPID,https://eupid.eu/#/concept,"EUPID provides a method for identity management, pseudonymisation and record linkage to bridge the gap between multiple contexts.",,"it_support, policy_officer, human_data" -EURISCO,https://eurisco.ipk-gatersleben.de,European Search Catalogue for Plant Genetic Resources,biotools:eurisco,"plants, researcher, data_manager" -Europe PMC,https://europepmc.org/,"Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines.",fairsharing:cmw6mm,researcher -European Joint Programme on Rare Diseases (EJP RD),https://www.ejprarediseases.org/,"A programme aiming to create an effective rare diseases research ecosystem for progress, innovation and for the benefit of everyone with a rare disease.",,rare_disease -European Joint Programme on Rare Diseases Metadata Model,https://github.com/ejp-rd-vp/resource-metadata-schema,"This core model is designed to represent data about a rare disease patient and biosample registries. The model is based on and builds on existing standards, such as the European Rare Disease Registry Infrastructure and the Common Data Elements from the rare disease community and other more generalised standards for data sharing such as the W3C DCAT vocabulary.",,rare_disease -European Joint Programme on Rare Diseases Virtual Platform (EJP RD),https://vp.ejprarediseases.org/,"The Virtual Platform is a federated ecosystem, in which resources are enhanced to be amenable to rare disease research, and made Findable, Accessible, Interoperable and Reusable: data stays at the source level but can be queyrable at distance from an EJP RD query point.",,rare_disease -European Nucleotide Archive (ENA),https://www.ebi.ac.uk/ena/browser/home,A record of sequence information scaling from raw sequcning reads to assemblies and functional annotation,fairsharing:dj8nt8,"micro_biotech, plant_geno_assembly, data_brokering" -European Rare Disease Registry Infrastructure directory of registries (ERDRI.dor),https://eu-rd-platform.jrc.ec.europa.eu/erdridor/,ERDRI.dor provides an overview of participating rare disease registries with their main characteristics and description.,,rare_disease -European Rare Disease Registry Infrastructure metadata repository (ERDRI.mdr),https://eu-rd-platform.jrc.ec.europa.eu/mdr/,"ERDRI.mdr serves to ease the integration of heterogeneous data from different rare disease registries. For this purpose, it contains a collection of metadata which specifies the used data elements of a registry including the designation of the used data elements, their definition and units of measurement.",,rare_disease -European Reference Networks (ERNs),https://health.ec.europa.eu/european-reference-networks_en,"Virtual networks involving healthcare providers across Europe. They aim to facilitate discussion on complex or rare diseases and conditions that require highly specialised treatment, and concentrated knowledge and resources.",,rare_disease -European Variation Archive (EVA),https://www.ebi.ac.uk/eva/,Open-access database of all types of genetic variation data from all species.,fairsharing:6824pv,plant_geno_assembly -Evidence and Conclusion Ontology (ECO),https://evidenceontology.org/,Controlled vocabulary that describes types of evidence and assertion methods,"fairsharing:wvpgwn, biotools:NA","existing_data, metadata" -FAERS,https://www.fda.gov/drugs/surveillance/questions-and-answers-fdas-adverse-event-reporting-system-faers,"The FDA Adverse Event Reporting System (FAERS) is an american resource that contains adverse event reports, medication error reports and product quality complaints submitted by healthcare professionals, consumers, and manufacturers. MedDRA ontology is used for coding adverse effects. Note that reports available in FAERS do not require a causal relationship between a product and an adverse event and further evaluations are conducted by FDA to monitor the safety of products.",biotools:faers,toxicology_data -FAIDARE,https://urgi.versailles.inra.fr/faidare/,FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI.,biotools:faidare,"researcher, data_manager, plants, ifb, plant_pheno_assembly" -FAIR Cookbook,https://fairplus.github.io/the-fair-cookbook/content/recipes/assessing-fairness.html#,"FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable (FAIR)",,"compliance, data_manager, transmed" -FAIR Data Point (FDP),https://www.fairdatapoint.org/,A FAIR Data Point stores metadata in a standardized and sharable way.,fairsharing:298,"rare_disease, metadata, it_support" -FAIR Evaluation Services,https://fairsharing.github.io/FAIR-Evaluator-FrontEnd/#!/#%2F!,Resources and guidelines to assess the FAIRness of digital resources.,,"compliance, data_manager, policy_officer" -FAIR Implementation Profile,https://www.go-fair.org/how-to-go-fair/fair-implementation-profile/,The FIP is a collection of FAIR implementation choices made by a community of practice for each of the FAIR Principles. ,,"dm_coordination, dmp, researcher, data_manager" -FAIR-Wizard,https://wwwdev.ebi.ac.uk/ait/fair-wizard/home,"The FAIR wizard utilizes FAIRification resources developed by the FAIRplus project and other platforms, suggests FAIRification materials based on the FAIRification requirements, and designs FAIRification solutions for data owners, data stewards, and other people involved in FAIRification.",,"compliance, data_manager, policy_officer" -FAIRassist.org,https://fairassist.org/#!/,Help you discover resources to measure and improve FAIRness.,,"compliance, data_manager, policy_officer" -FAIRDOM-SEEK,https://seek4science.org/,"A data Management Platform for organising, sharing and publishing research datasets, models, protocols, samples, publications and other research outcomes.",biotools:seek,"storage, it_support, nels, micro_biotech, ifb, machine_actionability, plant_pheno_assembly" -FAIRDOMHub,https://fairdomhub.org,"Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models etc. (public SEEK instance)",fairsharing:nnvcr9,"storage, researcher, nels, metadata, micro_biotech, machine_actionability, data_manager" -FAIRshake,https://fairshake.cloud,A System to Evaluate the FAIRness of Digital Objects,,"compliance, data_manager, it_support" -FAIRsharing,https://fairsharing.org/,"A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies.",fairsharing:2abjs5,"metadata, data_publication, policy_officer, data_manager, researcher, micro_biotech, existing_data" -FigShare,https://figshare.com/,Data publishing platform,fairsharing:drtwnh,"data_publication, biomol_sim, bioimaging_data" -FileZilla,https://filezilla-project.org,A free FTP solution,,"transfer, it_support" -FIP Wizard,https://fip-wizard.readthedocs.io/en/latest/,FIP Wizard is a toolset to facilitate the capture of data in FAIR Convergence Matrix questionnaire prompting communities to explicitly declare their FAIR Implementation Profiles. These profiles can be then stored and published as nanopublications.,,"dm_coordination, dmp, researcher, data_manager" -Free-IPA,https://www.freeipa.org/,FreeIPA is an integrated Identity and Authentication solution for Linux/UNIX networked environments.,,"it_support, transmed" -Freegenes,https://stanford.freegenes.org/collections/open-genes,Repository of IP-free synthetic biological parts,,micro_biotech -GA4GH Data Security Toolkit,https://www.ga4gh.org/genomic-data-toolkit/data-security-toolkit/,Principled and practical framework for the responsible sharing of genomic and health-related data.,,"data_publication, policy_officer, data_manager, it_support, human_data, sensitive" -GA4GH Genomic Data Toolkit,https://www.ga4gh.org/genomic-data-toolkit/,Open standards for genomic data sharing.,,"data_manager, it_support, human_data" -GA4GH Regulatory and Ethics toolkit,https://www.ga4gh.org/genomic-data-toolkit/regulatory-ethics-toolkit/,Framework for Responsible Sharing of Genomic and Health-Related Data,,"data_protection, sensitive, policy_officer, data_manager, it_support, human_data" -Galaxy,https://galaxyproject.org/,"Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.",biotools:galaxy,"nels, marine_assembly, data_analysis, researcher, it_support, ifb, galaxy" -GenBank,https://www.ncbi.nlm.nih.gov/genbank/,A database of genetic sequence information. GenBank may also refer to the data format used for storing information around genetic sequence data.,,micro_biotech -Gene Expression Omnibus (GEO),https://www.ncbi.nlm.nih.gov/geo/,A repository of MIAME-compliant genomics data from arrays and high-throughput sequencing,,"micro_biotech, data_publication, metadata, transfer, ome, bioimaging_data, toxicology_data" -GENEID,https://genome.crg.cat/software/geneid/index.html,Geneid is an ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms.,biotools:geneid,"data_analysis, researcher" -GHS Classification,https://pubchem.ncbi.nlm.nih.gov/ghs/,"GHS (Globally Harmonized System of Classification and Labelling of Chemicals) classification was developed by the United Nations in an attempt to align standards and chemical regulations in different countries. GHS includes criteria for the classification of health, physical and environmental hazards, and what information should be included on labels of hazardous chemicals and safety data sheets.",,toxicology_data -Git,https://git-scm.com/,Distributed version control system designed to handle everything from small to very large projects,,"data_organisation, data_manager, it_support" -GitHub,https://github.com,"Versioning system, used for sharing code, as well as for sharing of small data",fairsharing-coll:bsg-d001160,"data_publication, data_organisation, it_support, data_manager" -GitLab,https://gitlab.com/gitlab-org/gitlab,"GitLab is an open source end-to-end software development platform with built-in version control, issue tracking, code review, CI/CD, and more. Self-host GitLab on your own servers, in a container, or on a cloud provider.",,"data_organisation, data_publication, it_support, data_manager" -Globus,https://www.globus.org,"Globus lets you efficiently, securely, and reliably transfer data directly between systems separated by an office wall or an ocean. Focus on your research and offload your data transfer headaches to Globus",,"transfer, it_support" -GnpIS,https://urgi.versailles.inrae.fr/gnpis/,"A multispecies integrative information system dedicated to plant and fungi pests. It allows researchers to access genetic, phenotypic and genomic data. It is used by both large international projects and the French National Research Institute for Agriculture, Food and Environment.","fairsharing:dw22y3, biotools:gnpis",plants -Google Dataset Search,https://datasetsearch.research.google.com/,Search engine for datasets,,existing_data -Google Drive,https://www.google.com/intl/en_us/drive/,Cloud Storage for Work and Home,,"storage, transfer" -GPCRmd,http://gpcrmd.org/,Repository of GPCR protein simulations,biotools:GPCRmd,"biomol_sim, data_publication" -GRAPE 2.0,https://github.com/guigolab/grape-nf,"The GRAPE pipeline provides an extensive pipeline for RNA-Seq analyses. It allows the creation of an automated and integrated workflow to manage, analyse and visualize RNA-Seq data.",biotools:grape_2.0,data_analysis -Harvard Medical School - ELN Comparison Grid,https://datamanagement.hms.harvard.edu/analyze/electronic-lab-notebooks,ELN Comparison Grid by Hardvard Medical School,,"metadata, identifiers, researcher, data_manager" -Haz-Map,https://haz-map.com/,Haz-Map is an occupational health database that makes available information about the adverse effects of exposures to chemical and biological agents at the workplace. These associations have been established using current scientific evidence.,,toxicology_data -How to License Research Data - DCC,https://www.dcc.ac.uk/guidance/how-guides/license-research-data,Guidelines about how to license research data from Digital Curation Centre,,"licensing, researcher, data_manager, policy_officer" -Human Protein Atlas,https://www.proteinatlas.org/,The Human Protein Atlas contains information for a large majority of all human protein-coding genes regarding the expression and localization of the corresponding proteins based on both RNA and protein data.,fairsharing:j0t0pe,proteomics -HumanMine,https://www.humanmine.org/,"HumanMine integrates many types of human data and provides a powerful query engine, export for results, analysis for lists of data and FAIR access via web services.",biotools:humanmine,"data_organisation, data_manager, researcher, human_data, data_analysis" -iCloud,https://www.icloud.com/,Data sharing,,"storage, data_analysis, transfer" -Identifiers.org,http://identifiers.org,The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession).,"biotools:identifiers.org, fairsharing:n14rc8","identifiers, it_support, data_manager" -iGEM Parts Registry,http://parts.igem.org/Main_Page,A collection of standard biological parts to which all entrants in the iGEM competition must submit their parts,,micro_biotech -Image Data Resource (IDR),https://idr.openmicroscopy.org,A repository of image datasets from scientific publications,fairsharing:6wf1zw,"micro_biotech, data_publication, metadata, transfer, ome, bioimaging_data" -Informed Consent Ontology,http://purl.obolibrary.org/obo/ICO.owl,The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field.,fairsharing:b9znd5,"it_support, policy_officer, human_data" -International Compilation of Human Research Standards,https://www.hhs.gov/ohrp/sites/default/files/2020-international-compilation-of-human-research-standards.pdf,"The International Compilation of Human Research Standards enumerates over 1,000 laws, regulations, and guidelines (collectively referred to as standards) that govern human subject protections in 133 countries, as well as standards from a number of international and regional organizations",,human_data -International Nucleotide Sequence Database Collaboration (INSDC),http://www.insdc.org,"A collaborative database of genetic sequence datasets from DDBJ, EMBL-EBI and NCBI",,"micro_biotech, data_brokering" -International Society for the Advancement of Cytometry (ISAC),https://isac-net.org/page/Data-Standards,Data standards and formats for reporting flow cytometry data,biotools:NA,micro_biotech -International Union of Biochemistry and Molecular Biology (IUBMB),https://www.qmul.ac.uk/sbcs/iubmb/,Resource for naming standards in biochemistry and molecular biology,,micro_biotech -InterPro,https://www.ebi.ac.uk/interpro/,Functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites,fairsharing:pda11d, -IntoGen,https://www.intogen.org/search,IntoGen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes.,biotools:intogen,"data_analysis, human_data" -Intrinsically disordered proteins ontology (IDPO),https://disprot.org/about,Intrinsically disordered proteins ontology,,"idp, metadata" -IRIS,https://www.epa.gov/iris,The Integrated Risk Information System (IRIS) resource evaluates information on health that might arise after exposure to environmental contaminants.,,toxicology_data -iRODS,https://irods.org/,Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow.,biotools:irods,"storage, it_support, transmed, bioimaging_data" -ISA-tools,https://isa-tools.org/,"Open source framework and tools helping to manage a diverse set of life science, environmental and biomedical experiments using the Investigation Study Assay (ISA) standard",fairsharing:53gp75,"it_support, data_manager, micro_biotech, machine_actionability" -ISA4J,https://doi.org/10.12688/f1000research.27188.1,Open source software library that can be used to generate a ISA-TAB export from in-house data sets. These comprises e.g. local database or local file system based experimental.,biotools:isa4j,"plants, machine_actionability, plant_pheno_assembly" -ISO/IEC 27001,https://en.wikipedia.org/wiki/ISO/IEC_27001,International information security standard,,"data_protection, policy_officer, human_data" -IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN),https://www.qmul.ac.uk/sbcs/iupac/jcbn/,A collaborative resource from IUPAC and IUBMB for naming standards in biochemistry,,micro_biotech -JBEI-ICE,https://ice.jbei.org,A registry platform for biological parts,,micro_biotech -Jupyter,https://jupyter.org,"Jupyter notebooks allow to share code, documentation",,"it_support, data_analysis" -Keycloak,https://www.keycloak.org/,Keycloak is an open source identity and data access management solution.,,"it_support, transmed" -LimTox,http://limtox.bioinfo.cnio.es/,"The LiMTox system is a text mining approach that tries to extract associations between compounds and a particular toxicological endpoint at various levels of granularity and evidence types, all inspired by the content of toxicology reports. It integrates direct ranking of associations between compounds and hepatotoxicity through combination of heterogeneous complementary strategies from term co-mention, rules, and patterns to machine learning-based text classification. It also provides indirect associations to hepatotoxicity through the extraction of relations reflecting the effect of compounds at the level of metabolism and liver enzymes.",biotools:limtox,toxicology_data -Linked Open Vocabularies (LOV),https://lov.linkeddata.es/dataset/lov/,Web portal for finding ontologies,,"metadata, data_manager, researcher" -List of Prokaryotic names with Standing in Nomenclature (LPSN),https://lpsn.dsmz.de,A database of prokaryote specific biodiversity information,,micro_biotech -LUMI,https://www.lumi-supercomputer.eu/,EuroHPC world-class supercomputer,,"data_analysis, researcher, it_support, csc" -maDMP - Research Bridge,https://library.ust.hk/sc/machine-actionable-dmp/,Machine-Actionable Data Management Plan | Webinar (2016) on making a good data management plan.,,"dmp, it_support" -MarDB,https://mmp2.sfb.uit.no/mardb/,"MarDB includes all non-complete marine microbial genomes regardless of level of completeness. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation.",biotools:mardb,"marine_assembly, data_analysis" -MarFun,https://mmp2.sfb.uit.no/marfun/,MarFun is a manually curated marine fungi genome database.,,"marine_assembly, data_analysis" -Marine metagenomics portal,https://mmp2.sfb.uit.no/,High-quality curated and freely accessible microbial genomics and metagenomics resources for the marine scientific community,biotools:mmp,marine_assembly -MarRef,https://mmp2.sfb.uit.no/marref/,"MarRef is a manually curated marine microbial reference genome database that equenced genomes. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation information",biotools:marref,marine_assembly -MemProtMD,http://memprotmd.bioch.ox.ac.uk/,Database of over 5000 intrinsic membrane protein structures,,biomol_sim -Mendeley data,https://data.mendeley.com/,"Multidisciplinary, free-to-use open repository specialized for research data",fairsharing:3epmpp,"data_publication, biomol_sim" -MetabolomeXchange,http://www.metabolomexchange.org/site/,A repository of genomics data relating to the study of the metabolome,,"micro_biotech, data_publication" -MIADE,https://www.psidev.info/intrinsically-disordered-proteins-workgroup,Minimum Information About Disorder Experiments (MIADE) standard,,"metadata, researcher, data_manager, idp" -MIAPPE,https://www.miappe.org/,Minimum Information About a Plant Phenotyping Experiment,fairsharing:nd9ce9,"metadata, researcher, data_manager, plants, plant_geno_assembly, plant_pheno_assembly" -Microsoft Azure,https://azure.microsoft.com/en-gb/,Cloud storage and file sharing service from Microsoft,,"storage, it_support, transfer" -Microsoft OneDrive,https://www.microsoft.com/en-us/microsoft-365/onedrive/online-cloud-storage,Cloud storage and file sharing service from Microsoft,,"storage, it_support" -MIGS/MIMS,https://genomicsstandardsconsortium.github.io/mixs/,Minimum Information about a (Meta)Genome Sequence,fairsharing:va1hck,"metadata, researcher, data_manager, marine, micro_biotech" -MINT,https://mint.bio.uniroma2.it/,"MINT, the Molecular INTeraction database, focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators",fairsharing:2bdvmk, -MIxS,https://gensc.org/mixs/,Minimum Information about any (x) Sequence,fairsharing:9aa0zp,"metadata, researcher, data_manager, marine, plant_geno_assembly" -MobiDB,https://mobidb.org/,A database of protein disorder and mobility annotations,biotools:mobidb,"idp, researcher" -MoDEL,https://mmb.irbbarcelona.org/MoDEL/,Database of Protein Molecular Dynamics simulations representing different structural clusters of the PDB,"biotools:model, fairsharing:NA",biomol_sim -MoDEL Covid19,https://bioexcel-cv19.bsc.es/#/,Database of COVID-19 related atomistic Molecular Dynamic Trajectories,,biomol_sim -MoDEL-CNS,https://mmb.irbbarcelona.org/MoDEL-CNS/#/,Repository for Central Nervous System-related mainly membrane protein MD simulations,,"biomol_sim, data_publication" -ModelArchive,https://www.modelarchive.org/,Repository for theoretical models of macromolecular structures with DOIs for models,fairsharing:tpqndj,"biomol_sim, struct_bioinfo, data_publication" -Molgenis,https://molgenis.gitbooks.io/molgenis/content/,"Molgenis is a modular web application for scientific data. Molgenis provides researchers with user friendly and scalable software infrastructures to capture, exchange, and exploit the large amounts of data that is being produced by scientific organisations all around the world.",biotools:molgenis,"identifiers, it_support, data_manager" -MolMeDB,https://molmedb.upol.cz/,Database about interactions of molecules with membranes,"biotools:MolMeDB, fairsharing:cwzk3c",biomol_sim -MONARC,https://open-source-security-software.net/project/MONARC,A risk assessment tool that can be used to do Data Protection Impact Assessments,,"data_protection, policy_officer, human_data, transmed" -MRI2DICOM,https://github.com/szullino/XNAT-PIC,"a Magnetic Resonance Imaging (MRI) converter from ParaVision® (Bruker, Inc. Billerica, MA) file format to DICOM standard",,"researcher, data_manager, xnat-pic" -Multi-Crop Passport Descriptor (MCPD),https://www.bioversityinternational.org/e-library/publications/detail/faobioversity-multi-crop-passport-descriptors-v21-mcpd-v21/,The Multi-Crop Passport Descriptor is the metadata standard for plant genetic resources maintained ex situ by genbanks.,"biotools:NA, fairsharing:hn155r","metadata, researcher, it_support, policy_officer, plants" -MyTardis,http://www.mytardis.org/,A file-system based platform handling the transfer of data,,"data_manager, transfer, bioimaging_data" -National Center for Biotechnology Information (NCBI),https://www.ncbi.nlm.nih.gov,"Online database hosting a vast amount of biotechnological information including nucleic acids, proteins, genomes and publications. Also boasts integrated tools for analysis.",,micro_biotech -NBP,https://www.cdc.gov/biomonitoring/,The National Biomonitoring Program (NBP) is a public resource that offers an assessment of nutritional status and the exposure of the U.S. population to environmental chemicals and toxic substances.,,toxicology_data -NCBI Taxonomy,https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/,NCBI's taxonomy browser is a database of biodiversity information,,micro_biotech -NCIMB,https://www.ncimb.com/culture-collection/,"Hosts information relating to strains, cultures and more",,micro_biotech -Nettskjema,https://nettskjema.no/,"Form and survey tool, also for sensitive data",,"sensitive, tsd" -NextCloud,https://nextcloud.com,"As fully on-premises solution, Nextcloud Hub provides the benefits of online collaboration without the compliance and security risks.",,"storage, it_support, transfer" -Nextflow,https://www.nextflow.io,Nextflow is a framework for data analysis workflow execution,,"it_support, data_analysis" -NMRlipids,http://nmrlipids.blogspot.com/,Repository for lipid MD simulations to validate force fields with NMR data,,"biomol_sim, data_publication" -NPDS,https://www.aapcc.org/national-poison-data-system,The National Poison Data System (NPDS) is a resource that provides poisson exposure occurring in the US and some freely associated states.,,toxicology_data -OHDSI,https://ohdsi.org/,"Multi-stakeholder, interdisciplinary collaborative to bring out the value of health data through large-scale analytics. All our solutions are open-source.",biotools:ohdsi,"researcher, data_manager, data_analysis, storage, transmed, toxicology_data" -OMERO,https://www.openmicroscopy.org,"OMERO is an open-source client-server platform for managing, visualizing and analyzing microscopy images and associated metadata","biotools:omero, fairsharing:NA","metadata, data_manager, it_support, storage, ome, bioimaging_data" -OmicsDI,https://www.omicsdi.org,"Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics)","biotools:omicsdi, fairsharing:re1278","existing_data, proteomics" -OMOP-CDM,https://ohdsi.github.io/CommonDataModel/,OMOP is a common data model for the harmonisation for of observational health data.,,transmed -Ontobee,http://www.ontobee.org,A web portal to search and visualise ontologies,,"metadata, data_manager, researcher" -ONTOMATON,https://github.com/ISA-tools/OntoMaton,OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets.,,"researcher, data_manager, it_support, metadata, identifiers" -Open Definition Conformant Licenses,https://opendefinition.org/licenses/,Licenses that are conformant with the principles laid out in the Open Definition.,,"licensing, researcher, data_manager, policy_officer" -OpenAIRE Explore,https://explore.openaire.eu/search/find,Explore Open Access research outcomes from OpenAIRE network,,existing_data -OpenEBench,https://openebench.bsc.es/,ELIXIR benchmarking platform to support community-led scientific benchmarking efforts and the technical monitoring of bioinformatics reosurces,biotools:openebench,"data_analysis, data_manager, it_support" -OpenRefine,https://openrefine.org/,Data curation tool for working with messy data,,data_quality -OpenScienceFramework,https://osf.io/,"free and open source project management tool that supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery",fairsharing:g4z879,"data_publication, biomol_sim" -OpenStack,https://www.openstack.org/,OpenStack is an open source cloud computing infrastructure software project and is one of the three most active open source projects in the world,,"storage, data_analysis, transmed, ifb" -Orphadata,http://www.orphadata.org/cgi-bin/index.php,"The Orphadata platform provides the scientific community with comprehensive, high-quality datasets related to rare diseases and orphan drugs, in a reusable and computable format",fairsharing-coll:bsg-d001249, -OSF,https://osf.io,"OSF (Open Science Framework) is a free, open platform to support your research and enable collaboration.",,"storage, researcher, data_manager" -OTP,https://gitlab.com/one-touch-pipeline/otp,"One Touch Pipeline (OTP) is a data management platform for running bioinformatics pipelines in a high-throughput setting, and for organising the resulting data and metadata.",,"human_data, metadata, dmp, data_analysis" -ownCloud,https://owncloud.com,Cloud storage and file sharing service,,"storage, it_support, transfer, data_analysis" -PAA,https://bioconductor.org/packages/PAA/,PAA is an R/Bioconductor tool for protein microarray data analysis aimed at biomarker discovery.,biotools:paa,"data_analysis, researcher, human_data, proteomics" -PANGAEA,https://www.pangaea.de/,Data Publisher for Earth and Environmental Science,biotools:pangaea,"data_publication, metadata, researcher, data_manager" -PCDDB,https://pcddb.cryst.bbk.ac.uk/,The Protein Circular Dichroism Data Bank,biotools:pcddb,"idp, researcher" -PDB,https://www.wwpdb.org/,The Protein Data Bank (PDB),biotools:pdb,"researcher, idp, struct_bioinfo" -PDB-Dev,https://pdb-dev.wwpdb.org/,Prototype archiving system for structural models obtained using integrative or hybrid modeling,,"biomol_sim, struct_bioinfo" -PDBx/mmCIF format and tools,https://mmcif.wwpdb.org/,"Information about the standard PDB archive format PDBx/mmCIF, its dictionaries and related software tools",fairsharing:fd28en,struct_bioinfo -PDBx/mmCIF ModelCIF Extension Dictionary,https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/,Extension of the PDBx/mmCIF dictionary for theoretical models of macromolecular structures,,struct_bioinfo -PharmGKB,https://www.pharmgkb.org/,A resource that curates knowledge about the impact of genetic variation on drug response.,biotools:pharmgkb,toxicology_data -Pharos,https://pharosproject.net/,"Pharos provides hazard, use, and exposure information on 140,872 chemicals and 180 different kinds of building products.",biotools:pharos,toxicology_data -PHIS,http://www.phis.inra.fr/,The open-source Phenotyping Hybrid Information System (PHIS) manages and collects data from plants phenotyping and high throughput phenotyping experiments on a day to day basis.,,"plant_pheno_assembly, plants, ifb" -PIA - Protein Inference Algorithms,https://github.com/mpc-bioinformatics/pia,PIA is a toolbox for mass spectrometrey based protein inference and identification analysis.,biotools:pia,"data_analysis, researcher, proteomics" -pISA-tree,https://github.com/NIB-SI/pISA-tree,"A data management solution for intra-institutional organization and structured storage of life science project-associated research data, with emphasis on the generation of adequate metadata.",biotools:pisa-tree,"plants, micro_biotech, researcher, data_manager, data_organisation, metadata, plant_pheno_assembly" -PLAZA,https://bioinformatics.psb.ugent.be/plaza/,"Access point for plant comparative genomics, centralizing genomic data produced by different genome sequencing initiatives.",fairsharing:wBOua0,"plants, plant_geno_assembly, researcher" -PMut,http://mmb.irbbarcelona.org/PMut,Platform for the study of the impact of pathological mutations in protein stuctures.,biotools:pmut,"data_analysis, human_data" -PRIDE,https://www.ebi.ac.uk/pride/,PRoteomics IDEntifications (PRIDE) Archive database,fairsharing:e1byny,proteomics -ProteomeXchange,http://www.proteomexchange.org/,ProteomeXchange provides globally coordinated standard data submission and dissemination pipelines,fairsharing:92dt9d,proteomics -Proteomics Standards Initiative,https://www.psidev.info/,"The HUPO Proteomics Standards Initiative defines community standards for data representation in proteomics and interactomics to facilitate data comparison, exchange and verification.",,proteomics -protocols.io,https://www.protocols.io,A secure platform for developing and sharing reproducible methods.,,micro_biotech -PROV-DM: The PROV Data Model,https://www.w3.org/TR/prov-dm/,PROV-DM is the conceptual data model that forms a basis for the W3C provenance (PROV) family of specifications.,,data_provenance -R Markdown,https://rmarkdown.rstudio.com,"R Markdown documents are fully reproducible. Use a productive notebook interface to weave together narrative text and code to produce elegantly formatted output. Use multiple languages including R, Python, and SQL.",,"data_analysis, researcher" -RD-Connect Genome Phenome Analysis Platform,https://rd-connect.eu/what-we-do/omics/gpap/,The RD-Connect GPAP is an online tool for diagnosis and gene discovery in rare disease research.,,"researcher, human_data" -RDA Standards,https://rd-alliance.github.io/metadata-directory/standards/,"Directory of standard metadata, divided into different research areas",,"metadata, researcher, data_manager" -re3data,https://www.re3data.org/,Registry of Research Data Repositories,,existing_data -REACH registered substances,https://echa.europa.eu/information-on-chemicals/registered-substances,"Portal with public data submitted to ECHA in REACH registration dossiers by substance manufacturers, importers, or their representatives, as laid out by the REACH Regulation (see Understanding REACH regulation).",,toxicology_data -REDCap,https://projectredcap.org,"REDCap is a secure web application for building and managing online surveys and databases. While REDCap can be used to collect virtually any type of data in any environment, it is specifically geared to support online and offline data capture for research studies and operations.",biotools:redcap,"identifiers, it_support, data_manager, data_quality" -REDIportal,http://srv00.recas.ba.infn.it/atlas/,"Database of A-to-I (deamination of adenosines to inosines) events that enables to search RNA editing sites by genomic region, gene name and other relevant features as the tissue of origin.",biotools:rediportal,epitrans -REDItools,https://github.com/BioinfoUNIBA/REDItools,Python scripts to detect RNA editing events in RNAseq experiments,biotools:reditools,epitrans -REDItools2,https://github.com/BioinfoUNIBA/REDItools2,"REDItools2 is the optimized, parallel multi-node version of REDItools.",,epitrans -REMS,https://github.com/CSCfi/rems,"REMS (Resource Entitlement Management System), developed by CSC, is a tool that can be used to manage researchers’ access rights to datasets.",biotools:rems,"it_support, transmed" -Renamer4Mac,https://renamer.com/,File renaming software for Mac,,"data_organisation, data_manager, researcher" -Repository Finder,https://repositoryfinder.datacite.org,Repository Finder can help you find an appropriate repository to deposit your research data. The tool is hosted by DataCite and queries the re3data registry of research data repositories.,,"data_publication, researcher, data_manager" -Research Data Management Organiser,https://rdmorganiser.github.io/en,"Supports the systematic planning, organisation and implementation of research data management throughout the course of a project",,"dmp, researcher, data_manager, it_support" -Research Data Management Platform (RDMP),https://www.dundee.ac.uk/hic/data-team/researchdatamanagementplatform/,"Data management platform for automated loading, storage, linkage and provision of data sets",biotools:rdmp,"storage, it_support" -Research Management Plan,https://researcheracademy.elsevier.com/research-preparation/research-data-management/creating-good-research-data-management-plan,Machine actionable DMPs.,,"dmp, researcher, data_manager" -Research Object Crate (RO-Crate),https://w3id.org/ro/crate,"RO-Crate is a lightweight approach to packaging research data with their metadata, using schema.org. An RO-Crate is a structured archive of all the items that contributed to the research outcome, including their identifiers, provenance, relations and annotations.",fairsharing:wUoZKE,"metadata, storage, data_organisation, data_manager, researcher, micro_biotech, machine_actionability, data_provenance" -Reva,https://reva.link/,Reva connects cloud storages and application providers,,"data_analysis, transfer" -Rightfield,https://rightfield.org.uk,RightField is an open-source tool for adding ontology term selection to Excel spreadsheets,,"researcher, metadata, data_manager, micro_biotech, identifiers, machine_actionability" -Rstudio,https://rstudio.com,"Rstudio notebooks allow to share code, documentation",,"data_analysis, it_support, researcher" -Rucio,https://rucio.cern.ch/,Rucio - Scientific Data Management,,"storage, data_analysis, transfer" -RxNorm,https://www.nlm.nih.gov/research/umls/rxnorm/index.html,RxNorm is a normalized naming system for medications that is maintained by the National Library of Medicine. Rxnorm provides unique identifiers and allows unambiguous communication of drug-related information across the American health computer systems.,biotools:rxnorm,toxicology_data -salDB,https://mmp.sfb.uit.no/databases/saldb/,SalDB is a salmon specific database of genome sequenced prokaryotes representing the microbiota of fishes found in the taxonomic family of Salmonidae.,,marine_assembly -SASBDB,https://www.sasbdb.org/,Small Angle Scattering Biological Data Bank,,"idp, researcher" -SBOL Visual,https://sbolstandard.org/visual-glyphs/,A standard library of visual glyphs used to represent SBOL designs and interactions.,,micro_biotech -SBOLDesigner,https://sboldesigner.github.io,A CAD tool to create SBOL designs through the use of SBOL Visual glyphs.,,micro_biotech -Schema.org,https://schema.org,"Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond.",,"machine_actionability, it_support" -Schemapedia,https://schemapedia.com,Web portal for finding ontologies,,"metadata, data_manager, researcher" -ScienceMesh,https://sciencemesh.io/,ScienceMesh - frictionless scientific collaboration and access to research services,,"storage, data_analysis, transfer" -Scientific Data's Recommended Repositories,https://www.nature.com/sdata/policies/repositories,"List of respositories recommended by Scientific Data, contains both discipline-specific and general repositories.",,"data_publication, researcher, data_manager, it_support" -SeaFile,https://www.seafile.com/,SeaFile File Synchronization and Share Solution,,"storage, transfer" -Semantic data model of the set of common data elements for rare diseases registration,https://github.com/ejp-rd-vp/CDE-semantic-model,A semantic data model describing the common data elements for rare diseases registration.,,rare_disease -semares,www.genevention.com/products,"All-in-one platform for life science data management, semantic data integration, data analysis and visualization",,"researcher, data_manager, metadata, data_analysis, it_support, storage" -Set of common data elements for rare diseases registration,https://eu-rd-platform.jrc.ec.europa.eu/set-of-common-data-elements_en,"Contains 16 data elements to be registered by each rare disease registry across Europe, which are considered to be essential for further research.",,rare_disease -ShortBOL,http://shortbol.org,A scripting language for creating Synthetic Biology Open Language (SBOL) in a more abstract way.,,micro_biotech -SIFTS,https://www.ebi.ac.uk/pdbe/docs/sifts/,"Structure integration with function, taxonomy and sequence",,"researcher, idp" -Silva,https://www.arb-silva.de/,"SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).",fairsharing:5vtYGG, -Singularity,https://sylabs.io,Singularity is a container platform.,,"it_support, data_analysis, tsd" -SMASCH,https://smasch.pages.uni.lu,"SMASCH (Smart Scheduling) system, is a web-based tooldesigned for longitudinal clinical studies requiring recurrent follow-upvisits of the participants. SMASCH controls and simplifies the scheduling of big database of patients. Smasch is also used to organize the daily plannings (delegation of tasks) for the different medical professionals such as doctors, nurses and neuropsychologists.",,"data_organisation, transmed" -Snakemake,https://snakemake.github.io,Snakemake