feat: add rare disease ontology-first skill with bundled scripts#100
Merged
zqbake merged 1 commit intoaristoteleo:mainfrom Apr 28, 2026
Merged
Conversation
zqbake
reviewed
Apr 28, 2026
zqbake
reviewed
Apr 28, 2026
zqbake
reviewed
Apr 28, 2026
zqbake
reviewed
Apr 28, 2026
Collaborator
|
remove framework-level changes |
hazelian0619
force-pushed
the
feature/rare-disease-v2
branch
from
430748f to
bb70d68
Compare
Author
|
Superseded — previous branch accidentally included framework-level changes from v1. |
hazelian0619
force-pushed
the
feature/rare-disease-v2
branch
from
bb70d68 to
77a2309
Compare
Ship ontology query tools as CLI scripts inside the skill directory rather than as a framework-level ToolSet. Agents invoke them via the shell toolset — no changes to pantheon/toolsets or endpoint. - Add rd_ontology_first skill with ontology-before-online workflow - Bundle build_rd_ontology.py (ETL) and query_rd_ontology.py (CLI) inside skills/rare_disease/scripts/ - Use ~/.pantheon/rd_ontology/ as the global shared database path - Include 6 agent definitions and rare_disease_team template Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Add a rare disease ontology-first skill with self-contained CLI scripts shipped inside the skill directory. Uses
~/.pantheon/rd_ontology/as the global shared database path. No framework-level changes — agents invoke scripts via theshelltoolset.Supersedes #99.
What changed from v1
rd_ontologyToolSet registered in frameworkskills/rare_disease/scripts/pantheon/toolsets/__init__.pypantheon/endpoint/toolsets.pydata/rd_ontology_store/(project-local)~/.pantheon/rd_ontology/(global, shared)shellto invoke Python CLIFiles
New
skills/rare_disease/scripts/build_rd_ontology.py— ETL pipeline (Orphanet/OMIM/HPO → SQLite)skills/rare_disease/scripts/query_rd_ontology.py— CLI: resolve, disease, find_by_hpo, hpo_term, statsModified
skills/rare_disease/rd_ontology_first.md— updated for shell-based usage, global DB pathagents/rare_disease/evidence_researcher.md—rd_ontology→shelltoolsetagents/rare_disease/phenotype_structurer.md—rd_ontology→shelltoolsetUnchanged from upstream
agents/rare_disease/leader.md,auditor.md,genotype_analyst.md,reporter.mdteams/rare_disease_team.md🤖 Generated with Claude Code