diff --git a/.github/method_template.md b/.github/method_template.md new file mode 100644 index 0000000..8c26e9e --- /dev/null +++ b/.github/method_template.md @@ -0,0 +1,45 @@ +# {{method}} + + + +{{#method_description_content}}{{{method_description_content}}}{{/method_description_content}} + +## Method Details + +* **Vendor:** {{#vendor_content}}{{{vendor_content}}}{{/vendor_content}}{{^vendor_content}}Not available{{/vendor_content}} + +* **Catalog Number:** {{#catalog_number_content}}{{{catalog_number_content}}}{{/catalog_number_content}}{{^catalog_number_content}}Not available{{/catalog_number_content}} + +* **Catalog Webpage:** {{#catalog_webpage_url}}[{{{catalog_webpage_url}}}]({{{catalog_webpage_url}}}){{/catalog_webpage_url}}{{^catalog_webpage_url}}Not available{{/catalog_webpage_url}} + +* **VHP4Safety Workflow Stage:** {{#vhp4safety_workflow_stage_content}}{{{vhp4safety_workflow_stage_content}}}{{/vhp4safety_workflow_stage_content}}{{^vhp4safety_workflow_stage_content}}Not available{{/vhp4safety_workflow_stage_content}} + +* **Workflow Substage:** {{#workflow_substage_content}}{{{workflow_substage_content}}}{{/workflow_substage_content}}{{^workflow_substage_content}}Not available{{/workflow_substage_content}} + +* **Case Study:** {{#case_study_content}}{{{case_study_content}}}{{/case_study_content}}{{^case_study_content}}Not available{{/case_study_content}} + +* **Regulatory Question:** {{#regulatory_question_content}}{{{regulatory_question_content}}}{{/regulatory_question_content}}{{^regulatory_question_content}}Not available{{/regulatory_question_content}} + +## Additional Information + +* **Assay Name:** {{#assay_name_content}}{{{assay_name_content}}}{{/assay_name_content}}{{^assay_name_content}}Not available{{/assay_name_content}} + +* **Data Producer:** {{#data_producer_content}}{{{data_producer_content}}}{{/data_producer_content}}{{^data_producer_content}}Not available{{/data_producer_content}} + +* **Relevant AOP Wiki Key Event(s):** {{#relevant_aop_wiki_key_event(s)_to_the_assay_content}}{{{relevant_aop_wiki_key_event(s)_to_the_assay_content}}}{{/relevant_aop_wiki_key_event(s)_to_the_assay_content}}{{^relevant_aop_wiki_key_event(s)_to_the_assay_content}}Not available{{/relevant_aop_wiki_key_event(s)_to_the_assay_content}} + +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** {{#relevant_aop_wiki_adverse_outcome_pathway(s)_to_the_assay_content}}{{{relevant_aop_wiki_adverse_outcome_pathway(s)_to_the_assay_content}}}{{/relevant_aop_wiki_adverse_outcome_pathway(s)_to_the_assay_content}}{{^relevant_aop_wiki_adverse_outcome_pathway(s)_to_the_assay_content}}Not available{{/relevant_aop_wiki_adverse_outcome_pathway(s)_to_the_assay_content}} + +* **Available SOP or Protocol:** {{#available_sop_or_protocol_content}}{{{available_sop_or_protocol_content}}}{{/available_sop_or_protocol_content}}{{^available_sop_or_protocol_content}}Not available{{/available_sop_or_protocol_content}} + +* **Ontology Term:** {{#ontology_term_content}}[{{{ontology_term_content}}}]({{{ontology_term_content}}}){{/ontology_term_content}}{{^ontology_term_content}}Not available{{/ontology_term_content}} + +* **Citation:** {{#citation_content}}{{{citation_content}}}{{/citation_content}}{{^citation_content}}Not available{{/citation_content}} + +--- + +*Generated from issue #{{issue_number}}* + + diff --git a/.github/workflows/generate_method_markdown.yml b/.github/workflows/generate_method_markdown.yml index 3ae0479..966ecef 100644 --- a/.github/workflows/generate_method_markdown.yml +++ b/.github/workflows/generate_method_markdown.yml @@ -1,149 +1,59 @@ -name: Generate Method Markdown from JSON +name: Generate Method Documentation with Mustache on: workflow_dispatch: push: paths: - 'docs/methods/*.json' + - '.github/method_template.md' + - '.github/workflows/generate_method_markdown.yml' pull_request: paths: - 'docs/methods/*.json' + - '.github/method_template.md' + - '.github/workflows/generate_method_markdown.yml' jobs: - generate-markdown: + generate-docs: runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.11' - - - name: Install dependencies - run: | - pip install requests - - - name: Generate Markdown from JSON files - run: | - python - <<'EOF' - import os, json, glob, datetime - - def clean_field_name(field): - """Convert field names to human readable format""" - return field.replace('_content', '').replace('_', ' ').title() - - def format_value(value): - """Format field values for display""" - if isinstance(value, str): - # Handle URLs - if value.startswith('http'): - return f"[{value}]({value})" - if value.startswith('//'): # temp fix - return f"[https{value}](https{value})" - # Skip empty responses - if