diff --git a/cap/service_index.json b/cap/service_index.json index 8d02922..52c95ee 100644 --- a/cap/service_index.json +++ b/cap/service_index.json @@ -467,7 +467,7 @@ "png_file_name": "https://github.com/VHP4Safety/ui-design/blob/main/static/images/logo.png", "stage": "https://vhp4safety.github.io/glossary#VHP0000156", "main_url": "https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing", - "inst_url": "no_url", + "inst_url": "https://mct8-docking.vhp4safety.nl/#docking", "reg_q_1a": "", "reg_q_1b": "", "reg_q_2a": "", @@ -603,7 +603,7 @@ "png_file_name": "pcbi.1004085.g004.png", "stage": "https://vhp4safety.github.io/glossary#VHP0000156", "main_url": "https://pathvisio.org/", - "inst_url": "no_url", + "inst_url": "https://pathvisio.org/", "reg_q_1a": "false", "reg_q_1b": "false", "reg_q_2a": "false", @@ -722,7 +722,7 @@ "png_file_name": "https://github.com/VHP4Safety/ui-design/blob/main/static/images/logo.png", "stage": "https://vhp4safety.github.io/glossary#VHP0000153", "main_url": "http://cdk.github.io/", - "inst_url": "no_url", + "inst_url": "http://cdk.github.io/", "reg_q_1a": "false", "reg_q_1b": "false", "reg_q_2a": "false", @@ -773,7 +773,7 @@ "png_file_name": "txg_mapr.png", "stage": "https://vhp4safety.github.io/glossary#VHP0000156", "main_url": "https://txg-mapr.eu/", - "inst_url": "no_url", + "inst_url": "https://txg-mapr.eu/", "reg_q_1a": "false", "reg_q_1b": "false", "reg_q_2a": "false", @@ -790,7 +790,7 @@ "png_file_name": "vhp_glossary.png", "stage": "Other", "main_url": "https://glossary.vhp4safety.nl/", - "inst_url": "no_url", + "inst_url": "https://glossary.vhp4safety.nl/", "reg_q_1a": "true", "reg_q_1b": "true", "reg_q_2a": "true", @@ -807,7 +807,7 @@ "png_file_name": "VHP4Safety_ChemicalCompounds.png", "stage": "Other", "main_url": "https://compoundcloud.wikibase.cloud/", - "inst_url": "no_url", + "inst_url": "https://compoundcloud.wikibase.cloud/", "reg_q_1a": "false", "reg_q_1b": "false", "reg_q_2a": "false", @@ -824,7 +824,7 @@ "png_file_name": "wikipathways_aop.png", "stage": "https://vhp4safety.github.io/glossary#VHP0000156", "main_url": "https://aop.wikipathways.org/", - "inst_url": "no_url", + "inst_url": "https://aop.wikipathways.org/", "reg_q_1a": "false", "reg_q_1b": "false", "reg_q_2a": "false", diff --git a/docs/index.md b/docs/index.md index 67bbfed..9d857b0 100644 --- a/docs/index.md +++ b/docs/index.md @@ -101,10 +101,6 @@ A webservice for prediction of protein-structure and reactivity based (P450) sit An online tool for harmonizing in vitro toxicity test methods using Large Language Models, based on the ToxTemp template where it extracts details from protocols, publications or lab notes to create structured draft responses. [[more information](service/toxtemp_assistant.md)] -#### TXG-MAPr - -An online application for implementation of weighted gene co-expression network analysis (WGCNA) derived from publicly available transcriptomic datasets from the TG-GATEs database. [[more information](service/txg_mapr.md)] - #### VHP4Safety Glossary A collection of ontology with names, abrreviations and definitions of the terminology that is used within the VHP4Safety project. [[more information](service/vhp_glossary.md)] @@ -113,10 +109,6 @@ A collection of ontology with names, abrreviations and definitions of the termin A Wikibase instance for storing and presenting information about toxic, safe and potentially toxic compounds related to the VHP4Safety project. [[more information](service/wikibase.md)] -#### WikiPathways - AOP Portal - -An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecular basis of AOPs and their key events (KEs). [[more information](service/wikipathways_aop.md)] - #### xploreaop A web application for visualization of Adverse Outcome Pathway (AOP) networks and interactive exploration of AOPs for two liver outcomes. [[more information](service/xploreaop.md)] @@ -133,6 +125,10 @@ Open-source active-learning software for transparent and efficient systematic li A software tool for high-dimensional dose-response modeling