[Upstream sync] K-Dense-AI/scientific-agent-skills (github) — 78 added, 66 modified #29

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promptadmin wants to merge 144 commits from upstream-sync/scientific-agent-skills-20260724-757b63-dcry into main

promptadmin commented

2026-07-24 23:43:06 +00:00

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Upstream sync from `K-Dense-AI/scientific-agent-skills` (github)

Source: https://github.com/K-Dense-AI/scientific-agent-skills
Forge: github
Compare: 831d49eb...757b63b1

Scan summary

Category	Files
Prompt / Skill files	16
Catalogue / Reference files	128

Prompt files are stored under upstream/{owner}-{repo}/
Catalogue files are stored under upstream/{owner}-{repo}/catalogue/

Decision required

Option	Action
Accept	Merge this PR — changes ingested into PromptNotes
Reject	Close this PR — local version preserved unchanged
Modify	Edit files in this branch before merging

Backup rights: If the upstream repository is later deleted or made private,
the last accepted version in PromptNotes is retained under backup rights.

Files added (78)

skills/clinical-decision-support/assets/aggregate_cohort_table_template.json
skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json
skills/clinical-decision-support/assets/artifact_intended_use_template.json
skills/clinical-decision-support/assets/decision_logic_traceability_template.json
skills/clinical-decision-support/assets/deidentification_checklist_template.json
skills/clinical-decision-support/assets/evidence_profile_template.json
skills/clinical-decision-support/assets/survival_analysis_plan_template.json
skills/clinical-decision-support/references/cohort_evaluation.md
skills/clinical-decision-support/references/decision_logic_traceability.md
skills/clinical-decision-support/references/evidence_profiles.md
skills/clinical-decision-support/references/model_biomarker_evaluation.md
skills/clinical-decision-support/references/privacy_and_disclosure.md
skills/clinical-decision-support/references/regulatory_and_governance.md
skills/clinical-decision-support/references/safety_and_scope.md
skills/clinical-decision-support/references/security_validation.md
skills/clinical-decision-support/references/sources.md
skills/clinical-decision-support/references/study_reporting.md
skills/clinical-decision-support/references/survival_analysis.md
skills/clinical-reports/assets/case_report_template.json
skills/clinical-reports/assets/clinical_trial_csr_template.json
skills/clinical-reports/assets/clinical_trial_results_template.json
skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json
skills/clinical-reports/assets/consistency_manifest_template.json
skills/clinical-reports/assets/deidentification_process_checklist.json
skills/clinical-reports/assets/lab_report_template.json
skills/clinical-reports/assets/pathology_report_template.json
skills/clinical-reports/assets/provenance_manifest_template.json
skills/clinical-reports/assets/quality_review_checklist.json
skills/clinical-reports/assets/radiology_report_template.json
skills/clinical-reports/assets/research_summary_template.json
skills/clinical-reports/assets/terminology_manifest_template.json
skills/clinical-reports/assets/trial_protocol_reporting_checklist.json
skills/clinical-reports/references/privacy_and_deidentification.md
skills/clinical-reports/references/professional_review.md
skills/clinical-reports/references/report_type_routing.md
skills/clinical-reports/references/safety_reporting.md
skills/clinical-reports/references/sources.md
skills/dnanexus-integration/references/authentication.md
skills/dnanexus-integration/references/operations-and-troubleshooting.md
skills/dnanexus-integration/references/sources.md
… and 38 more

Files modified (66)

README.md
docs/examples.md
docs/open-source-sponsors.md
docs/skills.md
skills/clinical-decision-support/SKILL.md
skills/clinical-decision-support/references/README.md
skills/clinical-reports/SKILL.md
skills/clinical-reports/references/README.md
skills/clinical-reports/references/case_report_guidelines.md
skills/clinical-reports/references/clinical_trial_reporting.md
skills/clinical-reports/references/data_presentation.md
skills/clinical-reports/references/diagnostic_reports_standards.md
skills/clinical-reports/references/medical_terminology.md
skills/dnanexus-integration/SKILL.md
skills/dnanexus-integration/references/app-development.md
skills/dnanexus-integration/references/configuration.md
skills/dnanexus-integration/references/data-operations.md
skills/dnanexus-integration/references/job-execution.md
skills/dnanexus-integration/references/python-sdk.md
skills/etetoolkit/SKILL.md
skills/etetoolkit/references/api_reference.md
skills/etetoolkit/references/visualization.md
skills/etetoolkit/references/workflows.md
skills/exploratory-data-analysis/SKILL.md
skills/exploratory-data-analysis/assets/report_template.md
skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md
skills/exploratory-data-analysis/references/chemistry_molecular_formats.md
skills/exploratory-data-analysis/references/general_scientific_formats.md
skills/exploratory-data-analysis/references/microscopy_imaging_formats.md
skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md
skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md
skills/flowio/SKILL.md
skills/flowio/references/api_reference.md
skills/fluidsim/SKILL.md
skills/fluidsim/references/advanced_features.md
skills/fluidsim/references/installation.md
skills/fluidsim/references/output_analysis.md
skills/fluidsim/references/parameters.md
skills/fluidsim/references/simulation_workflow.md
skills/fluidsim/references/solvers.md
… and 26 more

