laboratoire-de-chemoinformatique/chemspacecopilot/chembl-to-gtm-report

ChEMBL To GTM Report

Use this skill when the user wants a complete ChEMBL retrieval, GTM density/activity landscape analysis, and report artifact.

Procedure

1. Run chembl_prepare_retrieval and resolve any clarification questions before retrieval.
2. Convert the clarified request with chembl_convert_to_chembl_query, then call chembl_fetch_compounds.
3. Describe the clean dataset with chembl_describe_dataset and use clean_dataset_path downstream.
4. Run chemspace_plan_analysis before GTM work.
5. Build a GTM with gtm_optimization and persist it with gtm_save_model_and_data, or reuse a suitable map with gtm_load_model_only / gtm_load_and_prep_data.
6. Create density artifacts with gtm_save_density_plot and summarize dense regions with gtm_get_density_summary when the request includes density or distribution analysis.
7. Create activity landscapes with gtm_create_activity_landscapes and summarize them with gtm_get_activity_landscape_summary when the request includes activity/SAR analysis.
8. Save a report with report_save_rich, referencing data, GTM, density/activity landscape, plot, and standardization artifacts.

Expected Outputs

• Clean ChEMBL dataset path.
• GTM model and projected dataset artifacts.
• Density plot and/or activity landscape CSV/plot artifacts.
• Rich HTML report path, plus PDF/Markdown companions when requested.