value in ['_No response_', 'N/A', 'n/a', 'TBD', 'tbd']: - return None - return value - - # Process all JSON files in docs/methods/ - json_files = glob.glob('docs/methods/*.json') - - for json_file in json_files: - try: - with open(json_file, 'r') as f: - data = json.load(f) - - method_id = data.get('id', 'unknown') - md_file = f'docs/methods/{method_id}.md' - - # Generate markdown content - with open(md_file, 'w') as f: - # Header - method_name = data.get('name_of_the_method_content', data.get('service', 'Unknown Method')) - method_name = method_name.replace('[METHOD]: ', '') - f.write(f"# {method_name}\n\n") - - # Description - description = data.get('method_description_content') - if description and description != '_No response_': - f.write(f"{description}\n\n") - - # Method Details - f.write("## Method Details\n\n") - - # Key fields to display in order - key_fields = [ - ('type_content', 'Type'), - ('vendor_content', 'Vendor'), - ('catalog_number_content', 'Catalog Number'), - ('catalog_webpage_url', 'Catalog Webpage'), - ('vhp4safety_workflow_stage_content', 'VHP4Safety Workflow Stage'), - ('workflow_substage_content', 'Workflow Substage'), - ('relevant_vhp4safety_regulatory_question(s)_content', 'Relevant VHP4Safety Regulatory Questions'), - ('relevant_AOP_Wiki_Key_Event(s)_content', 'Relevant AOP Wiki Key Event(s) to the assay'), - ('relevant_AOP_Wiki_AOP(s)_content', 'Relevant AOP Wiki Adverse Outcome Pathway(s) to the assay'), - ('case_study_content', 'Case Study'), - ('regulatory_question_content', 'Regulatory Question'), - ('available_sop_content', 'Available SOP or protocol'), - - ] - - for field_key, field_label in key_fields: - value = data.get(field_key) - formatted_value = format_value(value) - if formatted_value: - f.write(f"**{field_label}:** {formatted_value}\n\n") - - # Citation section - citation = data.get('citation_content') - if citation and citation != '_No response_': - f.write("## Citation\n\n") - f.write(f"{citation}\n\n") - - # Additional Information - f.write("## Additional Information\n\n") - - # Display other fields not already shown - skip_fields = { - 'id', 'service', 'issue_number', 'timestamp', - 'name_of_the_method_content', 'method_description_content', - 'citation_content' - } - skip_fields.update([field[0] for field in key_fields]) - - for key, value in data.items(): - if key not in skip_fields: - formatted_value = format_value(value) - if formatted_value: - clean_key = clean_field_name(key) - f.write(f"**{clean_key}:** {formatted_value}\n\n") - - # Footer - f.write("---\n\n") - f.write(f"*Generated from issue #{data.get('issue_number', 'unknown')} on {datetime.datetime.now().strftime('%Y-%m-%d')}*\n") - - print(f"Generated markdown: {md_file}") - - except Exception as e: - print(f"Error processing {json_file}: {e}") - - print("Markdown generation complete") - EOF - - - name: Commit generated markdown files - run: | - git config --global user.name "github-actions[bot]" - git config --global user.email "github-actions[bot]@users.noreply.github.com" - - if [ -n "$(git status --porcelain docs/methods/*.md 2>/dev/null)" ]; then + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Setup Node.js + uses: actions/setup-node@v4 + with: + node-version: '18' + + - name: Install mustache CLI + run: npm install -g mustache + + - name: Generate method documentation + run: | + for json_file in docs/methods/*.json; do + if [ -f "$json_file" ]; then + basename=$(basename "$json_file" .json) + + # Validate JSON + jq empty "$json_file" || { echo "Invalid JSON: $json_file"; exit 1; } + + # Generate markdown using mustache template + mustache "$json_file" .github/method_template.md > "docs/methods/${basename}.md" + + echo "Generated docs/methods/${basename}.md" + fi + done + + - name: Commit and push generated documentation + run: | + git config --global user.name 'GitHub Action' + git config --global user.email 'action@github.com' git pull git add docs/methods/*.md - git commit -m "Auto-generate method markdown files" - git push - else - echo "No markdown files to commit" - fi + if git diff --exit-code --staged; then + echo "No changes to commit" + else + git commit -m 'Generate method documentation from JSON files' + git push + fi diff --git a/docs/methods/5_cfda_assay_to_determine_cytotoxicity.md b/docs/methods/5_cfda_assay_to_determine_cytotoxicity.md index 8f3baeb..0320bd0 100644 --- a/docs/methods/5_cfda_assay_to_determine_cytotoxicity.md +++ b/docs/methods/5_cfda_assay_to_determine_cytotoxicity.md @@ -1,41 +1,45 @@ -# Unknown Method +# 5-CFDA assay to determine cytotoxicity + + Fluorescence-based determination of cell membrane damage ## Method Details -**Vendor:** Invitrogen +* **Vendor:** Invitrogen -**Catalog Number:** C1354 +* **Catalog Number:** C1354 -**Catalog Webpage:** [https://www.thermofisher.com/order/catalog/product/C1354](https://www.thermofisher.com/order/catalog/product/C1354) +* **Catalog Webpage:** [https://www.thermofisher.com/order/catalog/product/C1354](https://www.thermofisher.com/order/catalog/product/C1354) -**VHP4Safety Workflow Stage:** Adverse Outcome +* **VHP4Safety Workflow Stage:** Adverse Outcome -**Workflow Substage:** Cell death, Adverse outcome +* **Workflow Substage:** Cell death, Adverse outcome -**Case Study:** parkinson +* **Case Study:** parkinson -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** 5-CFDA assay to determine cytotoxicity - -**Assay Name:** 5-CFDA, AM (5-Carboxyfluorescein Diacetate, Acetoxymethyl Ester) +* **Assay Name:** 5-CFDA, AM (5-Carboxyfluorescein Diacetate, Acetoxymethyl Ester) -**Data Producer:** Julia Meerman +* **Data Producer:** Julia Meerman -**Relevant Aop Wiki Key Event(S) To The Assay:** KE1825 +* **Relevant AOP Wiki Key Event(s):** KE1825 -**Relevant Aop Wiki Adverse Outcome Pathway(S) To The Assay:** AOP464 +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** AOP464 -**Https:** [https//www.thermofisher.com/order/catalog/product/C1354](https//www.thermofisher.com/order/catalog/product/C1354) +* **Available SOP or Protocol:** No response -**Available Sop Or Protocol:** No response +* **Ontology Term:** [No response](No response) -**Ontology Term:** No response +* **Citation:** _No response_ --- -*Generated from issue #170 on 2025-12-03* +*Generated from issue #170* + + diff --git a/docs/methods/alamar_blue_assay_for_detection_of_mitochondrial_activity.md b/docs/methods/alamar_blue_assay_for_detection_of_mitochondrial_activity.md index 29a9783..e8f9442 100644 --- a/docs/methods/alamar_blue_assay_for_detection_of_mitochondrial_activity.md +++ b/docs/methods/alamar_blue_assay_for_detection_of_mitochondrial_activity.md @@ -1,45 +1,45 @@ -# Unknown Method +# Alamar Blue assay for detection of mitochondrial activity + + Fluorescence-based detection of mitochondrial metabolic activity ## Method Details -**Vendor:** Invitrogen +* **Vendor:** Invitrogen -**Catalog Number:** R12204 +* **Catalog Number:** R12204 -**Catalog Webpage:** [https://www.thermofisher.com/order/catalog/product/R12204?SID=srch-hj-R12204](https://www.thermofisher.com/order/catalog/product/R12204?SID=srch-hj-R12204) +* **Catalog Webpage:** [https://www.thermofisher.com/order/catalog/product/R12204?SID=srch-hj-R12204](https://www.thermofisher.com/order/catalog/product/R12204?SID=srch-hj-R12204) -**VHP4Safety Workflow Stage:** AOP +* **VHP4Safety Workflow Stage:** AOP -**Workflow Substage:** Mitochondrial dysfunction, mitochondrial damage +* **Workflow Substage:** Mitochondrial dysfunction, mitochondrial damage -**Case Study:** parkinson +* **Case Study:** parkinson -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** Alamar Blue assay for detection of mitochondrial activity - -**Assay Name:** Resazurin, Sodium Salt - -**Data Producer:** Julia Meerman +* **Assay Name:** Resazurin, Sodium Salt -**Http:** [https//id.nlm.nih.gov/mesh/C005843](https//id.nlm.nih.gov/mesh/C005843) +* **Data Producer:** Julia Meerman -**Type Url:** [http://id.nlm.nih.gov/mesh/C005843](http://id.nlm.nih.gov/mesh/C005843) +* **Relevant AOP Wiki Key Event(s):** KE177, KE1547 -**Relevant Aop Wiki Key Event(S) To The Assay:** KE177, KE1547 +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** AOP464 -**Relevant Aop Wiki Adverse Outcome Pathway(S) To The Assay:** AOP464 +* **Available SOP or Protocol:** No response -**Https:** [https//www.thermofisher.com/order/catalog/product/R12204?SID=srch-hj-R12204](https//www.thermofisher.com/order/catalog/product/R12204?SID=srch-hj-R12204) +* **Ontology Term:** [http://purl.enanomapper.org/onto/ENM_8000224](http://purl.enanomapper.org/onto/ENM_8000224) -**Available Sop Or Protocol:** No response - -**Ontology Term:** [http://purl.enanomapper.org/onto/ENM_8000224](http://purl.enanomapper.org/onto/ENM_8000224) +* **Citation:** _No response_ --- -*Generated from issue #166 on 2025-12-03* +*Generated from issue #166* + + diff --git a/docs/methods/cell_titer_fluor.md b/docs/methods/cell_titer_fluor.md index 2c1fbe8..e25d09c 100644 --- a/docs/methods/cell_titer_fluor.md +++ b/docs/methods/cell_titer_fluor.md @@ -1,31 +1,45 @@ -# Cell Titer Fluor +# [METHOD]: Cell Titer Fluor + + A Non-Lytic Fluorescence Assay That Measures the Relative Number of Viable Cells in Culture ## Method Details -**Type:** NA - -**Vendor:** Promega +* **Vendor:** Promega -**Catalog Number:** G6081 +* **Catalog Number:** G6081 -**Catalog