Files removed upstream (25)

Accepting this PR will NOT delete them from PromptNotes.

skills/clinical-decision-support/assets/example_gbm_cohort.md
skills/clinical-decision-support/assets/recommendation_strength_guide.md
skills/clinical-decision-support/references/biomarker_classification.md
skills/clinical-decision-support/references/clinical_decision_algorithms.md
skills/clinical-decision-support/references/evidence_synthesis.md
skills/clinical-decision-support/references/outcome_analysis.md
skills/clinical-decision-support/references/patient_cohort_analysis.md
skills/clinical-decision-support/references/treatment_recommendations.md
skills/clinical-reports/assets/case_report_template.md
skills/clinical-reports/assets/clinical_trial_csr_template.md
skills/clinical-reports/assets/clinical_trial_sae_template.md
skills/clinical-reports/assets/consult_note_template.md
skills/clinical-reports/assets/discharge_summary_template.md
skills/clinical-reports/assets/hipaa_compliance_checklist.md
skills/clinical-reports/assets/history_physical_template.md
skills/clinical-reports/assets/lab_report_template.md
skills/clinical-reports/assets/pathology_report_template.md
skills/clinical-reports/assets/quality_checklist.md
skills/clinical-reports/assets/radiology_report_template.md
skills/clinical-reports/assets/soap_note_template.md