is a framework for data analysis workflow execution,biotools:snakemake,"it_support, data_analysis" -SSBD:database,https://ssbd.riken.jp/database/,Added-value database for biological dynamics images,,"bioimaging_data, data_publication" -SSBD:repository,https://ssbd.riken.jp/repository/,An open data archive that stores and publishes bioimaging and biological quantitative datasets,,"bioimaging_data, data_publication" -Standards for Reporting Enzyme Data (STRENDA),https://www.beilstein-institut.de/en/projects/strenda/,Resource of standards for reporting enzyme data,,micro_biotech -STRING,https://string-db.org/,Known and predicted protein-protein interactions.,fairsharing:9b7wvk,proteomics -SynBioHub,https://synbiohub.org,A searchable design repository for biological constructs,,micro_biotech -Synthetic Biology Open Language (SBOL),https://sbolstandard.org,An open standard for the representation of in silico biological designs and their place in the Design-Build-Test-Learn cycle of synthetic biology.,,micro_biotech -Systems Biology Markup Language (SBML),http://sbml.org/Main_Page,An open format for computational models of biological processes,,micro_biotech -T3DB,http://www.t3db.ca/,"The Toxin and Toxin Target Database is a bioinformatics resource that combines exhaustive toxin data with toxin target information. Currently it presents more than 42,000 toxin-target associations extracted from other databases, government documents, books and scientific literature. Each toxin record includes data on chemical properties and descriptors, toxicity values and medical information.",biotools:t3db,toxicology_data -Talend,https://www.talend.com/,Talend is an open source data integration platform.,,"data_manager, researcher, transmed" -TG-GATES,https://toxico.nibiohn.go.jp/english/,"A toxicogenomics database that stores gene expression data and biochemistry, hematology, and histopathology findings derived from in vivo (rat) and in vitro (primary rat hepatocytes, primary human hepatocytes) exposure to 170 compounds at multiple dosages and time points.",biotools:open_tg-gates,toxicology_data -The Environment Ontology (EnvO),https://sites.google.com/site/environmentontology/,An ontology for expressing environmental terms,,micro_biotech -The European Genome-phenome Archive (EGA),https://ega-archive.org/,EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects,"biotools:ega, fairsharing:mya1ff","data_publication, human_data, policy_officer, csc, tsd" -The Genomic Standards Consortium (GSC),https://gensc.org/mixs/,Minimum Information about any (x) Sequence,"fairsharing:9aa0zp, biotools:NA","metadata, researcher, it_support, policy_officer, human_data" -The Open Biological and Biomedical Ontology (OBO) Foundry,http://obofoundry.org,Collaborative effort to develob interoperable ontologies for the biological sciences,fairsharing-coll:bsg-d001083,"metadata, data_manager, researcher" -Tox21_Toolbox,https://ntp.niehs.nih.gov/whatwestudy/tox21/toolbox/index.html,"The Toxicology in the 21st Century program, or Tox21, is a unique collaboration between several federal agencies to develop new ways to rapidly test whether substances adversely affect human health. The Tox21 Toolbox contains data-analysis tools for accessing and visualizing Tox21 quantitative high-throughput screening (qHTS) 10K library data, as well as integrating with other publicly available data.",,toxicology_data -ToxCast_data,https://www.epa.gov/chemical-research/exploring-toxcast-data-downloadable-data,"The Toxicology in the 21st Century program, or Tox21, is a unique collaboration between several federal agencies to develop new ways to rapidly test whether substances adversely affect human health. This portal contains diverse downloadable results of the ToxCast project.",,toxicology_data -TOXNET,https://www.nlm.nih.gov/toxnet/index.html,"The Toxicology Data Network (TOXNET) was a portal that allowed access to several relevant sources in the toxicological field. Nowadays, these sources have been integrated into other NLM resources.",,toxicology_data -tranSMART,https://github.com/transmart,"Knowledge management and high-content analysis platform enabling analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research.",biotools:transmart,"researcher, data_manager, data_analysis, storage, transmed" -Tryggve ELSI Checklist,https://scilifelab-data-guidelines.readthedocs.io/en/latest/docs/general/sensitive_data.html,"A list of Ethical, Legal, and Societal Implications (ELSI) to consider for research projects on human subjects",,"sensitive, policy_officer, data_manager, human_data, nels, csc, tsd" -TXG-MAPr,https://txg-mapr.eu/,"A tool that contains weighted gene co-expression networks obtained from the Primary Human Hepatocytes, rat kidney, and liver TG-GATEs dataset.",,"data_analysis, researcher, toxicology_data" -UMLS,https://www.nlm.nih.gov/research/umls/index.html,The Unified Medical Language System (UMLS) is a set of tools that establishes a mapping structure among different vocabularies in the biomedical sciences field to enable interoperativity between computer systems.,,toxicology_data -UniChem,https://www.ebi.ac.uk/unichem/,"UniChem is a very simple, large-scale non-redundant database of pointers between chemical structures and EMBL-EBI chemistry resources. Primarily, this service has been designed to maintain cross references between EBI chemistry resources. These include primary chemistry resources (ChEMBL and ChEBI), and other resources where the main focus is not small molecules, but which may nevertheless contain some small molecule information (eg: Gene Expression Atlas, PDBe).",,toxicology_data -UniProt,https://www.uniprot.org/,Comprehensive resource for protein sequence and annotation data,fairsharing:s1ne3g,"metadata, researcher, idp, micro_biotech, proteomics, struct_bioinfo" -University of Cambridge - Electronic Research Notebook Products,https://www.data.cam.ac.uk/data-management-guide/electronic-research-notebooks/electronic-research-notebook-products,List of Electronic Research Notebook Products by University of Cambridge,,"metadata, identifiers, researcher, data_manager" -VisBOL,http://visbol.org,A JavaScript library for the visualisation of SBOL.,,micro_biotech -Wellcome Open Research - Data Guidelines,https://wellcomeopenresearch.org/for-authors/data-guidelines,"Wellcome Open Research requires that the source data underlying the results are made available as soon as an article is published. This page provides information about data you need to include, where your data can be stored, and how your data should be presented.",,"data_publication, researcher, data_manager" -WinSCP,https://winscp.net/eng/index.php,"WinSCP is a popular SFTP client and FTP client for Microsoft Windows! Copy file between a local computer and remote servers using FTP, FTPS, SCP, SFTP, WebDAV or S3 file transfer protocols.",,"transfer, it_support" -WorkflowHub,https://workflowhub.eu,"WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows.",,"data_publication, data_manager, researcher" -XNAT,https://www.xnat.org/,"Open source imaging informatics platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data.",,"researcher, data_analysis, transmed, xnat-pic, bioimaging_data" -XNAT-PIC Pipelines,https://github.com/szullino/XNAT-PIC,Analysing of single or multiple subjects within the same project in XNAT,,"researcher, data_manager, data_analysis, xnat-pic" -XNAT-PIC Uploader,https://github.com/szullino/XNAT-PIC,Import tool for multimodal DICOM image datasets to XNAT,,"researcher, data_manager, xnat-pic" -Zenodo,https://zenodo.org/,Generalist research data repository built and developed by OpenAIRE and CERN,fairsharing:wy4egf,"data_publication, biomol_sim, bioimaging_data, plant_pheno_assembly" -Zooma,https://www.ebi.ac.uk/spot/zooma/,Find possible ontology mappings for free text terms in the ZOOMA repository.,,"metadata, data_manager, researcher" diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index d9ccfba5e..59836c450 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -1,559 +1,372 @@ - description: Network providing unified programmatic access to experimentally determined and predicted structure models + id: 3d-beacons name: 3D-Beacons - registry: - biotools: 3d-beacons - related_pages: - - struct_bioinfo url: https://3d-beacons.org - description: A standard schema for primary biodiversity data + id: access-to-biological-collection-data-schema-(abcd) name: Access to Biological Collection Data Schema (ABCD) - related_pages: - - micro_biotech + registry: + biotools: NA url: https://www.tdwg.org/standards/abcd/ - description: Ada is a performant and highly configurable system for secured integration, visualization, and collaborative analysis of heterogeneous data sets, primarily targeting clinical and experimental sources. + id: ada-discovery-analytics-(ada) name: Ada Discovery Analytics (Ada) - related_pages: - - data_analysis - - transmed url: https://ada-discovery.github.io/ - description: A searchable repository with a focus on plasmids + id: addgene name: Addgene - registry: - fairsharing: 8hcczk - related_pages: - - micro_biotech url: https://www.addgene.org/browse/ - description: Browser for ontologies for agricultural science based on NBCO BioPortal. + id: agroportal name: AgroPortal registry: biotools: AgroPortal - fairsharing: z4xpxx - related_pages: - - plant_pheno_assembly url: http://agroportal.lirmm.fr/ - description: Amazon Web Services + id: amazon-web-services name: Amazon Web Services - registry: - tess: Amazon Web Services - related_pages: - - storage - - data_analysis - - transfer url: https://aws.amazon.com/ - description: Amnesia is a GDPR compliant high accuracy data anonymization tool + id: amnesia name: Amnesia - related_pages: - - sensitive url: https://amnesia.openaire.eu/ - description: AOP4EUpest web server is devoted to the identification of pesticides involved in an Adverse Outcome Pathway via text mining approaches. + id: aop4eupest name: AOP4EUpest registry: biotools: aop4eupest - related_pages: - - toxicology_data url: http://www.biomedicale.parisdescartes.fr/aop4EUpest/home.php - description: APID (Agile Protein Interactomes DataServer) is a server that provides a comprehensive collection of protein interactomes for more than 400 organisms based in the integration of known experimentally validated protein-protein physical interactions (PPIs) + id: apid-interactomes name: APID Interactomes registry: biotools: apid - related_pages: - - idp url: http://apid.dep.usal.es/ - description: Plan and follow your data. Bring your Data Management Plans closer to where data are generated, analysed and stored. + id: argos name: Argos - related_pages: - - dmp - - researcher - - data_manager url: https://argos.openaire.eu/splash/ - description: A repository of array based genomics data + id: arrayexpress name: ArrayExpress - registry: - biotools: arrayexpress - fairsharing: 6k0kwd - tess: ArrayExpress - related_pages: - - micro_biotech - - data_publication url: https://www.ebi.ac.uk/arrayexpress/ - description: With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources. + id: arvados name: Arvados - related_pages: - - it_support - - policy_officer - - researcher - - data_analysis url: https://arvados.org - description: With fast file transfer and streaming solutions built on the award-winning IBM FASP protocol, IBM Aspera software moves data of any size across any distance + id: aspera-fasp name: Aspera Fasp - related_pages: - - transfer - - it_support url: https://www.ibm.com/products/aspera - description: Biological materials resource including cell-lines, strains and genomics tools + id: atcc name: ATCC - registry: - biotools: atcc - related_pages: - - micro_biotech url: https://www.lgcstandards-atcc.org/en.aspx# - description: Free, publicly available web-based, open-source software application developed by the OHDSI community to support the design and execution of observational analyses to generate real world evidence from patient level observational data. + id: atlas name: Atlas registry: - biotools: atlas - tess: Atlas - related_pages: - - data_manager - - researcher - - transmed + fairsharing: NA url: https://github.com/OHDSI/Atlas/wiki - description: Store and publish your research data. Can be used to bridge between domains + id: b2share name: b2share - registry: - fairsharing: da9307 - related_pages: - - storage - - data_publication - - bioimaging_data url: https://b2share.eudat.eu/ - description: A searchable database for bacteria specific information + id: bacdive name: BacDive - registry: - biotools: bacdive - related_pages: - - micro_biotech url: https://bacdive.dsmz.de - description: A repository specific to Bacillus strains + id: bacillus-genetic-stock-center-(bgsc) name: Bacillus Genetic Stock Center (BGSC) - related_pages: - - micro_biotech + registry: + biotools: NA url: http://www.bgsc.org/ - description: A search engine for academic web resources + id: base name: BASE - registry: - biotools: base - tess: BASE - related_pages: - - existing_data url: https://www.base-search.net/ - description: The ELSI Knowledge Base is an open-access resource platform that aims at providing practical know-how for responsible research. + id: bbmri-erics-elsi-knowledge-base name: BBMRI-ERIC's ELSI Knowledge Base - related_pages: - - data_protection - - sensitive - - policy_officer - - data_manager - - human_data url: https://www.bbmri-eric.eu/elsi/knowledge-base/ - description: The Beacon protocol defines an open standard for genomics data discovery. + id: beacon name: Beacon - registry: - biotools: beacon - fairsharing: 6fba91 - tess: Beacon - related_pages: - - researcher - - data_manager - - it_support - - human_data url: https://beacon-project.io/ - description: R&D Platform for Life Sciences + id: benchling name: Benchling - related_pages: - - micro_biotech url: https://www.benchling.com - description: BIAFLOWS is an open-soure web framework to reproducibly deploy and benchmark bioimage analysis workflows + id: biaflows name: BIAFLOWS registry: biotools: biaflows - related_pages: - - data_analysis url: https://biaflows.neubias.org/ - description: Repository for Nucleic Acids MD simulations + id: bignasim name: BigNASim registry: biotools: bignasim - related_pages: - - biomol_sim - - data_publication url: https://mmb.irbbarcelona.org/BigNASim/ - description: The BioImage Informatics Index is a registry of software tools, image databases for benchmarking, and training materials for bioimage analysis + id: biii name: BIII registry: biotools: BISE - related_pages: - - it_support - - data_analysis url: https://biii.eu/ - description: Public, web-accessible database of measured binding affinities + id: bindingdb name: BindingDB registry: biotools: bindingdb fairsharing: 3b36hk - related_pages: - - biomol_sim url: https://www.bindingdb.org/ - description: Bio-Formats is a software tool for reading and writing image data using standardized, open formats + id: bio-formats name: Bio-Formats registry: biotools: bio-formats - tess: Bio-Formats - related_pages: - - ome - - bioimaging_data url: https://www.openmicroscopy.org/bio-formats/ - description: Platform designed to efficiently generate bioactive conformers and speed up the drug discovery process. + id: bioactive-conformational-ensemble name: Bioactive Conformational Ensemble registry: biotools: bce - related_pages: - - biomol_sim url: https://mmb.irbbarcelona.org/BCE/ - description: Bioconda is a bioinformatics channel for the Conda package manager + id: bioconda name: Bioconda registry: biotools: bioconda - tess: Bioconda - related_pages: - - it_support - - data_analysis url: https://bioconda.github.io/ - description: Biodiversity Information Standards (TDWG), historically the Taxonomic Databases Working Group, work to develop biodiversity information standards + id: biodiversity-information-standards-(tdwg) name: Biodiversity Information Standards (TDWG) - related_pages: - - micro_biotech url: https://www.tdwg.org - description: Platform designed to provide web-access to atomistic-MD trajectories for macromolecules involved in the COVID-19 disease. + id: bioexcel-covid-19 name: BioExcel COVID-19 - related_pages: - - biomol_sim url: https://bioexcel-cv19.bsc.es/#/ - description: The BioImage Archive stores and distributes biological images that are useful to life-science researchers. + id: bioimagearchive name: BioImageArchive registry: fairsharing: x38D2k - related_pages: - - data_publication - - bioimaging_data url: https://www.ebi.ac.uk/bioimage-archive/ - description: A repository of mathematical models for application in biological sciences + id: biomodels name: BioModels registry: - biotools: biomodels fairsharing: paz6mh - tess: BioModels - related_pages: - - micro_biotech - - data_publication url: https://www.ebi.ac.uk/biomodels/ - description: BIONDA is a free and open-access biomarker database, which employs various text mining methods to extract structured information on biomarkers from abstracts of scientific publications + id: bionda name: BIONDA registry: biotools: bionda - related_pages: - - storage - - researcher - - human_data - - proteomics url: http://bionda.mpc.ruhr-uni-bochum.de/start.php - description: BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. + id: biosamples name: BioSamples registry: - biotools: biosamples fairsharing: ewjdq6 - tess: BioSamples - related_pages: - - plants - - plant_geno_assembly url: https://www.ebi.ac.uk/biosamples/ - description: Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials + id: bioschemas name: Bioschemas - registry: - fairsharing: f3a3ca - tess: Bioschemas - related_pages: - - machine_actionability - - it_support url: https://bioschemas.org - description: A database hosting datasets from biological studies. Useful for storing or accessing data that is not compliant for mainstream repositories. + id: biostudies name: BioStudies - registry: - biotools: biostudies - fairsharing: mtjvme - tess: BioStudies - related_pages: - - micro_biotech - - plants - - data_publication url: https://www.ebi.ac.uk/biostudies/ - description: Resource for management and analysis of 5D biological images + id: bisque name: BisQue - registry: - biotools: bisque - related_pages: - - data_organisation - - data_manager - - data_analysis - - bioimaging_data url: https://bioimage.ucsb.edu/bisque - description: Git based code hosting and collaboration tool, built for teams. + id: bitbucket name: Bitbucket - registry: - fairsharing: fc3431 - related_pages: - - data_organisation - - data_manager - - it_support url: https://bitbucket.org/ - description: Biological Magnetic Resonance Data Bank + id: bmrb name: BMRB - registry: - biotools: bmrb - related_pages: - - idp - - researcher url: https://bmrb.io/ - description: BoostDM is a method to score all possible point mutations (single base substitutions) in cancer genes for their potential to be involved in tumorigenesis. + id: boostdm name: BoostDM registry: biotools: boostdm - related_pages: - - data_analysis - - human_data url: https://www.intogen.org/boostdm/search - description: Cloud storage and file sharing service + id: box name: Box - registry: - tess: Box - related_pages: - - storage - - it_support - - transfer url: https://www.box.com - description: 'Specification for a standard API for plant data: plant material, plant phenotyping data' + id: brapi name: BrAPI - related_pages: - - it_support - - plants - - plant_pheno_assembly url: https://www.brapi.org - description: Database of enzyme and enzyme-ligand information, across all taxonomic groups, manually extracted from primary literature and extended by text mining procedures + id: brenda name: BRENDA registry: - biotools: brenda fairsharing: etp533 - tess: BRENDA - related_pages: - - micro_biotech url: https://www.brenda-enzymes.org/ - description: File renaming software for Windows + id: bulk-rename-utility name: Bulk Rename Utility - related_pages: - - data_organisation - - data_manager - - researcher url: https://www.bulkrenameutility.co.uk/ - description: A highly useful and flexible tool for calibration of targeted MS?based measurements. CalibraCurve enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays. The software uses a variety of measures to assess the accuracy of the calibration and provides intuitive visualizations. + id: calibracurve name: CalibraCurve registry: biotools: calibracurve - related_pages: - - data_analysis - - proteomics url: https://github.com/mpc-bioinformatics/CalibraCurve - description: Continuous evaluation of the accuracy and reliability of protein structure prediction methods in a fully automated manner + id: cameo name: CAMEO registry: biotools: cameo fairsharing: dq34p2 - related_pages: - - struct_bioinfo url: https://cameo3d.org - description: Cancer Genome Interpreter (CGI) is designed to support the identification of tumor alterations that drive the disease and detect those that may be therapeutically actionable. + id: cancer-genome-interpreter name: Cancer Genome Interpreter registry: biotools: cgi - related_pages: - - data_analysis - - human_data url: https://www.cancergenomeinterpreter.org/home - description: Critical assessment of structure prediction methods for protein-protein interactions + id: capri name: CAPRI - related_pages: - - struct_bioinfo url: https://www.ebi.ac.uk/pdbe/complex-pred/capri/ - description: The CAS Registry (Chemical Abstracts Service Registry) includes more than 188 million unique chemicals. CAS Registry Numbers are broadly used as a unique identifier for chemical substances. The Registry is maintained by CAS, a subdivision of the American Chemical Society. + id: cas-registry name: CAS Registry - registry: - fairsharing: r7Kwy7 - related_pages: - - toxicology_data url: https://www.cas.org/cas-data/cas-registry - description: Biennial critical assessment of techniques for protein structure prediction + id: casp name: CASP - registry: - biotools: casp - tess: CASP - related_pages: - - struct_bioinfo url: https://predictioncenter.org - description: Castor is an EDC system for researchers and institutions. With Castor, you can create and customize your own database in no time. Without any prior technical knowledge, you can build a study in just a few clicks using our intuitive Form Builder. Simply define your data points and start collecting high quality data, all you need is a web browser. + id: castor name: Castor registry: - biotools: castor - related_pages: - - identifiers - - it_support - - data_manager + fairsharing: NA url: https://www.castoredc.com - description: A hierarchical domain classification of protein structures in the Protein Data Bank. + id: cath name: CATH registry: - biotools: cath fairsharing: xgcyyn - tess: CATH url: http://www.cathdb.info/ - description: CEDAR is making data submission smarter and faster, so that scientific researchers and analysts can create and use better metadata. + id: cedar name: CEDAR - registry: - biotools: cedar - fairsharing: pmygc7 - related_pages: - - metadata - - machine_actionability - - researcher - - data_manager url: https://metadatacenter.org - description: A version management tool for modifying strains + id: cellrepo name: CellRepo - related_pages: - - micro_biotech url: https://cellrepo.herokuapp.com/ - description: An ontology for expressing cellular (or multi-cellular) terms with applications in microscopy + id: cellular-microscopy-phenotype-ontology-(cmpo) name: Cellular Microscopy Phenotype Ontology (CMPO) - registry: - tess: Cellular Microscopy Phenotype Ontology (CMPO) - related_pages: - - micro_biotech url: https://www.ebi.ac.uk/cmpo/ - description: CERNBox cloud data storage, sharing and synchronization + id: cernbox name: CERNBox - related_pages: - - storage url: https://cernbox.web.cern.ch/cernbox/ - description: Dictionary of molecular entities focused on 'small' chemical compounds + id: chebi name: ChEBI registry: - biotools: chebi fairsharing: 62qk8w - tess: ChEBI - related_pages: - - micro_biotech url: https://www.ebi.ac.uk/chebi/ - description: Database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties and abstracted bioactivities. + id: chembl name: ChEMBL registry: biotools: chembl fairsharing: m3jtpg - tess: ChEMBL - related_pages: - - data_analysis - - researcher - - toxicology_data url: https://www.ebi.ac.uk/chembl/ - description: ChIPSummitDB is a database of transcription factor binding sites and the distances of the binding sites relative to the peak summits. + id: chipsummitdb name: ChIPSummitDB registry: biotools: chipsummitdb - related_pages: - - human_data url: http://summit.med.unideb.hu/summitdb/ - description: Choose an open source license + id: choose-a-license name: Choose a license - related_pages: - - licensing - - researcher - - data_manager - - policy_officer url: https://choosealicense.com - description: ClinicalTrials.gov is a resource depending on the National Library of medicine which makes available private and public-funded clinical trials. + id: clinicaltrials.gov name: ClinicalTrials.gov - registry: - fairsharing: mewhad - related_pages: - - toxicology_data url: https://clinicaltrials.gov/ - description: A collection of software applications which enables creation, storing and publishing of "Common Data Elements" according to the CDE semantic model. + id: common-data-elements-(cde)-in-a-box- name: Common Data Elements (CDE) in a box - registry: - biotools: cde - related_pages: - - rare_disease url: https://github.com/ejp-rd-vp/cde-in-box - description: An open standard for describing workflows that are build from command line tools + id: common-workflow-language-(cwl) name: Common Workflow Language (CWL) registry: fairsharing: 8y5ayx - tess: Common Workflow Language (CWL) - related_pages: - - it_support - - researcher - - data_analysis url: https://www.commonwl.org - description: The CompTox Chemicals Dashboard provides toxicological information for over 800.000 chemical compounds. It is a part of a suite of databases and @@ -561,621 +374,413 @@ Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks. + id: comptox name: Comptox registry: biotools: comptox_chemistry_dashboard - fairsharing: tfj7gt - related_pages: - - toxicology_data url: https://comptox.epa.gov/dashboard - description: An initiative to bring together various formats and standard for computational models in biology + id: computational-modeling-in-biology-network-(combine) name: COmputational Modeling in BIology NEtwork (COMBINE) - related_pages: - - micro_biotech url: http://co.mbine.org - description: Open source package management system + id: conda name: Conda - registry: - tess: Conda - related_pages: - - it_support - - data_analysis url: https://docs.conda.io/en/latest/ - description: A resource for researchers when drafting consent forms so they can use language matching cutting-edge GA4GH international standards + id: consent-clauses-for-genomic-research name: Consent Clauses for Genomic Research - related_pages: - - human_data url: https://drive.google.com/file/d/1O5Ti7g7QJqS3h0ABm-LyTe02Gtq8wlKM/view?usp=sharing - description: A command-line utility that creates projects from cookiecutters (project templates), e.g. creating a Python package project from a Python package project template. + id: cookiecutter name: Cookiecutter - related_pages: - - data_organisation - - it_support - - data_manager url: https://github.com/cookiecutter/cookiecutter - description: Portal for scientists to broker more easily rich metadata alongside data to public repos. + id: copo name: COPO registry: biotools: copo fairsharing-coll: bsg-d001247 - related_pages: - - metadata - - researcher - - plants - - machine_actionability - - plant_pheno_assembly url: https://copo-project.org/ - description: COVID-19 Molecular Structure and Therapeutics Hub + id: covid-19-molecular-structure-and-therapeutics-hub name: COVID-19 Molecular Structure and Therapeutics Hub - related_pages: - - biomol_sim url: https://covid.bioexcel.eu/ - description: Examples and tools to create a codebook by the Data Documentation Initiative (DDI) + id: create-a-codebook name: Create a Codebook - related_pages: - - metadata - - researcher - - data_manager url: https://ddialliance.org/training/getting-started-new-content/create-a-codebook - description: It helps you choose the right Creative Commons license for your needs. + id: creative-commons-license-chooser name: Creative Commons License Chooser - related_pages: - - licensing - - researcher - - data_manager - - policy_officer url: https://creativecommons.org/choose/ - description: The Crop Ontology compiles concepts to curate phenotyping assays on crop plants, including anatomy, structure and phenotype. + id: crop-ontology name: Crop Ontology registry: fairsharing: wgfrmg - tess: Crop Ontology - related_pages: - - researcher - - data_manager - - it_support - - plants url: https://www.cropontology.org - description: A Python tool to encrypt, decrypt or re-encrypt files, according to the GA4GH encryption file format. + id: crypt4gh name: Crypt4GH - related_pages: - - human_data url: https://crypt4gh.readthedocs.io/en/latest/ - description: Cloud Storage Services for Synchronization and Sharing (CS3) + id: cs3 name: CS3 - related_pages: - - storage url: https://www.cs3community.org/ - description: A database that aims to advance understanding about how environmental exposures affect human health. + id: ctd name: CTD registry: biotools: ctd - related_pages: - - toxicology_data url: http://ctdbase.org/ - description: command line tool and library for transferring data with URLs + id: curl name: cURL - related_pages: - - transfer - - it_support url: https://curl.se - description: Image Data management + id: cytomine-ims name: Cytomine-IMS - related_pages: - - data_manager - - bioimaging_data url: https://github.com/cytomine/Cytomine-IMS - description: Data Information System to keep sensitive data inventory and meet GDPR accountability requirement. + id: daisy name: DAISY registry: biotools: Data_Information_System_DAISY - related_pages: - - it_support - - policy_officer - - human_data - - data_protection - - transmed url: https://daisy-demo.elixir-luxembourg.org - description: Unique collection of project-level metadata from large research initiatives in a diverse range of fields, including clinical, molecular and observational studies. Its aim is to improve the findability of these projects following FAIR data principles. + id: data-catalog name: Data Catalog - related_pages: - - metadata - - transmed + registry: + fairsharing: NA url: https://datacatalog.elixir-luxembourg.org/ - description: DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web. + id: data-catalog-vocabulary-(dcat) name: Data Catalog Vocabulary (DCAT) - related_pages: - - machine_actionability - - it_support - - rare_disease url: https://www.w3.org/TR/vocab-dcat-2/ - description: List of metadata standards + id: data-curation-centre-metadata-list name: Data Curation Centre Metadata list - related_pages: - - metadata - - researcher - - data_manager url: https://www.dcc.ac.uk/guidance/standards/metadata/list - description: Dataverse for life sciences and agronomic related data + id: data-inrae name: Data INRAE registry: fairsharing: 178BmT - related_pages: - - plants - - plant_geno_assembly - - researcher - - data_manager - - plant_pheno_assembly url: https://data.inrae.fr/ - description: Publicly available online tool for composing smart data management plans + id: data-stewardship-wizard name: Data Stewardship Wizard registry: biotools: Data_Stewardship_Wizard - tess: Data Stewardship Wizard - related_pages: - - dmp - - researcher - - data_manager - - it_support - - nels - - tsd - - plant_pheno_assembly url: https://ds-wizard.org/ - description: DUO allows to semantically tag datasets with restriction about their usage. + id: data-use-ontology name: Data Use Ontology registry: fairsharing: 5dnjs2 - tess: Data Use Ontology - related_pages: - - data_manager - - researcher - - human_data url: https://github.com/EBISPOT/DUO - description: Overview of typical licenses used for data resources + id: data.world-data-license-list name: data.world Data License list - related_pages: - - licensing - - biomol_sim url: https://help.data.world/hc/en-us/articles/115006114287-Common-license-types-for-datasets - description: A search engine for the complete collection of publicly available DataCite DOIs + id: datacite name: DataCite registry: fairsharing: yknezb - related_pages: - - existing_data url: https://search.datacite.org/ - description: Open source research data respository software. + id: dataverse name: DATAVERSE registry: - tess: DATAVERSE - related_pages: - - storage - - researcher - - data_manager - - it_support - - ifb + fairsharing: NA url: https://dataverse.org/ - description: The Data Agreement Wizard is a tool developed by ELIXIR-Luxembourg to facilitate data sharing agreements. + id: dawid name: DAWID - related_pages: - - data_protection - - policy_officer - - human_data url: https://dawid.elixir-luxembourg.org/ - description: The database of Genotypes and Phenotypes (dbGaP) archives and distributes data from studies investigating the interaction of genotype and phenotype in Humans + id: dbgap name: dbGAP registry: - biotools: dbgap fairsharing: 88v2k0 - tess: dbGAP - related_pages: - - data_publication - - researcher - - it_support - - human_data url: https://www.ncbi.nlm.nih.gov/gap/ - description: A discovery platform containing collections of genes and variants associated to human diseases. + id: disgenet name: DisGeNET registry: biotools: disgenet - fairsharing: fssydn - related_pages: - - data_analysis - - human_data - - researcher - - toxicology_data url: https://www.disgenet.org/ - description: A database of intrinsically disordered proteins + id: disprot name: DisProt registry: biotools: disprot - fairsharing: dt9z89 - tess: DisProt - related_pages: - - idp - - researcher url: https://disprot.org/ - description: Questionnaire, which generates a pre-filled a DMP + id: dmp-canvas-generator name: DMP Canvas Generator - related_pages: - - dmp - - researcher - - data_manager url: https://dmp.vital-it.ch - description: Semi-automatically generated, searchable catalogue of resources that are relevant to data management plans. + id: dmplanner name: DMPlanner - related_pages: - - dmp - - researcher - - data_manager url: https://dmplanner.athenarc.gr/ - description: DMP Roadmap is a Data Management Planning tool. + id: dmproadmap name: DMPRoadmap - related_pages: - - dmp - - researcher - - data_manager url: https://github.com/DMPRoadmap/roadmap - description: Build your Data Management Plan + id: dmptool name: DMPTool - related_pages: - - dmp - - researcher - - data_manager url: https://dmptool.org - description: A database of DNA sequences + id: dna-data-bank-of-japan-(ddbj) name: DNA Data Bank of Japan (DDBJ) - registry: - biotools: ddbj - related_pages: - - micro_biotech url: https://www.ddbj.nig.ac.jp/index-e.html - description: Docker is a software for the execution of applications in virtualized environments called containers. It is linked to DockerHub, a library for sharing container images + id: docker name: Docker registry: - fairsharing: afc2b3 fairsharing-coll: bsg-d001254 - tess: Docker - related_pages: - - it_support - - data_analysis url: https://www.docker.com/ - description: Cloud storage and file sharing service + id: dropbox name: DropBox - related_pages: - - storage - - it_support - - transfer url: https://www.dropbox.com/?landing=dbv2 - description: A toxicogenomic resource that provides access to the gene expression profiles of over 600 different compounds in several cell types from rats and primary rat hepatocytes. + id: drug-matrix name: Drug Matrix - related_pages: - - toxicology_data url: https://ntp.niehs.nih.gov/data/drugmatrix/ - description: Open-source, community-led data curation, publishing, and preservation platform for CC0 publicly available research data + id: dryad name: Dryad registry: fairsharing: wkggtx - related_pages: - - data_publication - - biomol_sim - - bioimaging_data url: https://datadryad.org/ - description: Database of folding / unfolding pathway of representatives from all known protein folds by MD simulation + id: dynameomics name: Dynameomics - related_pages: - - biomol_sim url: http://www.dynameomics.org/ - description: Electronic data archive library is a framework for publishing and sharing research data + id: e!dal name: e!DAL registry: biotools: edal - related_pages: - - storage - - it_support url: https://edal.ipk-gatersleben.de/ - description: Plant Genomics and Phenomics Research Data Repository + id: e!dal-pgp name: e!DAL-PGP registry: fairsharing: rf3m4g - related_pages: - - plants - - plant_geno_assembly - - researcher - - data_manager - - it_support - - data_publication - - metadata - - plant_pheno_assembly url: https://edal-pgp.ipk-gatersleben.de/ - description: The ECOTOXicology Knowledgebase (ECOTOX) is a comprehensive, publicly available Knowledgebase providing single chemical environmental toxicity data on aquatic life, terrestrial plants, and wildlife. + id: ecotox name: ECOTOX - related_pages: - - toxicology_data url: https://cfpub.epa.gov/ecotox/ - description: Hub for the identification of plant genetic resources in Europe + id: ecpgr name: ECPGR - related_pages: - - plants - - researcher - - data_manager url: https://www.ecpgr.cgiar.org/ - description: 'Endocrine Disruptor Knowledge Base is a platform designed to foster the development of computational predictive toxicology. This platform allows direct access to ten libraries containing the following resources: a biological activity database, QSAR training sets, in vitro and in vivo experimental data for more than 3,000 chemicals, literature citations, chemical-structure search capabilities.' + id: edkb name: EDKB - related_pages: - - toxicology_data url: https://www.fda.gov/science-research/bioinformatics-tools/endocrine-disruptor-knowledge-base - description: Set of European data resources of fundamental importance to the wider life-science community and the long-term preservation of biological data + id: elixir-core-data-resources name: ELIXIR Core Data Resources registry: fairsharing-coll: bsg-c000039 - related_pages: - - existing_data - - covid-19 url: https://elixir-europe.org/platforms/data/core-data-resources - description: List of discipline-specific deposition databases recommended by