Webpage:** [https://nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/fluorescent-cell-viability-assay/?catNum=G6081](https://nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/fluorescent-cell-viability-assay/?catNum=G6081) +* **Catalog Webpage:** [https://nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/fluorescent-cell-viability-assay/?catNum=G6081](https://nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/fluorescent-cell-viability-assay/?catNum=G6081) -**VHP4Safety Workflow Stage:** Adverse Outcome +* **VHP4Safety Workflow Stage:** Adverse Outcome -**Workflow Substage:** Increased Apoptosis +* **Workflow Substage:** Increased Apoptosis -**Case Study:** thyroid +* **Case Study:** thyroid -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: Cell Titer Fluor +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ -**Https:** [https//nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/fluorescent-cell-viability-assay/?catNum=G6081](https//nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/fluorescent-cell-viability-assay/?catNum=G6081) +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ + +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #136 on 2025-12-03* +*Generated from issue #136* + + diff --git a/docs/methods/cellrox__green_reagent_for_oxidative_stress_detection.md b/docs/methods/cellrox__green_reagent_for_oxidative_stress_detection.md index 26ebb7c..da42411 100644 --- a/docs/methods/cellrox__green_reagent_for_oxidative_stress_detection.md +++ b/docs/methods/cellrox__green_reagent_for_oxidative_stress_detection.md @@ -1,25 +1,45 @@ -# CellROX Green Reagent for oxidative stress detection +# [METHOD]: CellROX Green Reagent for oxidative stress detection + + ROS detection by fluorescent probe ## Method Details -**Vendor:** ThermoFisher Scientific +* **Vendor:** ThermoFisher Scientific + +* **Catalog Number:** C10444 -**Catalog Number:** C10444 +* **Catalog Webpage:** Not available -**VHP4Safety Workflow Stage:** AOP +* **VHP4Safety Workflow Stage:** AOP -**Workflow Substage:** _ROS increase_ +* **Workflow Substage:** _ROS increase_ -**Case Study:** thyroid +* **Case Study:** thyroid -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: CellROX Green Reagent for oxidative stress detection +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ + +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ + +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #139 on 2025-12-03* +*Generated from issue #139* + + diff --git a/docs/methods/celltiter_glo_20_assay_for_detection_of_cellular_atp_content.md b/docs/methods/celltiter_glo_20_assay_for_detection_of_cellular_atp_content.md index 10b64c0..d598736 100644 --- a/docs/methods/celltiter_glo_20_assay_for_detection_of_cellular_atp_content.md +++ b/docs/methods/celltiter_glo_20_assay_for_detection_of_cellular_atp_content.md @@ -1,41 +1,45 @@ -# Unknown Method +# CellTiter-Glo® 2.0 assay for detection of cellular ATP content + + Luminescence-based detection of cellular ATP content ## Method Details -**Vendor:** Promega +* **Vendor:** Promega -**Catalog Number:** G9242 +* **Catalog Number:** G9242 -**Catalog Webpage:** [https://nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?tabset0=0](https://nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?tabset0=0) +* **Catalog Webpage:** [https://nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?tabset0=0](https://nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?tabset0=0) -**VHP4Safety Workflow Stage:** AOP +* **VHP4Safety Workflow Stage:** AOP -**Workflow Substage:** Mitochondrial dysfunction +* **Workflow Substage:** Mitochondrial dysfunction -**Case Study:** parkinson +* **Case Study:** parkinson -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** CellTiter-Glo® 2.0 assay for detection of cellular ATP content - -**Assay Name:** CellTiter-Glo® 2.0 Cell Viability Assay +* **Assay Name:** CellTiter-Glo® 2.0 Cell Viability Assay -**Data Producer:** Julia Meerman +* **Data Producer:** Julia Meerman -**Relevant Aop Wiki Key Event(S) To The Assay:** KE177 +* **Relevant AOP Wiki Key Event(s):** KE177 -**Relevant Aop Wiki Adverse Outcome Pathway(S) To The Assay:** AOP464 +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** AOP464 -**Https:** [https//nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?tabset0=0](https//nld.