# Taxonomy Builder

Build a 2+ level taxonomy (`outline/taxonomy.yml`) from a core paper set and scope...

- Repository: https://github.com/WILLOSCAR/research-units-pipeline-skills (517 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-10-05
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add WILLOSCAR/research-units-pipeline-skills --skill taxonomy-builder -g -a claude-code -y`
Codex: `npx skills add WILLOSCAR/research-units-pipeline-skills --skill taxonomy-builder -g -a codex -y`
Cursor: `npx skills add WILLOSCAR/research-units-pipeline-skills --skill taxonomy-builder -g -a cursor -y`
Gemini CLI: `npx skills add WILLOSCAR/research-units-pipeline-skills --skill taxonomy-builder -g -a gemini-cli -y`

## Description

Build a 2+ level taxonomy (`outline/taxonomy.yml`) from a core paper set and scope constraints, with short descriptions per node.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Taxonomy Builder (router, compatibility mode)

## Triggers & routing

- **Trigger**: taxonomy, taxonomy builder, 分类, 主题树, taxonomy.yml.
- **Use when**: survey/snapshot 的结构阶段（NO PROSE），已有 `papers/core_set.csv`，需要生成可映射且读者友好的主题结构。
- **Skip if**: 已经有批准过且可映射的 taxonomy（不要无意义重构）。
- **Network**: none.
- **Guardrail**: 避免泛化占位桶；保持 2+ 层且每节点有具体描述。


Build `outline/taxonomy.yml` from `papers/core_set.csv`.

P0 compatibility note:
- The output contract stays the same (`outline/taxonomy.yml`, YAML list, >=2 levels, concrete descriptions).
- Curated domain taxonomies now live in `assets/domain_packs/*.yaml` instead of Python prose.
- `scripts/run.py` stays a deterministic scaffold/helper: detect domain pack -> load pack when available -> otherwise fall back to the generic builder.

## Load Order

1. `references/overview.md`
2. `references/taxonomy_principles.md`
3. If a domain pack applies, read its `references/domain_pack_<domain>.md` and `assets/domain_packs/<domain>.yaml`
4. Otherwise read `references/archetypes_generic.md`
5. Calibrate naming/description quality with `references/examples_good.md` and `references/examples_bad.md`

Current compatibility packs:
- `llm_agents`
- `gen_image`
- `embodied_ai`
- `rag_evaluation`

## Explicit refinement marker

Create `outline/taxonomy.refined.ok` only after reviewing a manually refined taxonomy. The marker is honored only while it is newer than the taxonomy, its upstream evidence, and the generator; stale markers are removed and the prior taxonomy is backed up before regeneration.

## Inputs

- `papers/core_set.csv` (required)
- Optional: `papers/papers_dedup.jsonl`
- Optional: `DECISIONS.md`, `GOAL.md`, `queries.md`

## Outputs

- `outline/taxonomy.yml`

## Asset contract

- `assets/taxonomy_schema.json`: machine-readable shape for domain packs / output expectations
- `assets/domain_packs/*.yaml`: compatibility domain packs for supported domains

## Script role

The rest: https://github.com/WILLOSCAR/research-units-pipeline-skills/blob/HEAD/.codex/skills/taxonomy-builder/SKILL.md