Auto-generated by PromptNotes upstream tracker v2 · 2026-07-24 23:42 UTC

## Upstream sync from `K-Dense-AI/scientific-agent-skills` (github) **Source:** https://github.com/K-Dense-AI/scientific-agent-skills **Forge:** github **Compare:** [831d49eb...757b63b1](https://github.com/K-Dense-AI/scientific-agent-skills/compare/831d49eb...757b63b1) --- ## Scan summary | Category | Files | |----------|-------| | Prompt / Skill files | 16 | | Catalogue / Reference files | 128 | > Prompt files are stored under `upstream/{owner}-{repo}/` > Catalogue files are stored under `upstream/{owner}-{repo}/catalogue/` --- ## Decision required | Option | Action | |--------|--------| | **Accept** | Merge this PR — changes ingested into PromptNotes | | **Reject** | Close this PR — local version preserved unchanged | | **Modify** | Edit files in this branch before merging | > **Backup rights:** If the upstream repository is later deleted or made private, > the last accepted version in PromptNotes is retained under backup rights. --- ## Files added (78) - `skills/clinical-decision-support/assets/aggregate_cohort_table_template.json` - `skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json` - `skills/clinical-decision-support/assets/artifact_intended_use_template.json` - `skills/clinical-decision-support/assets/decision_logic_traceability_template.json` - `skills/clinical-decision-support/assets/deidentification_checklist_template.json` - `skills/clinical-decision-support/assets/evidence_profile_template.json` - `skills/clinical-decision-support/assets/survival_analysis_plan_template.json` - `skills/clinical-decision-support/references/cohort_evaluation.md` - `skills/clinical-decision-support/references/decision_logic_traceability.md` - `skills/clinical-decision-support/references/evidence_profiles.md` - `skills/clinical-decision-support/references/model_biomarker_evaluation.md` - `skills/clinical-decision-support/references/privacy_and_disclosure.md` - `skills/clinical-decision-support/references/regulatory_and_governance.md` - `skills/clinical-decision-support/references/safety_and_scope.md` - `skills/clinical-decision-support/references/security_validation.md` - `skills/clinical-decision-support/references/sources.md` - `skills/clinical-decision-support/references/study_reporting.md` - `skills/clinical-decision-support/references/survival_analysis.md` - `skills/clinical-reports/assets/case_report_template.json` - `skills/clinical-reports/assets/clinical_trial_csr_template.json` - `skills/clinical-reports/assets/clinical_trial_results_template.json` - `skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json` - `skills/clinical-reports/assets/consistency_manifest_template.json` - `skills/clinical-reports/assets/deidentification_process_checklist.json` - `skills/clinical-reports/assets/lab_report_template.json` - `skills/clinical-reports/assets/pathology_report_template.json` - `skills/clinical-reports/assets/provenance_manifest_template.json` - `skills/clinical-reports/assets/quality_review_checklist.json` - `skills/clinical-reports/assets/radiology_report_template.json` - `skills/clinical-reports/assets/research_summary_template.json` - `skills/clinical-reports/assets/terminology_manifest_template.json` - `skills/clinical-reports/assets/trial_protocol_reporting_checklist.json` - `skills/clinical-reports/references/privacy_and_deidentification.md` - `skills/clinical-reports/references/professional_review.md` - `skills/clinical-reports/references/report_type_routing.md` - `skills/clinical-reports/references/safety_reporting.md` - `skills/clinical-reports/references/sources.md` - `skills/dnanexus-integration/references/authentication.md` - `skills/dnanexus-integration/references/operations-and-troubleshooting.md` - `skills/dnanexus-integration/references/sources.md` - … and 38 more ## Files modified (66) - `README.md` - `docs/examples.md` - `docs/open-source-sponsors.md` - `docs/skills.md` - `skills/clinical-decision-support/SKILL.md` - `skills/clinical-decision-support/references/README.md` - `skills/clinical-reports/SKILL.md` - `skills/clinical-reports/references/README.md` - `skills/clinical-reports/references/case_report_guidelines.md` - `skills/clinical-reports/references/clinical_trial_reporting.md` - `skills/clinical-reports/references/data_presentation.md` - `skills/clinical-reports/references/diagnostic_reports_standards.md` - `skills/clinical-reports/references/medical_terminology.md` - `skills/dnanexus-integration/SKILL.md` - `skills/dnanexus-integration/references/app-development.md` - `skills/dnanexus-integration/references/configuration.md` - `skills/dnanexus-integration/references/data-operations.md` - `skills/dnanexus-integration/references/job-execution.md` - `skills/dnanexus-integration/references/python-sdk.md` - `skills/etetoolkit/SKILL.md` - `skills/etetoolkit/references/api_reference.md` - `skills/etetoolkit/references/visualization.md` - `skills/etetoolkit/references/workflows.md` - `skills/exploratory-data-analysis/SKILL.md` - `skills/exploratory-data-analysis/assets/report_template.md` - `skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md` - `skills/exploratory-data-analysis/references/chemistry_molecular_formats.md` - `skills/exploratory-data-analysis/references/general_scientific_formats.md` - `skills/exploratory-data-analysis/references/microscopy_imaging_formats.md` - `skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md` - `skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md` - `skills/flowio/SKILL.md` - `skills/flowio/references/api_reference.md` - `skills/fluidsim/SKILL.md` - `skills/fluidsim/references/advanced_features.md` - `skills/fluidsim/references/installation.md` - `skills/fluidsim/references/output_analysis.md` - `skills/fluidsim/references/parameters.md` - `skills/fluidsim/references/simulation_workflow.md` - `skills/fluidsim/references/solvers.md` - … and 26 more ## Files removed upstream (25) > Accepting this PR will NOT delete them from PromptNotes. - `skills/clinical-decision-support/assets/example_gbm_cohort.md` - `skills/clinical-decision-support/assets/recommendation_strength_guide.md` - `skills/clinical-decision-support/references/biomarker_classification.md` - `skills/clinical-decision-support/references/clinical_decision_algorithms.md` - `skills/clinical-decision-support/references/evidence_synthesis.md` - `skills/clinical-decision-support/references/outcome_analysis.md` - `skills/clinical-decision-support/references/patient_cohort_analysis.md` - `skills/clinical-decision-support/references/treatment_recommendations.md` - `skills/clinical-reports/assets/case_report_template.md` - `skills/clinical-reports/assets/clinical_trial_csr_template.md` - `skills/clinical-reports/assets/clinical_trial_sae_template.md` - `skills/clinical-reports/assets/consult_note_template.md` - `skills/clinical-reports/assets/discharge_summary_template.md` - `skills/clinical-reports/assets/hipaa_compliance_checklist.md` - `skills/clinical-reports/assets/history_physical_template.md` - `skills/clinical-reports/assets/lab_report_template.md` - `skills/clinical-reports/assets/pathology_report_template.md` - `skills/clinical-reports/assets/quality_checklist.md` - `skills/clinical-reports/assets/radiology_report_template.md` - `skills/clinical-reports/assets/soap_note_template.md` --- *Auto-generated by PromptNotes upstream tracker v2 · 2026-07-24 23:42 UTC*