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?tabset0=0) +* **Available SOP or Protocol:** No response -**Available Sop Or Protocol:** No response +* **Ontology Term:** [No response](No response) -**Ontology Term:** No response +* **Citation:** _No response_ --- -*Generated from issue #168 on 2025-12-03* +*Generated from issue #168* + + diff --git a/docs/methods/cytotoxicity_detection_kitplusldh.md b/docs/methods/cytotoxicity_detection_kitplusldh.md index 1621c2f..b36214c 100644 --- a/docs/methods/cytotoxicity_detection_kitplusldh.md +++ b/docs/methods/cytotoxicity_detection_kitplusldh.md @@ -1,25 +1,45 @@ -# Cytotoxicity Detection KitPLUS (LDH) +# [METHOD]: Cytotoxicity Detection KitPLUS (LDH) + + Fluorescence-based detection of LDH ## Method Details -**Vendor:** Merck +* **Vendor:** Merck + +* **Catalog Number:** 4744926001 -**Catalog Number:** 4744926001 +* **Catalog Webpage:** Not available -**VHP4Safety Workflow Stage:** AOP, Adverse Outcome +* **VHP4Safety Workflow Stage:** AOP, Adverse Outcome -**Workflow Substage:** Dose-response toxicity +* **Workflow Substage:** Dose-response toxicity -**Case Study:** thyroid +* **Case Study:** thyroid -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: Cytotoxicity Detection KitPLUS (LDH) +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ + +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ + +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #144 on 2025-12-03* +*Generated from issue #144* + + diff --git a/docs/methods/h2dcfda_am_assay_for_detection_of_oxidative_stress_production.md b/docs/methods/h2dcfda_am_assay_for_detection_of_oxidative_stress_production.md index 3e45beb..c981de0 100644 --- a/docs/methods/h2dcfda_am_assay_for_detection_of_oxidative_stress_production.md +++ b/docs/methods/h2dcfda_am_assay_for_detection_of_oxidative_stress_production.md @@ -1,41 +1,45 @@ -# Unknown Method +# H2DCFDA-AM assay for detection of oxidative stress production + + Fluorescence-based detection of reactive oxygen species production ## Method Details -**Vendor:** Invitrogen +* **Vendor:** Invitrogen -**Catalog Number:** C6827 +* **Catalog Number:** C6827 -**Catalog Webpage:** [https://www.thermofisher.com/order/catalog/product/C6827?SID=srch-srp-C6827](https://www.thermofisher.com/order/catalog/product/C6827?SID=srch-srp-C6827) +* **Catalog Webpage:** [https://www.thermofisher.com/order/catalog/product/C6827?SID=srch-srp-C6827](https://www.thermofisher.com/order/catalog/product/C6827?SID=srch-srp-C6827) -**VHP4Safety Workflow Stage:** AOP +* **VHP4Safety Workflow Stage:** AOP -**Workflow Substage:** Oxidative stress +* **Workflow Substage:** Oxidative stress -**Case Study:** parkinson +* **Case Study:** parkinson -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** H2DCFDA-AM assay for detection of oxidative stress production - -**Assay Name:** H2DCFDA-AM +* **Assay Name:** H2DCFDA-AM -**Data Producer:** Julia Meerman +* **Data Producer:** Julia Meerman -**Relevant Aop Wiki Key Event(S) To The Assay:** KE1392 +* **Relevant AOP Wiki Key Event(s):** KE1392 -**Relevant Aop Wiki Adverse Outcome Pathway(S) To The Assay:** AOP464 +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** AOP464 -**Https:** [https//www.thermofisher.com/order/catalog/product/C6827?SID=srch-srp-C6827](https//www.thermofisher.com/order/catalog/product/C6827?SID=srch-srp-C6827) +* **Available SOP or Protocol:** No response -**Available Sop Or Protocol:** No response +* **Ontology Term:** [No response](No response) -**Ontology Term:** No response +* **Citation:** _No response_ --- -*Generated from issue #167 on 2025-12-03* +*Generated from issue #167* + + diff --git a/docs/methods/immunofluorescent_detection_of_collagen___1.md b/docs/methods/immunofluorescent_detection_of_collagen___1.md index 361e02d..50a7aa6 100644 --- a/docs/methods/immunofluorescent_detection_of_collagen___1.md +++ b/docs/methods/immunofluorescent_detection_of_collagen___1.md @@ -1,25 +1,45 @@ -# immunofluorescent detection of collagen - 1 +# [METHOD]: Collagen I Polyclonal Antibody + + immunofluorescent detection of collagen - 1 ## Method Details -**Vendor:** Thermofisher +* **Vendor:** Thermofisher + +* **Catalog Number:** PA5-90574 -**Catalog Number:** PA5-90574 +* **Catalog Webpage:** Not available -**VHP4Safety Workflow Stage:** AOP +* **VHP4Safety Workflow Stage:** AOP -**Workflow Substage:** Increase fibrosis +* **Workflow Substage:** Increase fibrosis -**Case Study:** thyroid +* **Case Study:** thyroid -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: Collagen I Polyclonal Antibody +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ + +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ + +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #142 on 2025-12-03* +*Generated from issue #142* + + diff --git a/docs/methods/intracellular_measurements.md b/docs/methods/intracellular_measurements.md index 8b271e0..c7ef739 100644 --- a/docs/methods/intracellular_measurements.md +++ b/docs/methods/intracellular_measurements.md @@ -1,27 +1,45 @@ -# Intracellular measurements +# [METHOD]: Intracellular measurements + + Intracellular measurements are determined in cell lysates using LCMS, normalized by protein expression that has been measured by 2D Quant ## Method Details -**Vendor:** Cytiva +* **Vendor:** Cytiva + +* **Catalog Number:** 80648356 -**Catalog Number:** 80648356 +* **Catalog Webpage:** [https://www.cytivalifesciences.com/en/us/shop/protein-analysis/protein-sample-preparation/sample-cleanup/2-d-quant-kit-p-02012](https://www.cytivalifesciences.com/en/us/shop/protein-analysis/protein-sample-preparation/sample-cleanup/2-d-quant-kit-p-02012) -**Catalog Webpage:** [https://www.cytivalifesciences.com/en/us/shop/protein-analysis/protein-sample-preparation/sample-cleanup/2-d-quant-kit-p-02012](https://www.cytivalifesciences.com/en/us/shop/protein-analysis/protein-sample-preparation/sample-cleanup/2-d-quant-kit-p-02012) +* **VHP4Safety Workflow Stage:** Kinetics -**VHP4Safety Workflow Stage:** Kinetics +* **Workflow Substage:** _No response_ -**Case Study:** thyroid +* **Case Study:** thyroid -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: Intracellular measurements +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ -**Https:** [https//www.cytivalifesciences.com/en/us/shop/protein-analysis/protein-sample-preparation/sample-cleanup/2-d-quant-kit-p-02012](https//www.cytivalifesciences.com/en/us/shop/protein-analysis/protein-sample-preparation/sample-cleanup/2-d-quant-kit-p-02012) +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ + +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #146 on 2025-12-03* +*Generated from issue #146* + + diff --git a/docs/methods/kim_1_staining.md b/docs/methods/kim_1_staining.md index 9120f00..bc2333a 100644 --- a/docs/methods/kim_1_staining.md +++ b/docs/methods/kim_1_staining.md @@ -1,27 +1,45 @@ -# KIM-1 staining +# [METHOD]: KIM-1 staining + + KIM-1 staining is an immunofluorescent staining of kidney injury molecule 1, an protein that is expressed when kidney injury takes place ## Method Details -**Vendor:** ThermoFisher Scientific +* **Vendor:** ThermoFisher Scientific + +* **Catalog Number:** PA5-20244 -**Catalog Number:** PA5-20244 +* **Catalog Webpage:** [https://www.thermofisher.com/antibody/product/TIM-1-Antibody-Polyclonal/PA5-20244](https://www.thermofisher.com/antibody/product/TIM-1-Antibody-Polyclonal/PA5-20244) -**Catalog Webpage:** [https://www.thermofisher.com/antibody/product/TIM-1-Antibody-Polyclonal/PA5-20244](https://www.thermofisher.com/antibody/product/TIM-1-Antibody-Polyclonal/PA5-20244) +* **VHP4Safety Workflow Stage:** AOP -**VHP4Safety Workflow Stage:** AOP +* **Workflow Substage:** _No response_ -**Case Study:** thyroid +* **Case Study:** thyroid -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: KIM-1 staining +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ -**Https:** [https//www.thermofisher.com/antibody/product/TIM-1-Antibody-Polyclonal/PA5-20244](https//www.thermofisher.com/antibody/product/TIM-1-Antibody-Polyclonal/PA5-20244) +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ + +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #147 on 2025-12-03* +*Generated from issue #147* + + diff --git a/docs/methods/ldh_activity_assay_to_determine_cell_death.md b/docs/methods/ldh_activity_assay_to_determine_cell_death.md index 544db67..7e91232 100644 --- a/docs/methods/ldh_activity_assay_to_determine_cell_death.md +++ b/docs/methods/ldh_activity_assay_to_determine_cell_death.md @@ -1,45 +1,45 @@ -# Unknown Method +# LDH activity assay to determine cell death + + Colorimetric determination of lactate dehydrogenase (LDH) activity ## Method Details -**Vendor:** Roche +* **Vendor:** Roche -**Catalog Number:** 11644793001 +* **Catalog Number:** 11644793001 -**Catalog Webpage:** [https://www.sigmaaldrich.com/NL/en/product/roche/11644793001](https://www.sigmaaldrich.com/NL/en/product/roche/11644793001) +* **Catalog Webpage:** [https://www.sigmaaldrich.com/NL/en/product/roche/11644793001](https://www.sigmaaldrich.com/NL/en/product/roche/11644793001) -**VHP4Safety Workflow Stage:** Adverse Outcome +* **VHP4Safety Workflow Stage:** Adverse Outcome -**Workflow Substage:** Cell death, Adverse outcome +* **Workflow Substage:** Cell death, Adverse outcome -**Case Study:** parkinson +* **Case Study:** parkinson -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** LDH activity assay to determine cell death - -**Assay Name:** Cytotoxicity Detection Kit (LDH) - -**Data Producer:** Julia Meerman +* **Assay Name:** Cytotoxicity Detection Kit (LDH) -**Http:** [https//www.bioassayontology.org/bao#BAO_0013056](https//www.bioassayontology.org/bao#BAO_0013056) +* **Data