and analysis. [[more information](service/bmdexpress_3.md)] +#### The Chemistry Development Kit + +A Java library for chem- and bioinformatics, with functionality to read/write chemical structures, calculate molecular descriptors, physicochemical properties, substructure and similarity searching, and much more. [[more information](service/cdk.md)] + #### CellDesigner An intuitive user interface for creating gene-regulatory and biochemical network diagrams. [[more information](service/celldesigner.md)] @@ -201,6 +197,14 @@ Desktop software to visualize, edit, and draw new pathways, which can be exporte An online service for conduction of literature review, data extraction and systematic review. [[more information](service/sysrev.md)] +#### TXG-MAPr + +An online application for implementation of weighted gene co-expression network analysis (WGCNA) derived from publicly available transcriptomic datasets from the TG-GATEs database. [[more information](service/txg_mapr.md)] + +#### WikiPathways - AOP Portal + +An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecular basis of AOPs and their key events (KEs). [[more information](service/wikipathways_aop.md)] + ------------------------------------------ ## Persona-Specific Catalogs diff --git a/docs/service/cdk.json b/docs/service/cdk.json index 94fb231..31b5bac 100644 --- a/docs/service/cdk.json +++ b/docs/service/cdk.json @@ -5,6 +5,10 @@ "stage": "https://vhp4safety.github.io/glossary#VHP0000153", "url": "http://cdk.github.io/", "doi": "10.1186/s13321-017-0220-4", + "instance": { + "type": "external", + "url": "http://cdk.github.io/" + }, "provider": { "contact": { "name": "Egon Willighagen", diff --git a/docs/service/cdk.md b/docs/service/cdk.md index 201da14..4402e9b 100644 --- a/docs/service/cdk.md +++ b/docs/service/cdk.md @@ -8,6 +8,7 @@ A Java library for chem- and bioinformatics, with functionality to read/write ch **Main Webpage:** [http://cdk.github.io/](http://cdk.github.io/) +**Tool Webpage:** [http://cdk.github.io/](http://cdk.github.io/) ## Contact @@ -54,13 +55,13 @@ A Java library for chem- and bioinformatics, with functionality to read/write ch * Sub-Stage: -* Development Cloud: Not available +* Development Cloud: [http://cdk.github.io/](http://cdk.github.io/) * Login Required: Not available * TRL: Not available -* Type: Not available +* Type: external * API Type: Not available @@ -102,6 +103,6 @@ A Java library for chem- and bioinformatics, with functionality to read/write ch "@id" : "https://vhp4safety.github.io/cloud/service/cdk", "name": "The Chemistry Development Kit", "description": "A Java library for chem- and bioinformatics, with functionality to read/write chemical structures, calculate molecular descriptors, physicochemical properties, substructure and similarity searching, and much more.", - "url": "" + "url": "http://cdk.github.io/" } diff --git a/docs/service/mct8-dock.json b/docs/service/mct8-dock.json index f8aca71..79c747e 100644 --- a/docs/service/mct8-dock.json +++ b/docs/service/mct8-dock.json @@ -7,9 +7,9 @@ "url": "https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing", "doi": "", "instance": { - "type": "External", + "type": "internal", "vhp-platform": "Development", - "url": "", + "url": "https://mct8-docking.vhp4safety.nl/#docking", "TRL": "" }, "intro": { diff --git a/docs/service/mct8-dock.md b/docs/service/mct8-dock.md index 2de0e58..0030e9e 100644 --- a/docs/service/mct8-dock.md +++ b/docs/service/mct8-dock.md @@ -8,6 +8,7 @@ A Python-based notebook for identifying potential MCT8 inhibitors and related mo **Main Webpage:** [https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing](https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing) +**Tool Webpage:** [https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing](https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing) ## Contact @@ -55,7 +56,7 @@ A Python-based notebook for identifying potential MCT8 inhibitors and related mo * Sub-Stage: -* Development Cloud: []() +* Development Cloud: [https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing](https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing) * Login Required: No @@ -103,6 +104,6 @@ A Python-based notebook for identifying potential MCT8 inhibitors and related mo "@id" : "https://vhp4safety.github.io/cloud/service/mct8-dock", "name": "MCT8 Docking for MIE Discovery", "description": "A Python-based notebook for identifying potential MCT8 inhibitors and related molecular events linked to developmental thyroid toxicity from maternal thyroid hormone deprivation.", - "url": "" + "url": "https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing" } diff --git a/docs/service/pathvisio.json b/docs/service/pathvisio.json index 9048a76..9f3915d 100644 --- a/docs/service/pathvisio.json +++ b/docs/service/pathvisio.json @@ -9,6 +9,7 @@ "doi": "10.1371/journal.pcbi.1004085", "instance": { "type": "external", + "url": "https://pathvisio.org/", "license": "Apache-2.0 license", "version": "3.3", "source": "https://github.com/PathVisio/pathvisio" diff --git a/docs/service/pathvisio.md b/docs/service/pathvisio.md index b1a7f93..dffba47 100644 --- a/docs/service/pathvisio.md +++ b/docs/service/pathvisio.md @@ -9,6 +9,7 @@ Desktop software to visualize, edit, and draw new pathways, which can be exporte **Main Webpage:** [https://pathvisio.org/](https://pathvisio.org/) +**Tool Webpage:** [https://pathvisio.org/](https://pathvisio.org/) ## Contact @@ -56,7 +57,7 @@ Desktop software to visualize, edit, and draw new pathways, which can be exporte * Sub-Stage: -* Development Cloud: Not available +* Development Cloud: [https://pathvisio.org/](https://pathvisio.org/) * Login Required: no @@ -104,6 +105,6 @@ Desktop software to visualize, edit, and draw new pathways, which can be exporte "@id" : "https://vhp4safety.github.io/cloud/service/pathvisio", "name": "PathVisio", "description": "Desktop software to visualize, edit, and draw new pathways, which can be exported in the GPML format, for example, to WikiPathways.", - "url": "" + "url": "https://pathvisio.org/" } diff --git a/docs/service/txg_mapr.json b/docs/service/txg_mapr.json index fbea0b7..083944e 100644 --- a/docs/service/txg_mapr.json +++ b/docs/service/txg_mapr.json @@ -8,8 +8,9 @@ "url": "https://txg-mapr.eu/", "doi": "10.1007/s00204-021-03141-w", "instance": { - "type": "internal", + "type": "external", "vhp-platform": "External", + "url": "https://txg-mapr.eu/", "license": "Proprietary" }, "provider": { diff --git a/docs/service/txg_mapr.md b/docs/service/txg_mapr.md index d6b43ee..6bee68b 100644 --- a/docs/service/txg_mapr.md +++ b/docs/service/txg_mapr.md @@ -9,6 +9,7 @@ An online application for implementation of weighted gene co-expression network **Main Webpage:** [https://txg-mapr.eu/](https://txg-mapr.eu/) +**Tool Webpage:** [https://txg-mapr.eu/](https://txg-mapr.eu/) ## Contact @@ -56,13 +57,13 @@ An online application for implementation of weighted gene co-expression network * Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000018 -* Development Cloud: Not available +* Development Cloud: [https://txg-mapr.eu/](https://txg-mapr.eu/) * Login Required: Yes * TRL: Not available -* Type: internal +* Type: external * API Type: Not available @@ -104,6 +105,6 @@ An online application for implementation of weighted gene co-expression network "@id" : "https://vhp4safety.github.io/cloud/service/txg_mapr", "name": "TXG-MAPr", "description": "An online application for implementation of weighted gene co-expression network analysis (WGCNA) derived from publicly available transcriptomic datasets from the TG-GATEs database.", - "url": "" + "url": "https://txg-mapr.eu/" } diff --git a/docs/service/vhp_glossary.json b/docs/service/vhp_glossary.json index 0ed7389..767ac3a 100644 --- a/docs/service/vhp_glossary.json +++ b/docs/service/vhp_glossary.json @@ -13,6 +13,7 @@ "instance": { "type": "internal", "vhp-platform": "development", + "url": "https://glossary.vhp4safety.nl/", "license": "CC-BY 4.0 International", "source": "https://github.com/VHP4Safety/glossary" }, diff --git a/docs/service/vhp_glossary.md b/docs/service/vhp_glossary.md index 64e80fc..2e88f41 100644 --- a/docs/service/vhp_glossary.md +++ b/docs/service/vhp_glossary.md @@ -9,6 +9,7 @@ A collection of ontology with names, abrreviations and definitions of the termin **Main Webpage:** [https://glossary.vhp4safety.nl/](https://glossary.vhp4safety.nl/) +**Tool Webpage:** [https://glossary.vhp4safety.nl/](https://glossary.vhp4safety.nl/) ## Contact @@ -56,7 +57,7 @@ A collection of ontology with names, abrreviations and definitions of the termin * Sub-Stage: Other -* Development Cloud: Not available +* Development Cloud: [https://glossary.vhp4safety.nl/](https://glossary.vhp4safety.nl/) * Login Required: no @@ -104,6 +105,6 @@ A collection of ontology with names, abrreviations and definitions of the termin "@id" : "https://vhp4safety.github.io/cloud/service/vhp_glossary", "name": "VHP4Safety Glossary", "description": "A collection of ontology with names, abrreviations and definitions of the terminology that is used within the VHP4Safety project.", - "url": "" + "url": "https://glossary.vhp4safety.nl/" } diff --git a/docs/service/wikibase.json b/docs/service/wikibase.json index 6827f55..4d8084c 100644 --- a/docs/service/wikibase.json +++ b/docs/service/wikibase.json @@ -8,7 +8,8 @@ "url": "https://compoundcloud.wikibase.cloud/", "doi": "10.5281/zenodo.13864849", "instance": { - "type": "internal" + "type": "internal", + "url": "https://compoundcloud.wikibase.cloud/" }, "provider": { "contact": { diff --git a/docs/service/wikibase.md b/docs/service/wikibase.md index e5fea46..123be5b 100644 --- a/docs/service/wikibase.md +++ b/docs/service/wikibase.md @@ -9,6 +9,7 @@ A Wikibase instance for storing and presenting information about toxic, safe and **Main Webpage:** [https://compoundcloud.wikibase.cloud/](https://compoundcloud.wikibase.cloud/) +**Tool Webpage:** [https://compoundcloud.wikibase.cloud/](https://compoundcloud.wikibase.cloud/) ## Contact @@ -56,7 +57,7 @@ A Wikibase instance for storing and presenting information about toxic, safe and * Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000148 -* Development Cloud: Not available +* Development Cloud: [https://compoundcloud.wikibase.cloud/](https://compoundcloud.wikibase.cloud/) * Login Required: No @@ -104,6 +105,6 @@ A Wikibase instance for storing and presenting information about toxic, safe and "@id" : "https://vhp4safety.github.io/cloud/service/wikibase", "name": "VHP4Safety Wikibase", "description": "A Wikibase instance for storing and presenting information about toxic, safe and potentially toxic compounds related to the VHP4Safety project.", - "url": "" + "url": "https://compoundcloud.wikibase.cloud/" } diff --git a/docs/service/wikipathways_aop.json b/docs/service/wikipathways_aop.json index f436c60..095d901 100644 --- a/docs/service/wikipathways_aop.json +++ b/docs/service/wikipathways_aop.json @@ -8,9 +8,9 @@ "url": "https://aop.wikipathways.org/", "doi": "10.3389/fgene.2018.00661", "instance": { - "type": "internal", + "type": "external", "vhp-platform": "External", - "url": "", + "url": "https://aop.wikipathways.org/", "license": "[CC0](https://creativecommons.org/share-your-work/public-domain/cc0/)", "version": "", "source": "", diff --git a/docs/service/wikipathways_aop.md b/docs/service/wikipathways_aop.md index 5c4ec36..965609a 100644 --- a/docs/service/wikipathways_aop.md +++ b/docs/service/wikipathways_aop.md @@ -9,6 +9,7 @@ An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecu **Main Webpage:** [https://aop.wikipathways.org/](https://aop.wikipathways.org/) +**Tool Webpage:** [https://aop.wikipathways.org/](https://aop.wikipathways.org/) ## Contact @@ -56,13 +57,13 @@ An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecu * Sub-Stage: https://vhp4safety.github.io/glossary#VHP0000023 -* Development Cloud: []() +* Development Cloud: [https://aop.wikipathways.org/](https://aop.wikipathways.org/) * Login Required: No * TRL: -* Type: internal +* Type: external * API Type: SPARQL @@ -104,6 +105,6 @@ An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecu "@id" : "https://vhp4safety.github.io/cloud/service/wikipathways_aop", "name": "WikiPathways - AOP Portal", "description": "An Adverse Outcome Pathway (AOP) portal on WikiPathways for exploring the molecular basis of AOPs and their key events (KEs).", - "url": "" + "url": "https://aop.wikipathways.org/" } diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 4421657..bd395f2 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -4,7 +4,7 @@ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.sitemaps.org/schemas/sitemap/0.9 http://www.sitemaps.org/schemas/sitemap/0.9/sitemap.xsd"> - + diff --git a/docs/tools.tsv b/docs/tools.tsv index 24a6057..b9ef635 100644 --- a/docs/tools.tsv +++ b/docs/tools.tsv @@ -9,7 +9,7 @@ biomodels BioModels https://www.ebi.ac.uk/biomodels/ NA biotransformer BioTransformer https://biotransformer.ca/ NA bmdexpress_3 BMDExpress-3 https://github.com/auerbachs/BMDExpress-3 NA bridgedb BridgeDb https://www.bridgedb.org/ https://bridgedb.cloud.vhp4safety.nl/ -cdk The Chemistry Development Kit http://cdk.github.io/ NA +cdk The Chemistry Development Kit http://cdk.github.io/ http://cdk.github.io/ cdkdepict CDK Depict https://www.simolecule.com/cdkdepict/depict.html https://cdkdepict.cloud.vhp4safety.nl/ celldesigner CellDesigner https://www.celldesigner.org/ NA comptox CompTox https://comptox.epa.gov/dashboard/ NA @@ -28,7 +28,7 @@ google Google Search https://google.com/ NA gscholar Google Scholar https://scholar.google.com/ NA jrc_data_catalogue Joint Research Centre Data Catalogue https://data.jrc.ec.europa.eu/ NA llemy Llemy NA https://llemy.vhp4safety.nl/ -mct8-dock MCT8 Docking for MIE Discovery https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing +mct8-dock MCT8 Docking for MIE Discovery https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing https://colab.research.google.com/drive/1vhy61p0z_AGnSEidwD83RwBzsW2AxAAT?usp=sharing molaopanalyser MolAOP analyser https://molaop-analyser.vhp4safety.nl/ https://molaop-analyser.vhp4safety.nl/ molaopbuilder Molecular AOP Builder https://github.com/marvinm2/KE-WP-mapping https://molaop-builder.vhp4safety.nl/ oecd_qsar_toolbox The OECD QSAR Toolbox https://qsartoolbox.org/ @@ -36,7 +36,7 @@ ontox_physiological_maps ONTOX Physiological Maps https://sites.google.com/view/ oppbk_model OP PBK Model http://oppbk.cloud.vhp4safety.nl/ http://oppbk.cloud.vhp4safety.nl/ opsin OPSIN: Open Parser for Systematic IUPAC nomenclature https://www.ebi.ac.uk/opsin/ NA oqt_assistant O-QT — OECD QSAR Toolbox AI Assistant https://github.com/VHP4Safety/O-QT-OECD-QSAR-Toolbox-AI-assistant https://o-qt-oecd.vhp4safety.nl/ -pathvisio PathVisio https://pathvisio.org/ NA +pathvisio PathVisio https://pathvisio.org/ https://pathvisio.org/ qaop_app qAOP-App https://qaop.vhp4safety.nl/ https://qaop.vhp4safety.nl/ qsprpred QSPRpred https://qsprpred.cloud.vhp4safety.nl/ https://qsprpred.cloud.vhp4safety.nl/ r_odaf R-ODAF Shiny NA https://r-odaf.nl/ @@ -44,8 +44,8 @@ robot ROBOT https://robot.vhp4safety.nl/ui sombie SOM Prediction https://sombie.cloud.vhp4safety.nl/ https://sombie.cloud.vhp4safety.nl/ sysrev SysRev https://sysrev.com/ NA toxtemp_assistant ToxTempAssistant https://toxtempassistant.vhp4safety.nl/ https://toxtempassistant.vhp4safety.nl/ -txg_mapr TXG-MAPr https://txg-mapr.eu/ NA -vhp_glossary VHP4Safety Glossary https://glossary.vhp4safety.nl/ NA -wikibase VHP4Safety Wikibase https://compoundcloud.wikibase.cloud/ NA -wikipathways_aop WikiPathways - AOP Portal https://aop.wikipathways.org/ +txg_mapr TXG-MAPr https://txg-mapr.eu/ https://txg-mapr.eu/ +vhp_glossary VHP4Safety Glossary https://glossary.vhp4safety.nl/ https://glossary.vhp4safety.nl/ +wikibase VHP4Safety Wikibase https://compoundcloud.wikibase.cloud/ https://compoundcloud.wikibase.cloud/ +wikipathways_aop WikiPathways - AOP Portal https://aop.wikipathways.org/ https://aop.wikipathways.org/ xploreaop xploreaop https://xploreaop.cloud.vhp4safety.nl/ https://xploreaop.cloud.vhp4safety.nl/