ELIXIR. + id: elixir-deposition-databases-for-biomolecular-data name: ELIXIR Deposition Databases for Biomolecular Data registry: fairsharing-coll: bsg-c000039 - related_pages: - - data_publication - - researcher - - data_manager - - it_support - - covid-19 - - nels - - ifb - - csc url: https://elixir-europe.org/platforms/data/elixir-deposition-databases - description: The ELIXIR Authentication and Authorisation Infrastructure (AAI) + id: elixir-aai name: ELIXIR-AAI - registry: - tess: ELIXIR-AAI - related_pages: - - sensitive - - nels - - tsd - - transmed url: https://elixir-europe.org/services/compute/aai - description: "EMBL-EBI\u2019s web portal for finding ontologies" + id: embl-ebi-ontology-lookup-service name: EMBL-EBI Ontology Lookup Service - related_pages: - - metadata - - data_manager - - researcher url: https://www.ebi.ac.uk/ols/index - description: EMBL-EBI's wizard for finding the right EMBL-EBI repository for your data. + id: embl-ebis-data-submission-wizard name: EMBL-EBI's data submission wizard - related_pages: - - data_publication - - researcher - - data_manager url: https://www.ebi.ac.uk/submission/ - description: Electron Microscopy Public Image Archive is a public resource for raw, 2D electron microscopy images. You can browse, upload and download the raw images used to build a 3D structure + id: empiar name: EMPIAR - registry: - tess: EMPIAR - related_pages: - - data_publication - - ome - - bioimaging_data url: https://www.ebi.ac.uk/pdbe/emdb/empiar/ - description: This tool carries out data hub set up at the European Nucleotide Archive (ENA). + id: ena-compare-data-hubs name: ENA COMPARE Data Hubs - related_pages: - - dm_coordination - - it_support - - data_manager url: https://github.com/nadimm-rahman/ena-datahub-setup - description: The program submits experimental data and respective metadata to the European Nucleotide Archive (ENA). + id: ena-upload-tool name: ENA upload tool - related_pages: - - it_support - - data_manager - - researcher - - data_brokering url: https://github.com/usegalaxy-eu/ena-upload-cli - description: Genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. + id: ensembl name: Ensembl registry: - biotools: ensembl fairsharing: fx0mw7 - tess: Ensembl url: https://www.ensembl.org/index.html - description: Comparative analysis, data mining and visualisation for the genomes of non-vertebrate species + id: ensembl-genomes name: Ensembl Genomes registry: - biotools: ensembl_genomes fairsharing: 923a0p - tess: Ensembl Genomes url: https://ensemblgenomes.org/ - description: Open-access database of full genomes of plant species. + id: ensembl-plants name: Ensembl Plants registry: fairsharing: j8g2cv - tess: Ensembl Plants - related_pages: - - plant_geno_assembly url: https://plants.ensembl.org/ - description: Web-based tool allowing users to create and manage a register of personal data processing activities (ROPA). + id: erpa name: ERPA - related_pages: - - policy_officer - - human_data - - data_protection url: https://gitlab.sib.swiss/clinbio/erpa-app - description: Regulation (eu) 2016/679 of the european parliament and of the council on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing directive 95/46/ec (general data protection regulation). + id: eu-general-data-protection-regulation name: EU General Data Protection Regulation - related_pages: - - data_protection - - policy_officer - - human_data - - tsd url: https://eur-lex.europa.eu/legal-content/EN/TXT/HTML/?uri=CELEX:32016R0679&from=EN - description: EUDAT's wizard for finding the right licence for your data or code. + id: eudat-licence-selector-wizard name: EUDAT licence selector wizard - related_pages: - - licensing - - researcher - - data_manager - - policy_officer url: https://ufal.github.io/public-license-selector/ - description: The European database of suspected adverse drug reaction reports is a public resource aimed to provide access to reported suspected side-effects of drugs. Side-effects are defined according to the MedDRA ontology. + id: eudravigilance name: EudraVigilance - related_pages: - - toxicology_data url: https://www.ema.europa.eu/en/human-regulatory/research-development/pharmacovigilance/eudravigilance - description: EUPID provides a method for identity management, pseudonymisation and record linkage to bridge the gap between multiple contexts. + id: eupid name: EUPID - related_pages: - - it_support - - policy_officer - - human_data url: https://eupid.eu/#/concept - description: European Search Catalogue for Plant Genetic Resources + id: eurisco name: EURISCO registry: biotools: eurisco - related_pages: - - plants - - researcher - - data_manager url: https://eurisco.ipk-gatersleben.de - description: Europe PMC is a repository, providing access to worldwide life sciences articles, books, patents and clinical guidelines. + id: europe-pmc name: Europe PMC registry: - biotools: europe_pmc fairsharing: cmw6mm - tess: Europe PMC - related_pages: - - researcher url: https://europepmc.org/ - description: A programme aiming to create an effective rare diseases research ecosystem for progress, innovation and for the benefit of everyone with a rare disease. + id: european-joint-programme-on-rare-diseases-(ejp-rd) name: European Joint Programme on Rare Diseases (EJP RD) - related_pages: - - rare_disease url: https://www.ejprarediseases.org/ - description: This core model is designed to represent data about a rare disease patient and biosample registries. The model is based on and builds on existing standards, such as the European Rare Disease Registry Infrastructure and the Common Data Elements from the rare disease community and other more generalised standards for data sharing such as the W3C DCAT vocabulary. + id: european-joint-programme-on-rare-diseases-metadata-model name: European Joint Programme on Rare Diseases Metadata Model - related_pages: - - rare_disease url: https://github.com/ejp-rd-vp/resource-metadata-schema - description: 'The Virtual Platform is a federated ecosystem, in which resources are enhanced to be amenable to rare disease research, and made Findable, Accessible, Interoperable and Reusable: data stays at the source level but can be queyrable at distance from an EJP RD query point.' + id: european-joint-programme-on-rare-diseases-virtual-platform-(ejp-rd) name: European Joint Programme on Rare Diseases Virtual Platform (EJP RD) - related_pages: - - rare_disease url: https://vp.ejprarediseases.org/ - description: A record of sequence information scaling from raw sequcning reads to assemblies and functional annotation + id: european-nucleotide-archive-(ena) name: European Nucleotide Archive (ENA) registry: - biotools: ena fairsharing: dj8nt8 - tess: European Nucleotide Archive (ENA) - related_pages: - - micro_biotech - - plant_geno_assembly - - data_brokering url: https://www.ebi.ac.uk/ena/browser/home - description: ERDRI.dor provides an overview of participating rare disease registries with their main characteristics and description. + id: european-rare-disease-registry-infrastructure-directory-of-registries-(erdri.dor) name: European Rare Disease Registry Infrastructure directory of registries (ERDRI.dor) - related_pages: - - rare_disease url: https://eu-rd-platform.jrc.ec.europa.eu/erdridor/ - description: ERDRI.mdr serves to ease the integration of heterogeneous data from different rare disease registries. For this purpose, it contains a collection of metadata which specifies the used data elements of a registry including the designation of the used data elements, their definition and units of measurement. + id: european-rare-disease-registry-infrastructure-metadata-repository-(erdri.mdr) name: European Rare Disease Registry Infrastructure metadata repository (ERDRI.mdr) - related_pages: - - rare_disease url: https://eu-rd-platform.jrc.ec.europa.eu/mdr/ - description: Virtual networks involving healthcare providers across Europe. They aim to facilitate discussion on complex or rare diseases and conditions that require highly specialised treatment, and concentrated knowledge and resources. + id: european-reference-networks-(erns) name: European Reference Networks (ERNs) - registry: - tess: European Reference Networks (ERNs) - related_pages: - - rare_disease url: https://health.ec.europa.eu/european-reference-networks_en - description: Open-access database of all types of genetic variation data from all species. + id: european-variation-archive-(eva) name: European Variation Archive (EVA) registry: - biotools: eva fairsharing: 6824pv - tess: European Variation Archive (EVA) - related_pages: - - plant_geno_assembly url: https://www.ebi.ac.uk/eva/ - description: Controlled vocabulary that describes types of evidence and assertion methods + id: evidence-and-conclusion-ontology-(eco) name: Evidence and Conclusion Ontology (ECO) registry: + biotools: NA fairsharing: wvpgwn - related_pages: - - existing_data - - metadata url: https://evidenceontology.org/ - description: The FDA Adverse Event Reporting System (FAERS) is an american resource that contains adverse event reports, medication error reports and product quality @@ -1183,239 +788,137 @@ MedDRA ontology is used for coding adverse effects. Note that reports available in FAERS do not require a causal relationship between a product and an adverse event and further evaluations are conducted by FDA to monitor the safety of products. + id: faers name: FAERS registry: biotools: faers - related_pages: - - toxicology_data url: https://www.fda.gov/drugs/surveillance/questions-and-answers-fdas-adverse-event-reporting-system-faers - description: FAIDARE is a tool allowing to search data across dinstinct databases that implemented BrAPI. + id: faidare name: FAIDARE registry: biotools: faidare - related_pages: - - researcher - - data_manager - - plants - - ifb - - plant_pheno_assembly url: https://urgi.versailles.inra.fr/faidare/ - description: FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable (FAIR) + id: fair-cookbook name: FAIR Cookbook - related_pages: - - compliance - - data_manager - - transmed url: https://fairplus.github.io/the-fair-cookbook/content/recipes/assessing-fairness.html# - description: A FAIR Data Point stores metadata in a standardized and sharable way. + id: fair-data-point-(fdp) name: FAIR Data Point (FDP) registry: fairsharing: '298' - tess: FAIR Data Point - related_pages: - - rare_disease - - metadata - - it_support url: https://www.fairdatapoint.org/ - description: Resources and guidelines to assess the FAIRness of digital resources. + id: fair-evaluation-services name: FAIR Evaluation Services - related_pages: - - compliance - - data_manager - - policy_officer url: https://fairsharing.github.io/FAIR-Evaluator-FrontEnd/#!/#%2F! - description: The FIP is a collection of FAIR implementation choices made by a community of practice for each of the FAIR Principles. + id: fair-implementation-profile name: FAIR Implementation Profile - related_pages: - - dm_coordination - - dmp - - researcher - - data_manager url: https://www.go-fair.org/how-to-go-fair/fair-implementation-profile/ - description: The FAIR wizard utilizes FAIRification resources developed by the FAIRplus project and other platforms, suggests FAIRification materials based on the FAIRification requirements, and designs FAIRification solutions for data owners, data stewards, and other people involved in FAIRification. + id: fair-wizard name: FAIR-Wizard - related_pages: - - compliance - - data_manager - - policy_officer url: https://wwwdev.ebi.ac.uk/ait/fair-wizard/home - description: Help you discover resources to measure and improve FAIRness. + id: fairassist.org name: FAIRassist.org - related_pages: - - compliance - - data_manager - - policy_officer url: https://fairassist.org/#!/ - description: A data Management Platform for organising, sharing and publishing research datasets, models, protocols, samples, publications and other research outcomes. + id: fairdom-seek name: FAIRDOM-SEEK registry: biotools: seek - tess: FAIRDOM-SEEK - related_pages: - - storage - - it_support - - nels - - micro_biotech - - ifb - - machine_actionability - - plant_pheno_assembly url: https://seek4science.org/ - description: Data, model and SOPs management for projects, from preliminary data to publication, support for running SBML models etc. (public SEEK instance) + id: fairdomhub name: FAIRDOMHub registry: fairsharing: nnvcr9 - related_pages: - - storage - - researcher - - nels - - metadata - - micro_biotech - - machine_actionability - - data_manager url: https://fairdomhub.org - description: A System to Evaluate the FAIRness of Digital Objects + id: fairshake name: FAIRshake - related_pages: - - compliance - - data_manager - - it_support url: https://fairshake.cloud - description: A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. + id: fairsharing name: FAIRsharing registry: fairsharing: 2abjs5 - tess: FAIRsharing - related_pages: - - metadata - - data_publication - - policy_officer - - data_manager - - researcher - - micro_biotech - - existing_data url: https://fairsharing.org/ - description: Data publishing platform + id: figshare name: FigShare registry: fairsharing: drtwnh - tess: FigShare - related_pages: - - data_publication - - biomol_sim - - bioimaging_data url: https://figshare.com/ - description: A free FTP solution + id: filezilla name: FileZilla - related_pages: - - transfer - - it_support url: https://filezilla-project.org - description: FIP Wizard is a toolset to facilitate the capture of data in FAIR Convergence Matrix questionnaire prompting communities to explicitly declare their FAIR Implementation Profiles. These profiles can be then stored and published as nanopublications. + id: fip-wizard name: FIP Wizard - related_pages: - - dm_coordination - - dmp - - researcher - - data_manager url: https://fip-wizard.readthedocs.io/en/latest/ - description: FreeIPA is an integrated Identity and Authentication solution for Linux/UNIX networked environments. + id: free-ipa name: Free-IPA - related_pages: - - it_support - - transmed url: https://www.freeipa.org/ - description: Repository of IP-free synthetic biological parts + id: freegenes name: Freegenes - related_pages: - - micro_biotech url: https://stanford.freegenes.org/collections/open-genes - description: Principled and practical framework for the responsible sharing of genomic and health-related data. + id: ga4gh-data-security-toolkit name: GA4GH Data Security Toolkit - related_pages: - - data_publication - - policy_officer - - data_manager - - it_support - - human_data - - sensitive url: https://www.ga4gh.org/genomic-data-toolkit/data-security-toolkit/ - description: Open standards for genomic data sharing. + id: ga4gh-genomic-data-toolkit name: GA4GH Genomic Data Toolkit - related_pages: - - data_manager - - it_support - - human_data url: https://www.ga4gh.org/genomic-data-toolkit/ - description: Framework for Responsible Sharing of Genomic and Health-Related Data + id: ga4gh-regulatory-and-ethics-toolkit name: GA4GH Regulatory and Ethics toolkit - related_pages: - - data_protection - - sensitive - - policy_officer - - data_manager - - it_support - - human_data url: https://www.ga4gh.org/genomic-data-toolkit/regulatory-ethics-toolkit/ - description: Open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. + id: galaxy name: Galaxy registry: biotools: galaxy - tess: Galaxy - related_pages: - - nels - - marine_assembly - - data_analysis - - researcher - - it_support - - ifb - - galaxy url: https://galaxyproject.org/ - description: A database of genetic sequence information. GenBank may also refer to the data format used for storing information around genetic sequence data. + id: genbank name: GenBank - registry: - biotools: genbank - fairsharing: 9kahy4 - tess: GenBank - related_pages: - - micro_biotech url: https://www.ncbi.nlm.nih.gov/genbank/ - description: A repository of MIAME-compliant genomics data from arrays and high-throughput sequencing + id: gene-expression-omnibus-(geo) name: Gene Expression Omnibus (GEO) - related_pages: - - micro_biotech - - data_publication - - metadata - - transfer - - ome - - bioimaging_data - - toxicology_data url: https://www.ncbi.nlm.nih.gov/geo/ - description: Geneid is an ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms. + id: geneid name: GENEID registry: biotools: geneid - related_pages: - - data_analysis - - researcher url: https://genome.crg.cat/software/geneid/index.html - description: GHS (Globally Harmonized System of Classification and Labelling of Chemicals) classification was developed by the United Nations in an attempt to @@ -1423,318 +926,215 @@ criteria for the classification of health, physical and environmental hazards, and what information should be included on labels of hazardous chemicals and safety data sheets. + id: ghs-classification name: GHS Classification - related_pages: - - toxicology_data url: https://pubchem.ncbi.nlm.nih.gov/ghs/ - description: Distributed version control system designed to handle everything from small to very large projects + id: git name: Git - registry: - tess: Git - related_pages: - - data_organisation - - data_manager - - it_support url: https://git-scm.com/ - description: Versioning system, used for sharing code, as well as for sharing of small data + id: github name: GitHub registry: - fairsharing: c55d5e fairsharing-coll: bsg-d001160 - tess: GitHub - related_pages: - - data_publication - - data_organisation - - it_support - - data_manager url: https://github.com - description: GitLab is an open source end-to-end software development platform with built-in version control, issue tracking, code review, CI/CD, and more. Self-host GitLab on your own servers, in a container, or on a cloud provider. + id: gitlab name: GitLab - registry: - fairsharing: 530e61 - tess: GitLab - related_pages: - - data_organisation - - data_publication - - it_support - - data_manager url: https://gitlab.com/gitlab-org/gitlab - description: Globus lets you efficiently, securely, and reliably transfer data directly between systems separated by an office wall or an ocean. Focus on your research and offload your data transfer headaches to Globus + id: globus name: Globus - related_pages: - - transfer - - it_support url: https://www.globus.org - description: A multispecies integrative information system dedicated to plant and fungi pests. It allows researchers to access genetic, phenotypic and genomic data. It is used by both large international projects and the French National Research Institute for Agriculture, Food and Environment. + id: gnpis name: GnpIS registry: biotools: gnpis fairsharing: dw22y3 - related_pages: - - plants url: https://urgi.versailles.inrae.fr/gnpis/ - description: Search engine for datasets + id: google-dataset-search name: Google Dataset Search - related_pages: - - existing_data url: https://datasetsearch.research.google.com/ - description: Cloud Storage for Work and Home + id: google-drive name: Google Drive - related_pages: - - storage - - transfer url: https://www.google.com/intl/en_us/drive/ - description: Repository of GPCR protein simulations + id: gpcrmd name: GPCRmd registry: biotools: GPCRmd - related_pages: - - biomol_sim - - data_publication url: http://gpcrmd.org/ - description: