survey-seed-harvest

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Identify survey/review papers in a retrieved set and extract taxonomy seeds into `outline/taxonomy.yml` (topics/subtopics/terminology).**Trigger**: survey seed harvest, taxonomy seeds, 从 survey 提 taxonomy, bootstrap taxonomy.**Use when**: retrieval/dedup 后想快速从已有 survey/review 论文中提取术语与主题结构，用于加速 `taxonomy-builder`。**Skip if**: 已经有高质量 taxonomy（或你不想被 survey 既有框架限制）。**Network**: none.**Guardrail**: 产物是 seed，必须经 `taxonomy-builder` 重写与对齐 scope；避免生成泛化占位节点。

⭐1stars🔀0forks📁View on GitHub🕐Updated Jan 8, 2026
[Academic Research]

When & Why to Use This Skill

The Survey Seed Harvest skill automates the extraction of taxonomy structures and key terminology from academic survey and review papers. It streamlines the initial phase of research organization by bootstrapping hierarchical topic frameworks, enabling researchers to quickly map out a domain's landscape based on established literature and accelerate the creation of structured knowledge bases.

Use Cases

  • Rapidly bootstrapping a domain taxonomy by extracting established hierarchical structures and terminology from existing meta-analyses and review papers.
  • Identifying core sub-topics and research trends within a specific scientific field to guide systematic literature reviews and information organization.
  • Accelerating the early stages of research by providing a pre-structured outline of a domain, reducing the manual effort required to categorize large sets of papers.
  • Generating actionable taxonomy seeds for downstream tools like taxonomy-builder to ensure domain-aligned and high-quality knowledge categorization.
namesurvey-seed-harvest
description|
**Trigger**survey seed harvest, taxonomy seeds, 从 survey 提 taxonomy, bootstrap taxonomy.
**Use when**retrieval/dedup 后想快速从已有 survey/review 论文中提取术语与主题结构，用于加速 `taxonomy-builder`。
**Skip if**已经有高质量 taxonomy（或你不想被 survey 既有框架限制）。
**Network**none.
**Guardrail**产物是 seed，必须经 `taxonomy-builder` 重写与对齐 scope；避免生成泛化占位节点。

Survey Seed Harvest

Bootstrap taxonomy seeds from existing survey/review papers inside your retrieved set.

This is an accelerator for the early structure stage: it should make taxonomy-builder easier, not replace it.

Inputs

  • papers/papers_dedup.jsonl (deduped paper metadata with titles/abstracts)

Outputs

  • outline/taxonomy.yml (seed taxonomy; expected to be refined)

Workflow (heuristic)

Uses: papers/papers_dedup.jsonl.

  1. Find likely survey/review papers:
    • title/abstract contains “survey”, “review”, “systematic”, “meta-analysis”
  2. Extract candidate topic terms and group them into:
    • ~4–10 top-level nodes (“chapters”)
    • 2–6 children per node (mappable leaves)
  3. Write short, actionable descriptions:
    • what belongs here / what does not
    • (optional) list 2–5 representative titles as seeds
  4. Treat the result as a starting point:
    • pass it to taxonomy-builder for domain-meaningful rewriting and scope alignment.

Quality checklist

  • outline/taxonomy.yml exists and is valid YAML.
  • Taxonomy has at least 2 levels (children used) and every node has a description.
  • Avoid generic placeholder nodes like “Overview/Benchmarks/Open Problems” unless they are truly content-based for your domain.

Script (optional helper)

Quick Start

  • python .codex/skills/survey-seed-harvest/scripts/run.py --help
  • python .codex/skills/survey-seed-harvest/scripts/run.py --workspace <workspace_dir>

All Options

  • --top-k <n>: number of candidate terms to consider
  • --min-freq <n>: minimum frequency threshold

Examples

  • More conservative term selection:
    • python .codex/skills/survey-seed-harvest/scripts/run.py --workspace <ws> --top-k 80 --min-freq 3

Notes

  • This helper is keyword-based; treat the output as seeds and refine with taxonomy-builder.

Troubleshooting

Issue: no survey/review papers are detected in the set

Fix:

  • Broaden retrieval (add “survey”, “review”, “benchmark” variants) or manually seed a few known surveys, then rerun.

Issue: taxonomy seeds look like generic buckets

Fix:

  • Keep seeds concrete (named methods/benchmarks/tasks) and rely on taxonomy-builder to rewrite under the actual scope.