Add instance.url to 7 tools

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",

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

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",

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/"
   }
 </script>

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": {

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"
   }
 </script>

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"

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/"
   }
 </script>

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": {

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/"
   }
 </script>

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"
   },

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/"
   }
 </script>

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": {

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/"
   }
 </script>

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": "",

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/"
   }
 </script>

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">
-<!-- Sitemap created on 2026-04-17 13:15:33.501041. -->
+<!-- Sitemap created on 2026-04-17 13:39:01.146856. -->
 
 <!-- parsing file: docs/service/aop-builder.json -->
 <url>