The GRAPE pipeline provides an extensive pipeline for RNA-Seq analyses. It allows the creation of an automated and integrated workflow to manage, analyse and visualize RNA-Seq data. + id: grape-2.0 name: GRAPE 2.0 registry: biotools: grape_2.0 - related_pages: - - data_analysis url: https://github.com/guigolab/grape-nf - description: ELN Comparison Grid by Hardvard Medical School + id: harvard-medical-school---eln-comparison-grid name: Harvard Medical School - ELN Comparison Grid - related_pages: - - metadata - - identifiers - - researcher - - data_manager url: https://datamanagement.hms.harvard.edu/analyze/electronic-lab-notebooks - description: Haz-Map is an occupational health database that makes available information about the adverse effects of exposures to chemical and biological agents at the workplace. These associations have been established using current scientific evidence. + id: haz-map name: Haz-Map - related_pages: - - toxicology_data url: https://haz-map.com/ - description: Guidelines about how to license research data from Digital Curation Centre + id: how-to-license-research-data---dcc name: How to License Research Data - DCC - related_pages: - - licensing - - researcher - - data_manager - - policy_officer url: https://www.dcc.ac.uk/guidance/how-guides/license-research-data - description: The Human Protein Atlas contains information for a large majority of all human protein-coding genes regarding the expression and localization of the corresponding proteins based on both RNA and protein data. + id: human-protein-atlas name: Human Protein Atlas registry: fairsharing: j0t0pe - tess: Human Protein Atlas - related_pages: - - proteomics url: https://www.proteinatlas.org/ - description: HumanMine integrates many types of human data and provides a powerful query engine, export for results, analysis for lists of data and FAIR access via web services. + id: humanmine name: HumanMine registry: biotools: humanmine - fairsharing: RJ99Pj - tess: HumanMine - related_pages: - - data_organisation - - data_manager - - researcher - - human_data - - data_analysis url: https://www.humanmine.org/ - description: Data sharing + id: icloud name: iCloud - related_pages: - - storage - - data_analysis - - transfer url: https://www.icloud.com/ - description: The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession). + id: identifiers.org name: Identifiers.org registry: biotools: identifiers.org fairsharing: n14rc8 - related_pages: - - identifiers - - it_support - - data_manager url: http://identifiers.org - description: A collection of standard biological parts to which all entrants in the iGEM competition must submit their parts + id: igem-parts-registry name: iGEM Parts Registry - related_pages: - - micro_biotech url: http://parts.igem.org/Main_Page - description: A repository of image datasets from scientific publications + id: image-data-resource-(idr) name: Image Data Resource (IDR) registry: - biotools: idr fairsharing: 6wf1zw - related_pages: - - micro_biotech - - data_publication - - metadata - - transfer - - ome - - bioimaging_data url: https://idr.openmicroscopy.org - description: The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. + id: informed-consent-ontology name: Informed Consent Ontology registry: fairsharing: b9znd5 - related_pages: - - it_support - - policy_officer - - human_data url: http://purl.obolibrary.org/obo/ICO.owl - description: The International Compilation of Human Research Standards enumerates over 1,000 laws, regulations, and guidelines (collectively referred to as standards) that govern human subject protections in 133 countries, as well as standards from a number of international and regional organizations + id: international-compilation-of-human-research-standards name: International Compilation of Human Research Standards - related_pages: - - human_data url: https://www.hhs.gov/ohrp/sites/default/files/2020-international-compilation-of-human-research-standards.pdf - description: A collaborative database of genetic sequence datasets from DDBJ, EMBL-EBI and NCBI + id: international-nucleotide-sequence-database-collaboration-(insdc) name: International Nucleotide Sequence Database Collaboration (INSDC) - registry: - biotools: insdc - related_pages: - - micro_biotech - - data_brokering url: http://www.insdc.org - description: Data standards and formats for reporting flow cytometry data + id: international-society-for-the-advancement-of-cytometry-(isac) name: International Society for the Advancement of Cytometry (ISAC) - related_pages: - - micro_biotech + registry: + biotools: NA url: https://isac-net.org/page/Data-Standards - description: Resource for naming standards in biochemistry and molecular biology + id: international-union-of-biochemistry-and-molecular-biology-(iubmb) name: International Union of Biochemistry and Molecular Biology (IUBMB) - related_pages: - - micro_biotech url: https://www.qmul.ac.uk/sbcs/iubmb/ - description: Functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites + id: interpro name: InterPro registry: - biotools: interpro fairsharing: pda11d - tess: InterPro url: https://www.ebi.ac.uk/interpro/ - description: IntoGen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes. + id: intogen name: IntoGen registry: biotools: intogen - related_pages: - - data_analysis - - human_data url: https://www.intogen.org/search - description: Intrinsically disordered proteins ontology + id: intrinsically-disordered-proteins-ontology-(idpo) name: Intrinsically disordered proteins ontology (IDPO) - registry: - biotools: idpo - related_pages: - - idp - - metadata url: https://disprot.org/about - description: The Integrated Risk Information System (IRIS) resource evaluates information on health that might arise after exposure to environmental contaminants. + id: iris name: IRIS - registry: - biotools: iris - tess: IRIS - related_pages: - - toxicology_data url: https://www.epa.gov/iris - description: Integrated Rule-Oriented Data System (iRODS) is open source data management software for a cancer genome analysis workflow. + id: irods name: iRODS registry: biotools: irods - related_pages: - - storage - - it_support - - transmed - - bioimaging_data url: https://irods.org/ - description: Open source framework and tools helping to manage a diverse set of life science, environmental and biomedical experiments using the Investigation Study Assay (ISA) standard + id: isa-tools name: ISA-tools registry: fairsharing: 53gp75 - related_pages: - - it_support - - data_manager - - micro_biotech - - machine_actionability url: https://isa-tools.org/ - description: Open source software library that can be used to generate a ISA-TAB export from in-house data sets. These comprises e.g. local database or local file system based experimental. + id: isa4j name: ISA4J registry: biotools: isa4j - related_pages: - - plants - - machine_actionability - - plant_pheno_assembly url: https://doi.org/10.12688/f1000research.27188.1 - description: International information security standard + id: iso/iec-27001 name: ISO/IEC 27001 - related_pages: - - data_protection - - policy_officer - - human_data url: https://en.wikipedia.org/wiki/ISO/IEC_27001 - description: A collaborative resource from IUPAC and IUBMB for naming standards in biochemistry + id: iupac-iubmb-joint-commission-on-biochemical-nomenclature-(jcbn) name: IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN) - related_pages: - - micro_biotech url: https://www.qmul.ac.uk/sbcs/iupac/jcbn/ - description: A registry platform for biological parts + id: jbei-ice name: JBEI-ICE - related_pages: - - micro_biotech url: https://ice.jbei.org - description: Jupyter notebooks allow to share code, documentation + id: jupyter name: Jupyter - registry: - tess: Jupyter - related_pages: - - it_support - - data_analysis url: https://jupyter.org - description: Keycloak is an open source identity and data access management solution. + id: keycloak name: Keycloak - registry: - tess: Keycloak - related_pages: - - it_support - - transmed url: https://www.keycloak.org/ - description: The LiMTox system is a text mining approach that tries to extract associations between compounds and a particular toxicological endpoint at various levels of @@ -1744,1162 +1144,770 @@ rules, and patterns to machine learning-based text classification. It also provides indirect associations to hepatotoxicity through the extraction of relations reflecting the effect of compounds at the level of metabolism and liver enzymes. + id: limtox name: LimTox registry: biotools: limtox - related_pages: - - toxicology_data url: http://limtox.bioinfo.cnio.es/ - description: Web portal for finding ontologies + id: linked-open-vocabularies-(lov) name: Linked Open Vocabularies (LOV) - related_pages: - - metadata - - data_manager - - researcher url: https://lov.linkeddata.es/dataset/lov/ - description: A database of prokaryote specific biodiversity information + id: list-of-prokaryotic-names-with-standing-in-nomenclature-(lpsn) name: List of Prokaryotic names with Standing in Nomenclature (LPSN) - related_pages: - - micro_biotech url: https://lpsn.dsmz.de - description: EuroHPC world-class supercomputer + id: lumi name: LUMI - registry: - biotools: lumi - related_pages: - - data_analysis - - researcher - - it_support - - csc url: https://www.lumi-supercomputer.eu/ - description: Machine-Actionable Data Management Plan | Webinar (2016) on making a good data management plan. + id: madmp---research-bridge name: maDMP - Research Bridge - related_pages: - - dmp - - it_support url: https://library.ust.hk/sc/machine-actionable-dmp/ - description: MarDB includes all non-complete marine microbial genomes regardless of level of completeness. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation. + id: mardb name: MarDB registry: biotools: mardb - related_pages: - - marine_assembly - - data_analysis url: https://mmp2.sfb.uit.no/mardb/ - description: MarFun is a manually curated marine fungi genome database. + id: marfun name: MarFun - related_pages: - - marine_assembly - - data_analysis url: https://mmp2.sfb.uit.no/marfun/ - description: High-quality curated and freely accessible microbial genomics and metagenomics resources for the marine scientific community + id: marine-metagenomics-portal name: Marine metagenomics portal registry: biotools: mmp - related_pages: - - marine_assembly url: https://mmp2.sfb.uit.no/ - description: MarRef is a manually curated marine microbial reference genome database that equenced genomes. Each entry contains 120 metadata fields including information about sampling environment or host, organism and taxonomy, phenotype, pathogenicity, assembly and annotation information + id: marref name: MarRef registry: biotools: marref - related_pages: - - marine_assembly url: https://mmp2.sfb.uit.no/marref/ - description: Database of over 5000 intrinsic membrane protein structures + id: memprotmd name: MemProtMD - related_pages: - - biomol_sim url: http://memprotmd.bioch.ox.ac.uk/ - description: Multidisciplinary, free-to-use open repository specialized for research data + id: mendeley-data name: Mendeley data registry: fairsharing: 3epmpp - related_pages: - - data_publication - - biomol_sim url: https://data.mendeley.com/ - description: A repository of genomics data relating to the study of the metabolome + id: metabolomexchange name: MetabolomeXchange - registry: - biotools: metabolomexchange - related_pages: - - micro_biotech - - data_publication url: http://www.metabolomexchange.org/site/ - description: Minimum Information About Disorder Experiments (MIADE) standard + id: miade name: MIADE - related_pages: - - metadata - - researcher - - data_manager - - idp url: https://www.psidev.info/intrinsically-disordered-proteins-workgroup - description: Minimum Information About a Plant Phenotyping Experiment + id: miappe name: MIAPPE registry: fairsharing: nd9ce9 - tess: MIAPPE - related_pages: - - metadata - - researcher - - data_manager - - plants - - plant_geno_assembly - - plant_pheno_assembly url: https://www.miappe.org/ - description: Cloud storage and file sharing service from Microsoft + id: microsoft-azure name: Microsoft Azure - related_pages: - - storage - - it_support - - transfer url: https://azure.microsoft.com/en-gb/ - description: Cloud storage and file sharing service from Microsoft + id: microsoft-onedrive name: Microsoft OneDrive - related_pages: - - storage - - it_support url: https://www.microsoft.com/en-us/microsoft-365/onedrive/online-cloud-storage - description: Minimum Information about a (Meta)Genome Sequence + id: migs/mims name: MIGS/MIMS registry: fairsharing: va1hck - related_pages: - - metadata - - researcher - - data_manager - - marine - - micro_biotech url: https://genomicsstandardsconsortium.github.io/mixs/ - description: MINT, the Molecular INTeraction database, focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators + id: mint name: MINT registry: - biotools: mint fairsharing: 2bdvmk url: https://mint.bio.uniroma2.it/ - description: Minimum Information about any (x) Sequence + id: mixs name: MIxS registry: fairsharing: 9aa0zp - tess: MIxS - related_pages: - - metadata - - researcher - - data_manager - - marine - - plant_geno_assembly url: https://gensc.org/mixs/ - description: A database of protein disorder and mobility annotations + id: mobidb name: MobiDB registry: biotools: mobidb - fairsharing: jwra3e - tess: MobiDB - related_pages: - - idp - - researcher url: https://mobidb.org/ - description: Database of Protein Molecular Dynamics simulations representing different structural clusters of the PDB + id: model name: MoDEL registry: biotools: model - tess: MoDEL - related_pages: - - biomol_sim + fairsharing: NA url: https://mmb.irbbarcelona.org/MoDEL/ - description: Database of COVID-19 related atomistic Molecular Dynamic Trajectories + id: model-covid19 name: MoDEL Covid19 - related_pages: - - biomol_sim url: https://bioexcel-cv19.bsc.es/#/ - description: Repository for Central Nervous System-related mainly membrane protein MD simulations + id: model-cns name: MoDEL-CNS - related_pages: - - biomol_sim - - data_publication url: https://mmb.irbbarcelona.org/MoDEL-CNS/#/ - description: Repository for theoretical models of macromolecular structures with DOIs for models + id: modelarchive name: ModelArchive registry: fairsharing: tpqndj - related_pages: - - biomol_sim - - struct_bioinfo - - data_publication url: https://www.modelarchive.org/ - description: Molgenis is a modular web application for scientific data. Molgenis provides researchers with user friendly and scalable software infrastructures to capture, exchange, and exploit the large amounts of data that is being produced by scientific organisations all around the world. + id: molgenis name: Molgenis registry: biotools: molgenis - related_pages: - - identifiers - - it_support - - data_manager url: https://molgenis.gitbooks.io/molgenis/content/ - description: Database about interactions of molecules with membranes + id: molmedb name: MolMeDB registry: biotools: MolMeDB fairsharing: cwzk3c - related_pages: - - biomol_sim url: https://molmedb.upol.cz/ - description: A risk assessment tool that can be used to do Data Protection Impact Assessments + id: monarc name: MONARC - registry: - fairsharing: b2979t - related_pages: - - data_protection - - policy_officer - - human_data - - transmed url: https://open-source-security-software.net/project/MONARC - description: "a Magnetic Resonance Imaging (MRI) converter from ParaVision\xAE (Bruker,\ \ Inc. Billerica, MA) file format to DICOM standard" + id: mri2dicom name: MRI2DICOM - related_pages: - - researcher - - data_manager - - xnat-pic url: https://github.com/szullino/XNAT-PIC - description: The Multi-Crop Passport Descriptor is the metadata standard for plant genetic resources maintained ex situ by genbanks. + id: multi-crop-passport-descriptor-(mcpd) name: Multi-Crop Passport Descriptor (MCPD) registry: + biotools: NA fairsharing: hn155r - related_pages: - - metadata - - researcher - - it_support - - policy_officer - - plants url: https://www.bioversityinternational.org/e-library/publications/detail/faobioversity-multi-crop-passport-descriptors-v21-mcpd-v21/ - description: A file-system based platform handling the transfer of data + id: mytardis name: MyTardis - related_pages: - - data_manager - - transfer - - bioimaging_data url: http://www.mytardis.org/ - description: Online database hosting a vast amount of biotechnological information including nucleic acids, proteins, genomes and publications. Also boasts integrated tools for analysis. + id: national-center-for-biotechnology-information-(ncbi) name: National Center for Biotechnology Information (NCBI) - related_pages: - - micro_biotech url: https://www.ncbi.nlm.nih.gov - description: The National Biomonitoring Program (NBP) is a public resource that offers an assessment of nutritional status and the exposure of the U.S. population to environmental chemicals and toxic substances. + id: nbp name: NBP - related_pages: - - toxicology_data url: https://www.cdc.gov/biomonitoring/ - description: NCBI's taxonomy browser is a database of biodiversity information + id: ncbi-taxonomy name: NCBI Taxonomy - registry: - fairsharing: fj07xj - related_pages: - - micro_biotech url: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ - description: Hosts information relating to strains, cultures and more + id: ncimb name: NCIMB - related_pages: - - micro_biotech url: https://www.ncimb.com/culture-collection/ - description: Form and survey tool, also for sensitive data + id: nettskjema name: Nettskjema - related_pages: - - sensitive - - tsd url: https://nettskjema.no/ - description: As fully on-premises solution, Nextcloud Hub provides the benefits of online collaboration without the compliance and security risks. + id: nextcloud name: NextCloud - related_pages: - - storage - - it_support - - transfer url: https://nextcloud.com - description: Nextflow is a framework for data analysis workflow execution + id: nextflow name: Nextflow - registry: - biotools: nextflow - tess: Nextflow - related_pages: - - it_support - - data_analysis url: https://www.nextflow.io - description: Repository for lipid MD simulations to validate force fields with NMR data + id: nmrlipids name: NMRlipids - related_pages: - - biomol_sim - - data_publication url: http://nmrlipids.blogspot.com/ - description: The National Poison Data System (NPDS) is a resource that provides poisson exposure occurring in the US and some freely associated states. + id: npds name: NPDS - related_pages: - - toxicology_data url: https://www.aapcc.org/national-poison-data-system - description: Multi-stakeholder, interdisciplinary collaborative to bring out the value of health data through large-scale analytics. All our solutions are open-source. + id: ohdsi name: OHDSI registry: biotools: ohdsi - related_pages: - - researcher - - data_manager - - data_analysis - - storage - - transmed - - toxicology_data url: https://ohdsi.org/ - description: OMERO is an open-source client-server platform for managing, visualizing and analyzing microscopy images and associated metadata + id: omero name: OMERO registry: biotools: omero - tess: OMERO - related_pages: - - metadata - - data_manager - - it_support - - storage - - ome - - bioimaging_data + fairsharing: NA url: https://www.openmicroscopy.org - description: Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics) + id: omicsdi name: OmicsDI registry: biotools: omicsdi fairsharing: re1278 - tess: OmicsDI - related_pages: - - existing_data - - proteomics url: https://www.omicsdi.org - description: OMOP is a common data model for the harmonisation for of observational health data. + id: omop-cdm name: OMOP-CDM - related_pages: - - transmed url: https://ohdsi.github.io/CommonDataModel/ - description: A web portal to search and visualise ontologies + id: ontobee name: Ontobee - registry: - fairsharing: q8fx1b - related_pages: - - metadata - - data_manager - - researcher url: http://www.ontobee.org - description: OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets. + id: ontomaton name: ONTOMATON - related_pages: - - researcher - - data_manager - - it_support - - metadata - - identifiers url: https://github.com/ISA-tools/OntoMaton - description: Licenses that are conformant with the principles laid out in the Open Definition. + id: open-definition-conformant-licenses name: Open Definition Conformant Licenses - related_pages: - - licensing - - researcher - - data_manager - - policy_officer url: https://opendefinition.org/licenses/ - description: Explore Open Access research outcomes from OpenAIRE network + id: openaire-explore name: OpenAIRE Explore - related_pages: - - existing_data url: https://explore.openaire.eu/search/find - description: ELIXIR benchmarking platform to support community-led scientific benchmarking efforts and the technical monitoring of bioinformatics reosurces + id: openebench name: OpenEBench registry: biotools: openebench - related_pages: - - data_analysis - - data_manager - - it_support url: https://openebench.bsc.es/ - description: Data curation tool for working with messy data + id: openrefine name: OpenRefine - registry: - tess: OpenRefine - related_pages: - - data_quality url: https://openrefine.org/ - description: 'free and open source project management tool that supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery' + id: openscienceframework name: OpenScienceFramework registry: fairsharing: g4z879 - related_pages: - - data_publication - - biomol_sim url: https://osf.io/ - description: OpenStack is an open source cloud computing infrastructure software project and is one of the three most active open source projects in the world + id: openstack name: OpenStack - registry: - tess: OpenStack - related_pages: - - storage - - data_analysis - - transmed - - ifb url: https://www.openstack.org/ - description: The Orphadata platform provides the scientific community with comprehensive, high-quality datasets related to rare diseases and orphan drugs, in a reusable and computable format + id: orphadata name: Orphadata registry: - biotools: orphadata - fairsharing: d1a667 fairsharing-coll: bsg-d001249 url: http://www.orphadata.org/cgi-bin/index.php - description: OSF (Open Science Framework) is a free, open platform to support your research and enable collaboration. + id: osf name: OSF - registry: - tess: OSF - related_pages: - - storage - - researcher - - data_manager url: https://osf.io - description: One Touch Pipeline (OTP) is a data management platform for running bioinformatics pipelines in a high-throughput setting, and for organising the resulting data and metadata. + id: otp name: OTP - registry: - biotools: otp - related_pages: - - human_data - - metadata - - dmp - - data_analysis url: https://gitlab.com/one-touch-pipeline/otp - description: Cloud storage and file sharing service + id: owncloud name: ownCloud - related_pages: - - storage - - it_support - - transfer - - data_analysis url: https://owncloud.com - description: PAA is an R/Bioconductor tool for protein microarray data analysis aimed at biomarker discovery. + id: paa name: PAA registry: biotools: paa - related_pages: - - data_analysis - - researcher - - human_data - - proteomics url: https://bioconductor.org/packages/PAA/ - description: Data Publisher for Earth and Environmental Science + id: pangaea name: PANGAEA registry: biotools: pangaea - fairsharing: 6yw6cp - related_pages: - - data_publication - - metadata - - researcher - - data_manager url: https://www.pangaea.de/ - description: The Protein Circular Dichroism Data Bank + id: pcddb name: PCDDB registry: biotools: pcddb - related_pages: - - idp - - researcher url: https://pcddb.cryst.bbk.ac.uk/ - description: The Protein Data Bank (PDB) + id: pdb name: PDB registry: biotools: pdb - tess: PDB - related_pages: - - researcher - - idp - - struct_bioinfo url: https://www.wwpdb.org/ - description: Prototype archiving system for structural models obtained using integrative or hybrid modeling + id: pdb-dev name: PDB-Dev - related_pages: - - biomol_sim - - struct_bioinfo url: https://pdb-dev.wwpdb.org/ - description: Information about the standard PDB archive format PDBx/mmCIF, its dictionaries and related software tools + id: pdbx/mmcif-format-and-tools name: PDBx/mmCIF format and tools registry: fairsharing: fd28en - related_pages: - - struct_bioinfo url: https://mmcif.wwpdb.org/ - description: Extension of the PDBx/mmCIF dictionary for theoretical models of macromolecular structures + id: pdbx/mmcif-modelcif-extension-dictionary name: PDBx/mmCIF ModelCIF Extension Dictionary - related_pages: - - struct_bioinfo url: https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/ - description: A resource that curates knowledge about the impact of genetic variation on drug response. + id: pharmgkb name: PharmGKB registry: biotools: pharmgkb - related_pages: - - toxicology_data url: https://www.pharmgkb.org/ - description: Pharos provides hazard, use, and exposure information on 140,872 chemicals and 180 different kinds of building products. + id: pharos name: Pharos registry: biotools: pharos - related_pages: - - toxicology_data url: https://pharosproject.net/ - description: The open-source Phenotyping Hybrid Information System (PHIS) manages and collects data from plants phenotyping and high throughput phenotyping experiments on a day to day basis. + id: phis name: PHIS - registry: - tess: PHIS - related_pages: - - plant_pheno_assembly - - plants - - ifb url: http://www.phis.inra.fr/ - description: PIA is a toolbox for mass spectrometrey based protein inference and identification analysis. + id: pia---protein-inference-algorithms name: PIA - Protein Inference Algorithms registry: biotools: pia - related_pages: - - data_analysis - - researcher - - proteomics url: https://github.com/mpc-bioinformatics/pia - description: A data management solution for intra-institutional organization and structured storage of life science project-associated research data, with emphasis on the generation of adequate metadata. + id: pisa-tree name: pISA-tree registry: biotools: pisa-tree - related_pages: - - plants - - micro_biotech - - researcher - - data_manager - - data_organisation - - metadata - - plant_pheno_assembly url: https://github.com/NIB-SI/pISA-tree - description: Access point for plant comparative genomics, centralizing genomic data produced by different genome sequencing initiatives. + id: plaza name: PLAZA registry: fairsharing: wBOua0 - tess: PLAZA - related_pages: - - plants - - plant_geno_assembly - - researcher url: https://bioinformatics.psb.ugent.be/plaza/ - description: Platform for the study of the impact of pathological mutations in protein stuctures. + id: pmut name: PMut registry: biotools: pmut - related_pages: - - data_analysis - - human_data url: http://mmb.irbbarcelona.org/PMut - description: PRoteomics IDEntifications (PRIDE) Archive database + id: pride name: PRIDE registry: - biotools: pride fairsharing: e1byny - tess: PRIDE - related_pages: - - proteomics url: https://www.ebi.ac.uk/pride/ - description: ProteomeXchange provides globally coordinated standard data submission and dissemination pipelines + id: proteomexchange name: ProteomeXchange registry: - biotools: proteomexchange fairsharing: 92dt9d - tess: ProteomeXchange - related_pages: - - proteomics url: http://www.proteomexchange.org/ - description: The HUPO Proteomics Standards Initiative defines community standards for data representation in proteomics and interactomics to facilitate data comparison, exchange and verification. + id: proteomics-standards-initiative name: Proteomics Standards Initiative - registry: - fairsharing: 46e1e9 - related_pages: - - proteomics url: https://www.psidev.info/ - description: A secure platform for developing and sharing reproducible methods. + id: protocols.io name: protocols.io - registry: - fairsharing: 132b10 - related_pages: - - micro_biotech url: https://www.protocols.io - description: PROV-DM is the conceptual data model that forms a basis for the W3C provenance (PROV) family of specifications. + id: prov-dm:-the-prov-data-model name: 'PROV-DM: The PROV Data Model' - related_pages: - - data_provenance url: https://www.w3.org/TR/prov-dm/ - description: R Markdown documents are fully reproducible. Use a productive notebook interface to weave together narrative text and code to produce elegantly formatted output. Use multiple languages including R, Python, and SQL. + id: r-markdown name: R Markdown - related_pages: - - data_analysis - - researcher url: https://rmarkdown.rstudio.com - description: The RD-Connect GPAP is an online tool for diagnosis and gene discovery in rare disease research. + id: rd-connect-genome-phenome-analysis-platform name: RD-Connect Genome Phenome Analysis Platform - registry: - tess: RD-Connect Genome Phenome Analysis Platform - related_pages: - - researcher - - human_data url: https://rd-connect.eu/what-we-do/omics/gpap/ - description: Directory of standard metadata, divided into different research areas + id: rda-standards name: RDA Standards - related_pages: - - metadata - - researcher - - data_manager url: https://rd-alliance.github.io/metadata-directory/standards/ - description: Registry of Research Data Repositories + id: re3data name: re3data - registry: - tess: re3data - related_pages: - - existing_data url: https://www.re3data.org/ - description: Portal with public data submitted to ECHA in REACH registration dossiers by substance manufacturers, importers, or their representatives, as laid out by the REACH Regulation (see Understanding REACH regulation). + id: reach-registered-substances name: REACH registered substances - related_pages: - - toxicology_data url: https://echa.europa.eu/information-on-chemicals/registered-substances - description: REDCap is a secure web application for building and managing online surveys and databases. While REDCap can be used to collect virtually any type of data in any environment, it is specifically geared to support online and offline data capture for research studies and operations. + id: redcap name: REDCap registry: biotools: redcap - tess: REDCap - related_pages: - - identifiers - - it_support - - data_manager - - data_quality url: https://projectredcap.org - description: Database of A-to-I (deamination of adenosines to inosines) events that enables to search RNA editing sites by genomic region, gene name and other relevant features as the tissue of origin. + id: rediportal name: REDIportal registry: biotools: rediportal - related_pages: - - epitrans url: http://srv00.recas.ba.infn.it/atlas/ - description: Python scripts to detect RNA editing events in RNAseq experiments + id: reditools name: REDItools registry: biotools: reditools - related_pages: - - epitrans url: https://github.com/BioinfoUNIBA/REDItools - description: REDItools2 is the optimized, parallel multi-node version of REDItools. + id: reditools2 name: REDItools2 - related_pages: - - epitrans url: https://github.com/BioinfoUNIBA/REDItools2 - description: "REMS (Resource Entitlement Management System), developed by CSC, is\ \ a tool that can be used to manage researchers\u2019 access rights to datasets." + id: rems name: REMS registry: biotools: rems - tess: REMS - related_pages: - - it_support - - transmed url: https://github.com/CSCfi/rems - description: File renaming software for Mac + id: renamer4mac name: Renamer4Mac - related_pages: - - data_organisation - - data_manager - - researcher url: https://renamer.com/ - description: Repository Finder can help you find an appropriate repository to deposit your research data. The tool is hosted by DataCite and queries the re3data registry of research data repositories. + id: repository-finder name: Repository Finder - related_pages: - - data_publication - - researcher - - data_manager url: https://repositoryfinder.datacite.org - description: Supports the systematic planning, organisation and implementation of research data management throughout the course of a project + id: research-data-management-organiser name: Research Data Management Organiser - related_pages: - - dmp - - researcher - - data_manager - - it_support url: https://rdmorganiser.github.io/en - description: Data management platform for automated loading, storage, linkage and provision of data sets + id: research-data-management-platform-(rdmp) name: Research Data Management Platform (RDMP) registry: biotools: rdmp - related_pages: - - storage - - it_support url: https://www.dundee.ac.uk/hic/data-team/researchdatamanagementplatform/ - description: Machine actionable DMPs. + id: research-management-plan name: Research Management Plan - related_pages: - - dmp - - researcher - - data_manager url: https://researcheracademy.elsevier.com/research-preparation/research-data-management/creating-good-research-data-management-plan - description: RO-Crate is a lightweight approach to packaging research data with their metadata, using schema.org. An RO-Crate is a structured archive of all the items that contributed to the research outcome, including their identifiers, provenance, relations and annotations. + id: research-object-crate-(ro-crate) name: Research Object Crate (RO-Crate) registry: fairsharing: wUoZKE - related_pages: - - metadata - - storage - - data_organisation - - data_manager - - researcher - - micro_biotech - - machine_actionability - - data_provenance url: https://w3id.org/ro/crate - description: Reva connects cloud storages and application providers + id: reva name: Reva - registry: - biotools: reva - tess: Reva - related_pages: - - data_analysis - - transfer url: https://reva.link/ - description: RightField is an open-source tool for adding ontology term selection to Excel spreadsheets + id: rightfield name: Rightfield - registry: - biotools: rightfield - related_pages: - - researcher - - metadata - - data_manager - - micro_biotech - - identifiers - - machine_actionability url: https://rightfield.org.uk - description: Rstudio notebooks allow to share code, documentation + id: rstudio name: Rstudio - registry: - biotools: rstudio - tess: Rstudio - related_pages: - - data_analysis - - it_support - - researcher url: https://rstudio.com - description: Rucio - Scientific Data Management + id: rucio name: Rucio - related_pages: - - storage - - data_analysis - - transfer url: https://rucio.cern.ch/ - description: RxNorm is a normalized naming system for medications that is maintained by the National Library of Medicine. Rxnorm provides unique identifiers and allows unambiguous communication of drug-related information across the American health computer systems. + id: rxnorm name: RxNorm registry: biotools: rxnorm - fairsharing: 36pf8q - related_pages: - - toxicology_data url: https://www.nlm.nih.gov/research/umls/rxnorm/index.html - description: SalDB is a salmon specific database of genome sequenced prokaryotes representing the microbiota of fishes found in the taxonomic family of Salmonidae. + id: saldb name: salDB - related_pages: - - marine_assembly url: https://mmp.sfb.uit.no/databases/saldb/ - description: Small Angle Scattering Biological Data Bank + id: sasbdb name: SASBDB - related_pages: - - idp - - researcher url: https://www.sasbdb.org/ - description: A standard library of visual glyphs used to represent SBOL designs and interactions. + id: sbol-visual name: SBOL Visual - related_pages: - - micro_biotech url: https://sbolstandard.org/visual-glyphs/ - description: A CAD tool to create SBOL designs through the use of SBOL Visual glyphs. + id: sboldesigner name: SBOLDesigner - related_pages: - - micro_biotech url: https://sboldesigner.github.io - description: Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond. + id: schema.org name: Schema.org - registry: - fairsharing: hzdzq8 - tess: Schema.org - related_pages: - - machine_actionability - - it_support url: https://schema.org - description: Web portal for finding ontologies + id: schemapedia name: Schemapedia - related_pages: - - metadata - - data_manager - - researcher url: https://schemapedia.com - description: ScienceMesh - frictionless scientific collaboration and access to research services + id: sciencemesh name: ScienceMesh - related_pages: - - storage - - data_analysis - - transfer url: https://sciencemesh.io/ - description: List of respositories recommended by Scientific Data, contains both discipline-specific and general repositories. + id: scientific-datas-recommended-repositories name: Scientific Data's Recommended Repositories - related_pages: - - data_publication - - researcher - - data_manager - - it_support url: https://www.nature.com/sdata/policies/repositories - description: SeaFile File Synchronization and Share Solution + id: seafile name: SeaFile - related_pages: - - storage - - transfer url: https://www.seafile.com/ - description: A semantic data model describing the common data elements for rare diseases registration. + id: semantic-data-model-of-the-set-of-common-data-elements-for-rare-diseases-registration name: Semantic data model of the set of common data elements for rare diseases registration - related_pages: - - rare_disease url: https://github.com/ejp-rd-vp/CDE-semantic-model - description: All-in-one platform for life science data management, semantic data integration, data analysis and visualization + id: semares name: semares - related_pages: - - researcher - - data_manager - - metadata - - data_analysis - - it_support - - storage url: www.genevention.com/products - description: Contains 16 data elements to be registered by each rare disease registry across Europe, which are considered to be essential for further research. + id: set-of-common-data-elements-for-rare-diseases-registration name: Set of common data elements for rare diseases registration - related_pages: - - rare_disease url: https://eu-rd-platform.jrc.ec.europa.eu/set-of-common-data-elements_en - description: A scripting language for creating Synthetic Biology Open Language (SBOL) in a more abstract way. + id: shortbol name: ShortBOL - related_pages: - - micro_biotech url: http://shortbol.org - description: Structure integration with function, taxonomy and sequence + id: sifts name: SIFTS - related_pages: - - researcher - - idp url: https://www.ebi.ac.uk/pdbe/docs/sifts/ - description: SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). + id: silva name: Silva registry: - biotools: silva fairsharing: 5vtYGG - tess: Silva url: https://www.arb-silva.de/ - description: Singularity is a container platform. + id: singularity name: Singularity - registry: - tess: Singularity - related_pages: - - it_support - - data_analysis - - tsd url: https://sylabs.io - description: SMASCH (Smart Scheduling) system, is a web-based tooldesigned for longitudinal clinical studies requiring recurrent follow-upvisits of the participants. SMASCH controls and simplifies the scheduling of big database of patients. Smasch is also used to organize the daily plannings (delegation of tasks) for the different medical professionals such as doctors, nurses and neuropsychologists. + id: smasch name: SMASCH - related_pages: - - data_organisation - - transmed url: https://smasch.pages.uni.lu - description: Snakemake is a framework for data analysis workflow execution + id: snakemake name: Snakemake registry: biotools: snakemake - tess: Snakemake - related_pages: - - it_support - - data_analysis url: https://snakemake.github.io - description: Added-value database for biological dynamics images + id: ssbd:database name: SSBD:database - related_pages: - - bioimaging_data - - data_publication url: https://ssbd.riken.jp/database/ - description: An open data archive that stores and publishes bioimaging and biological quantitative datasets + id: ssbd:repository name: SSBD:repository - related_pages: - - bioimaging_data - - data_publication url: https://ssbd.riken.jp/repository/ - description: Resource of standards for reporting enzyme data + id: standards-for-reporting-enzyme-data-(strenda) name: Standards for Reporting Enzyme Data (STRENDA) - related_pages: - - micro_biotech url: https://www.beilstein-institut.de/en/projects/strenda/ - description: Known and predicted protein-protein interactions. + id: string name: STRING registry: - biotools: string fairsharing: 9b7wvk - tess: STRING - related_pages: - - proteomics url: https://string-db.org/ - description: A searchable design repository for biological constructs + id: synbiohub name: SynBioHub - registry: - biotools: synbiohub - fairsharing: 7CVoS6 - related_pages: - - micro_biotech url: https://synbiohub.org - description: An open standard for the representation of in silico biological designs and their place in the Design-Build-Test-Learn cycle of synthetic biology. + id: synthetic-biology-open-language-(sbol) name: Synthetic Biology Open Language (SBOL) - registry: - biotools: sbol - related_pages: - - micro_biotech url: https://sbolstandard.org - description: An open format for computational models of biological processes + id: systems-biology-markup-language-(sbml) name: Systems Biology Markup Language (SBML) - registry: - biotools: sbml - related_pages: - - micro_biotech url: http://sbml.org/Main_Page - description: The Toxin and Toxin Target Database is a bioinformatics resource that combines exhaustive toxin data with toxin target information. Currently it presents more than 42,000 toxin-target associations extracted from other databases, government documents, books and scientific literature. Each toxin record includes data on chemical properties and descriptors, toxicity values and medical information. + id: t3db name: T3DB registry: biotools: t3db - related_pages: - - toxicology_data url: http://www.t3db.ca/ - description: Talend is an open source data integration platform. + id: talend name: Talend - related_pages: - - data_manager - - researcher - - transmed url: https://www.talend.com/ - description: A toxicogenomics database that stores gene expression data and biochemistry, hematology, and histopathology findings derived from in vivo (rat) and in vitro (primary rat hepatocytes, primary human hepatocytes) exposure to 170 compounds at multiple dosages and time points. + id: tg-gates name: TG-GATES registry: biotools: open_tg-gates - related_pages: - - toxicology_data url: https://toxico.nibiohn.go.jp/english/ - description: An ontology for expressing environmental terms + id: the-environment-ontology-(envo) name: The Environment Ontology (EnvO) - related_pages: - - micro_biotech url: https://sites.google.com/site/environmentontology/ - description: EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects + id: the-european-genome-phenome-archive-(ega) name: The European Genome-phenome Archive (EGA) registry: biotools: ega fairsharing: mya1ff - tess: The European Genome-phenome Archive (EGA) - related_pages: - - data_publication - - human_data - - policy_officer - - csc - - tsd url: https://ega-archive.org/ - description: Minimum Information about any (x) Sequence + id: the-genomic-standards-consortium-(gsc) name: The Genomic Standards Consortium (GSC) registry: + biotools: NA fairsharing: 9aa0zp - related_pages: - - metadata - - researcher - - it_support - - policy_officer - - human_data url: https://gensc.org/mixs/ - description: Collaborative effort to develob interoperable ontologies for the biological sciences + id: the-open-biological-and-biomedical-ontology-(obo)-foundry name: The Open Biological and Biomedical Ontology (OBO) Foundry registry: fairsharing-coll: bsg-d001083 - related_pages: - - metadata - - data_manager - - researcher url: http://obofoundry.org - description: The Toxicology in the 21st Century program, or Tox21, is a unique collaboration between several federal agencies to develop new ways to rapidly test whether substances adversely affect human health. The Tox21 Toolbox contains data-analysis tools for accessing and visualizing Tox21 quantitative high-throughput screening (qHTS) 10K library data, as well as integrating with other publicly available data. + id: tox21_toolbox name: Tox21_Toolbox - related_pages: - - toxicology_data url: https://ntp.niehs.nih.gov/whatwestudy/tox21/toolbox/index.html - description: The Toxicology in the 21st Century program, or Tox21, is a unique collaboration between several federal agencies to develop new ways to rapidly test whether substances adversely affect human health. This portal contains diverse downloadable results of the ToxCast project. + id: toxcast_data name: ToxCast_data - related_pages: - - toxicology_data url: https://www.epa.gov/chemical-research/exploring-toxcast-data-downloadable-data - description: The Toxicology Data Network (TOXNET) was a portal that allowed access to several relevant sources in the toxicological field. Nowadays, these sources have been integrated into other NLM resources. + id: toxnet name: TOXNET - related_pages: - - toxicology_data url: https://www.nlm.nih.gov/toxnet/index.html - description: Knowledge management and high-content analysis platform enabling analysis of integrated data for the purposes of hypothesis generation, hypothesis validation, and cohort discovery in translational research. + id: transmart name: tranSMART registry: biotools: transmart - related_pages: - - researcher - - data_manager - - data_analysis - - storage - - transmed url: https://github.com/transmart - description: A list of Ethical, Legal, and Societal Implications (ELSI) to consider for research projects on human subjects + id: tryggve-elsi-checklist name: Tryggve ELSI Checklist - related_pages: - - sensitive - - policy_officer - - data_manager - - human_data - - nels - - csc - - tsd url: https://scilifelab-data-guidelines.readthedocs.io/en/latest/docs/general/sensitive_data.html - description: A tool that contains weighted gene co-expression networks obtained from the Primary Human Hepatocytes, rat kidney, and liver TG-GATEs dataset. + id: txg-mapr name: TXG-MAPr - registry: - biotools: txg-mapr - related_pages: - - data_analysis - - researcher - - toxicology_data url: https://txg-mapr.eu/ - description: The Unified Medical Language System (UMLS) is a set of tools that establishes a mapping structure among different vocabularies in the biomedical sciences field to enable interoperativity between computer systems. + id: umls name: UMLS - related_pages: - - toxicology_data url: https://www.nlm.nih.gov/research/umls/index.html - description: 'UniChem is a very simple, large-scale non-redundant database of pointers between chemical structures and EMBL-EBI chemistry resources. Primarily, this @@ -2907,113 +1915,63 @@ These include primary chemistry resources (ChEMBL and ChEBI), and other resources where the main focus is not small molecules, but which may nevertheless contain some small molecule information (eg: Gene Expression Atlas, PDBe).' + id: unichem name: UniChem - registry: - tess: UniChem - related_pages: - - toxicology_data url: https://www.ebi.ac.uk/unichem/ - description: Comprehensive resource for protein sequence and annotation data + id: uniprot name: UniProt registry: - biotools: uniprot fairsharing: s1ne3g - tess: UniProt - related_pages: - - metadata - - researcher - - idp - - micro_biotech - - proteomics - - struct_bioinfo url: https://www.uniprot.org/ - description: List of Electronic Research Notebook Products by University of Cambridge + id: university-of-cambridge---electronic-research-notebook-products name: University of Cambridge - Electronic Research Notebook Products - related_pages: - - metadata - - identifiers - - researcher - - data_manager url: https://www.data.cam.ac.uk/data-management-guide/electronic-research-notebooks/electronic-research-notebook-products - description: A JavaScript library for the visualisation of SBOL. + id: visbol name: VisBOL - related_pages: - - micro_biotech url: http://visbol.org - description: Wellcome Open Research requires that the source data underlying the results are made available as soon as an article is published. This page provides information about data you need to include, where your data can be stored, and how your data should be presented. + id: wellcome-open-research---data-guidelines name: Wellcome Open Research - Data Guidelines - related_pages: - - data_publication - - researcher - - data_manager url: https://wellcomeopenresearch.org/for-authors/data-guidelines - description: WinSCP is a popular SFTP client and FTP client for Microsoft Windows! Copy file between a local computer and remote servers using FTP, FTPS, SCP, SFTP, WebDAV or S3 file transfer protocols. + id: winscp name: WinSCP - related_pages: - - transfer - - it_support url: https://winscp.net/eng/index.php - description: WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows. + id: workflowhub name: WorkflowHub - registry: - biotools: workflowhub - fairsharing: 07cf72 - related_pages: - - data_publication - - data_manager - - researcher url: https://workflowhub.eu - description: Open source imaging informatics platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. + id: xnat name: XNAT - related_pages: - - researcher - - data_analysis - - transmed - - xnat-pic - - bioimaging_data url: https://www.xnat.org/ - description: Analysing of single or multiple subjects within the same project in XNAT + id: xnat-pic-pipelines name: XNAT-PIC Pipelines - related_pages: - - researcher - - data_manager - - data_analysis - - xnat-pic url: https://github.com/szullino/XNAT-PIC - description: Import tool for multimodal DICOM image datasets to XNAT + id: xnat-pic-uploader name: XNAT-PIC Uploader - related_pages: - - researcher - - data_manager - - xnat-pic url: https://github.com/szullino/XNAT-PIC - description: Generalist research data repository built and developed by OpenAIRE and CERN + id: zenodo name: Zenodo registry: fairsharing: wy4egf - tess: Zenodo - related_pages: - - data_publication - - biomol_sim - - bioimaging_data - - plant_pheno_assembly url: https://zenodo.org/ - description: Find possible ontology mappings for free text terms in the ZOOMA repository. + id: zooma name: Zooma - registry: - biotools: zooma - tess: Zooma - related_pages: - - metadata - - data_manager - - researcher url: https://www.ebi.ac.uk/spot/zooma/ diff --git a/_includes/dev-info.html b/_includes/dev-info.html deleted file mode 100644 index 05854b96b..000000000 --- a/_includes/dev-info.html +++ /dev/null @@ -1,3 +0,0 @@ - diff --git a/_plugins/jekyll-github-metadata-fix.rb b/_plugins/jekyll-github-metadata-fix.rb deleted file mode 100644 index 206efcc49..000000000 --- a/_plugins/jekyll-github-metadata-fix.rb +++ /dev/null @@ -1,16 +0,0 @@ -# As GitHub Actions are used for GitHub Pages, the branch must be set via environment variable -module Jekyll - module GitHubMetadata - module RepositoryFix - def source - { - "branch" => ENV["GITHUB_BRANCH"] || super["branch"], - "path" => ENV["BASE_PATH"] || super["path"], - } - end - end - class Repository - prepend RepositoryFix - end - end -end diff --git a/index.html b/index.html index 438649883..e4ebbaf4d 100644 --- a/index.html +++ b/index.html @@ -8,7 +8,6 @@ {% include head.html %} - {% if jekyll.environment == "development" %}{% include dev-info.html %}{% endif %} {% include topnav.html search=false %}
diff --git a/pages/your_tasks/data_publication.md b/pages/your_tasks/data_publication.md index f02e782ec..591d3440c 100644 --- a/pages/your_tasks/data_publication.md +++ b/pages/your_tasks/data_publication.md @@ -58,12 +58,12 @@ The most suitable repository will depend on the data type and your discipline. * The [licence](licensing) that should be applied to your metadata and data. * Check if/what discipline-specific repositories can apply the necessary access conditions and licences to your (meta)data. * Discipline-specific repositories: if a discipline-specific repository, recognised by the community, exists this should be your first choice since discipline-specific repositories often increases the FAIRness of the data. - * The [EMBL-EBI's data submission wizard](https://www.ebi.ac.uk/submission/) will help you choose a suitable repository based on your data type. + * The {% tool "embl-ebis-data-submission-wizard" %} will help you choose a suitable repository based on your data type. * Lists of discipline-specific, community-recognised repositories can be found in the following links: - * [ELIXIR Deposition Databases](https://elixir-europe.org/platforms/data/elixir-deposition-databases). + * {% tool "elixir-deposition-databases-for-biomolecular-data" %} * [Scientific Data journal's recommended repositories](https://www.nature.com/sdata/policies/repositories). * General-purpose and institutional repositories: For other cases, a repository that accepts data of different types and disciplines should be considered. It could be a [general-purpose repository](https://www.nature.com/sdata/policies/repositories#general) or a centralised repository provided by your institution or university. -* [re3data.org](https://www.re3data.org) or [Repository Finder](https://repositoryfinder.datacite.org) gathers information about existing repositories and allows you to filter them based on access and licence types. +* [re3data.org](https://www.re3data.org) or {% tool "repository-finder" %} gathers information about existing repositories and allows you to filter them based on access and licence types. * [re3data.org](https://www.re3data.org) and [FAIRsharing](https://fairsharing.org) websites gather features of repositories, which you can filter by discipline, data type, taxonomy and many other features. ## How do you prepare your data for publication in data repositories? From 510b95d18a270c0daf7905d0688707d816b16403 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Wed, 14 Dec 2022 16:55:27 +0100 Subject: [PATCH 005/126] latest version --- Gemfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile b/Gemfile index 3bb8d8f10..a9fb1628d 100644 --- a/Gemfile +++ b/Gemfile @@ -1,6 +1,6 @@ source "https://rubygems.org" -gem "elixir-toolkit-theme-plugins", ">= 0.1.0" +gem "elixir-toolkit-theme-plugins", ">= 0.1.1" gem "webrick", "~> 1.7" gem "jekyll", "~> 4.3.1" gem "jemoji", "~> 0.13.0" From 71eaa1520dc4014e60101828009ff07914f53a49 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Wed, 14 Dec 2022 17:01:53 +0100 Subject: [PATCH 006/126] latest version --- Gemfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile b/Gemfile index a9fb1628d..2b2620385 100644 --- a/Gemfile +++ b/Gemfile @@ -1,6 +1,6 @@ source "https://rubygems.org" -gem "elixir-toolkit-theme-plugins", ">= 0.1.1" +gem "elixir-toolkit-theme-plugins", ">= 0.1.2" gem "webrick", "~> 1.7" gem "jekyll", "~> 4.3.1" gem "jemoji", "~> 0.13.0" From 4387baa33e18ee34369d637c94c3d0ed19102e09 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Thu, 15 Dec 2022 08:41:01 +0100 Subject: [PATCH 007/126] fixed version --- Gemfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile b/Gemfile index 2b2620385..5624bc8d0 100644 --- a/Gemfile +++ b/Gemfile @@ -1,6 +1,6 @@ source "https://rubygems.org" -gem "elixir-toolkit-theme-plugins", ">= 0.1.2" +gem "elixir-toolkit-theme-plugins", "~> 0.1.2" gem "webrick", "~> 1.7" gem "jekyll", "~> 4.3.1" gem "jemoji", "~> 0.13.0" From 5c90a166f48b086b74f73314891b3df4e4f355f4 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Thu, 15 Dec 2022 09:52:11 +0100 Subject: [PATCH 008/126] dev banner --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index e4ebbaf4d..1ac4646c6 100644 --- a/index.html +++ b/index.html @@ -6,8 +6,8 @@ {% include head.html %} - + {% if jekyll.environment == "development" %}{% include dev-info.html %}{% endif %} {% include topnav.html search=false %}
From fd72a8411a8eed0a370dc7419831d915be30d016 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Thu, 15 Dec 2022 12:16:26 +0100 Subject: [PATCH 009/126] test with no branch variable --- .github/workflows/jekyll.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml index 4ca216380..8fe419ecb 100644 --- a/.github/workflows/jekyll.yml +++ b/.github/workflows/jekyll.yml @@ -49,7 +49,6 @@ jobs: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" env: PAGES_REPO_NWO: ${{ github.repository }} - GITHUB_BRANCH: ${{ github.ref_name }} JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }} JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} From 206cc66c72c3765a61aafd2d613f9e0f527073ff Mon Sep 17 00:00:00 2001 From: bedroesb Date: Fri, 16 Dec 2022 13:35:30 +0100 Subject: [PATCH 010/126] GITHUB_BRANCH --- .github/workflows/jekyll.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml index 8fe419ecb..4ca216380 100644 --- a/.github/workflows/jekyll.yml +++ b/.github/workflows/jekyll.yml @@ -49,6 +49,7 @@ jobs: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" env: PAGES_REPO_NWO: ${{ github.repository }} + GITHUB_BRANCH: ${{ github.ref_name }} JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }} JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} From dce68dd9b18e4f580f53f1e7dd5b8025075576a4 Mon Sep 17 00:00:00 2001 From: bedroesb Date: Mon, 19 Dec 2022 11:31:41 +0100 Subject: [PATCH 011/126] test with branch --- .github/workflows/jekyll.yml | 2 ++ index.html | 1 + 2 files changed, 3 insertions(+) diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml index 4ca216380..5f0a1377f 100644 --- a/.github/workflows/jekyll.yml +++ b/.github/workflows/jekyll.yml @@ -16,6 +16,8 @@ jobs: steps: - name: Checkout uses: actions/checkout@v3 + with: + ref: ${{ github.event.inputs.branch }} - name: Setup Ruby uses: ruby/setup-ruby@v1.127.0 diff --git a/index.html b/index.html index 1ac4646c6..bd4438dd2 100644 --- a/index.html +++ b/index.html @@ -20,6 +20,7 @@

The Research Data Management toolkit for Life Sciences

What can we help you find?

+ {{site.github.source}}