Producer:** Julia Meerman -**Type Url:** [http://www.bioassayontology.org/bao#BAO_0013056](http://www.bioassayontology.org/bao#BAO_0013056) +* **Relevant AOP Wiki Key Event(s):** KE1825 -**Relevant Aop Wiki Key Event(S) To The Assay:** KE1825 +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** AOP464 -**Relevant Aop Wiki Adverse Outcome Pathway(S) To The Assay:** AOP464 +* **Available SOP or Protocol:** No response -**Https:** [https//www.sigmaaldrich.com/NL/en/product/roche/11644793001](https//www.sigmaaldrich.com/NL/en/product/roche/11644793001) +* **Ontology Term:** [No response](No response) -**Available Sop Or Protocol:** No response - -**Ontology Term:** No response +* **Citation:** _No response_ --- -*Generated from issue #169 on 2025-12-03* +*Generated from issue #169* + + diff --git a/docs/methods/lysotracker_green_dnd_26.md b/docs/methods/lysotracker_green_dnd_26.md index ef4a847..e6c9ded 100644 --- a/docs/methods/lysotracker_green_dnd_26.md +++ b/docs/methods/lysotracker_green_dnd_26.md @@ -1,23 +1,45 @@ -# LysoTracker Green DND-26 +# [METHOD]: LysoTracker Green DND-26 + + Fluorescent - based detection of lysosomes ## Method Details -**Vendor:** Thermofisher +* **Vendor:** Thermofisher + +* **Catalog Number:** L7526 + +* **Catalog Webpage:** Not available -**Catalog Number:** L7526 +* **VHP4Safety Workflow Stage:** Adverse Outcome -**VHP4Safety Workflow Stage:** Adverse Outcome +* **Workflow Substage:** _No response_ -**Case Study:** thyroid +* **Case Study:** thyroid -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: LysoTracker Green DND-26 +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ + +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ + +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #145 on 2025-12-03* +*Generated from issue #145* + + diff --git a/docs/methods/method-148.md b/docs/methods/method-148.md index 70fd0cd..7baefab 100644 --- a/docs/methods/method-148.md +++ b/docs/methods/method-148.md @@ -1,25 +1,45 @@ -# P-gp Staining +# + + Immunofluorescent staining of P-gp protein, the efflux transporter of tacrolimus ## Method Details -**Vendor:** Proteintech +* **Vendor:** Proteintech + +* **Catalog Number:** 22336-1-AP + +* **Catalog Webpage:** Not available -**Catalog Number:** 22336-1-AP +* **VHP4Safety Workflow Stage:** Kinetics -**VHP4Safety Workflow Stage:** Kinetics +* **Workflow Substage:** _No response_ -**Relevant VHP4Safety Regulatory Questions:** Kidney Disease (b) +* **Case Study:** Not available + +* **Regulatory Question:** Not available ## Additional Information -**Https:** [https//ptglab.com/products/ABCB1-Antibody-22336-1-AP.htm](https//ptglab.com/products/ABCB1-Antibody-22336-1-AP.htm) +* **Assay Name:** Not available + +* **Data Producer:** Not available -**Regulatory Question:** Q1 +* **Relevant AOP Wiki Key Event(s):** Not available -**Case Study:** thyroid +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** Not available + +* **Available SOP or Protocol:** Not available + +* **Ontology Term:** Not available + +* **Citation:** _No response_ --- -*Generated from issue #148 on 2025-12-03* +*Generated from issue #148* + + diff --git a/docs/methods/mitoprobe_jc_1_assay_kit.md b/docs/methods/mitoprobe_jc_1_assay_kit.md index ab56233..6099fdd 100644 --- a/docs/methods/mitoprobe_jc_1_assay_kit.md +++ b/docs/methods/mitoprobe_jc_1_assay_kit.md @@ -1,25 +1,45 @@ -# MitoProbe™ JC-1 Assay Kit +# [METHOD]: MitoProbe™ JC-1 Assay Kit + + mitochondrial membrane potential assay ## Method Details -**Vendor:** Thermofisher +* **Vendor:** Thermofisher + +* **Catalog Number:** M34152 -**Catalog Number:** M34152 +* **Catalog Webpage:** Not available -**VHP4Safety Workflow Stage:** AOP +* **VHP4Safety Workflow Stage:** AOP -**Workflow Substage:** Mitochondrial dysfuntion +* **Workflow Substage:** Mitochondrial dysfuntion -**Case Study:** thyroid +* **Case Study:** thyroid -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: MitoProbe™ JC-1 Assay Kit +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ + +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ + +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #138 on 2025-12-03* +*Generated from issue #138* + + diff --git a/docs/methods/mitotracker_deep_red_fm_assay.md b/docs/methods/mitotracker_deep_red_fm_assay.md index 2518785..cbf304a 100644 --- a/docs/methods/mitotracker_deep_red_fm_assay.md +++ b/docs/methods/mitotracker_deep_red_fm_assay.md @@ -1,25 +1,45 @@ -# MitoTracker Deep Red FM assay +# [METHOD]: MitoTracker Deep Red FM + + Fluorescent-based assay to label mitochondria ## Method Details -**Vendor:** ThermoFisher Scientific +* **Vendor:** ThermoFisher Scientific + +* **Catalog Number:** M22426 -**Catalog Number:** M22426 +* **Catalog Webpage:** Not available -**VHP4Safety Workflow Stage:** AOP +* **VHP4Safety Workflow Stage:** AOP -**Workflow Substage:** Mitochondrial dysfunction +* **Workflow Substage:** Mitochondrial dysfunction -**Case Study:** thyroid +* **Case Study:** thyroid -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: MitoTracker Deep Red FM +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ + +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ + +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #140 on 2025-12-03* +*Generated from issue #140* + + diff --git a/docs/methods/p_gp_staining.md b/docs/methods/p_gp_staining.md index ac0bfd3..15c159b 100644 --- a/docs/methods/p_gp_staining.md +++ b/docs/methods/p_gp_staining.md @@ -1,29 +1,45 @@ -# P-gp Staining +# [METHOD]: P-gp Staining + + Immunofluorescent staining of P-gp protein, the efflux transporter of tacrolimus ## Method Details -**Vendor:** Proteintech +* **Vendor:** Proteintech -**Catalog Number:** 22336-1-AP +* **Catalog Number:** 22336-1-AP -**Catalog Webpage:** [https://ptglab.com/products/ABCB1-Antibody-22336-1-AP.htm](https://ptglab.com/products/ABCB1-Antibody-22336-1-AP.htm) +* **Catalog Webpage:** [https://ptglab.com/products/ABCB1-Antibody-22336-1-AP.htm](https://ptglab.com/products/ABCB1-Antibody-22336-1-AP.htm) -**VHP4Safety Workflow Stage:** Kinetics +* **VHP4Safety Workflow Stage:** Kinetics -**Relevant VHP4Safety Regulatory Questions:** Kidney Disease (b) +* **Workflow Substage:** _No response_ -**Case Study:** thyroid +* **Case Study:** thyroid -**Regulatory Question:** Q1 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: P-gp Staining +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ + +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ -**Https:** [https//ptglab.com/products/ABCB1-Antibody-22336-1-AP.htm](https//ptglab.com/products/ABCB1-Antibody-22336-1-AP.htm) +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #148 on 2025-12-03* +*Generated from issue #148* + + diff --git a/docs/methods/real_time_polymerase_chain_reaction.md b/docs/methods/real_time_polymerase_chain_reaction.md index 52c062b..d67467b 100644 --- a/docs/methods/real_time_polymerase_chain_reaction.md +++ b/docs/methods/real_time_polymerase_chain_reaction.md @@ -1,31 +1,45 @@ -# Real-time polymerase chain reaction +# [METHOD]: RT-qPCR + + Technology used for measuring RNA using PCR ## Method Details -**Vendor:** NA +* **Vendor:** NA -**Catalog Number:** NA +* **Catalog Number:** NA -**Relevant VHP4Safety Regulatory Questions:** Kidney Disease (b) +* **Catalog Webpage:** Not available -**Case Study:** thyroid +* **VHP4Safety Workflow Stage:** _No response_ -**Regulatory Question:** Q1 +* **Workflow Substage:** _No response_ -## Citation +* **Case Study:** thyroid -10.1016/j.mam.2005.12.007 +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: RT-qPCR +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ -**Catalog Webpage:** NA +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ -**Ontology Term:** [http://id.nlm.nih.gov/mesh/D060888](http://id.nlm.nih.gov/mesh/D060888) +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [http://id.nlm.nih.gov/mesh/D060888](http://id.nlm.nih.gov/mesh/D060888) + +* **Citation:** 10.1016/j.mam.2005.12.007 --- -*Generated from issue #141 on 2025-12-03* +*Generated from issue #141* + + diff --git a/docs/methods/rna_sequencing.md b/docs/methods/rna_sequencing.md index 71a018f..d90e6fa 100644 --- a/docs/methods/rna_sequencing.md +++ b/docs/methods/rna_sequencing.md @@ -1,21 +1,45 @@ -# RNA-sequencing +# [METHOD]: RNA-sequencing + + next-generation sequencing technique used to quantify and identify RNA molecules in a biological sample ## Method Details -**Vendor:** Utrecht Sequencing Facility (USEQ) +* **Vendor:** Utrecht Sequencing Facility (USEQ) + +* **Catalog Number:** _No response_ + +* **Catalog Webpage:** Not available -**Relevant VHP4Safety Regulatory Questions:** Kidney Disease (b) +* **VHP4Safety Workflow Stage:** _No response_ -**Case Study:** thyroid +* **Workflow Substage:** _No response_ -**Regulatory Question:** Q1 +* **Case Study:** thyroid + +* **Regulatory Question:** Q1 ## Additional Information -**Method:** [METHOD]: RNA-sequencing +* **Assay Name:** Not available + +* **Data Producer:** Not available + +* **Relevant AOP Wiki Key Event(s):** _No response_ + +* **Relevant AOP Wiki Adverse Outcome Pathway(s):** _No response_ + +* **Available SOP or Protocol:** _No response_ + +* **Ontology Term:** [_No response_](_No response_) + +* **Citation:** _No response_ --- -*Generated from issue #143 on 2025-12-03* +*Generated from issue #143* + +