Survey Seed Harvest Skill for Codex

| Identify survey/review papers in a retrieved set and extract taxonomy seeds into `outline/taxonomy.yml` (topics/subtopics/terminology).

1k tokens

context cost

the whole folder, loaded on every use

files

ships runnable scripts

copies elsewhere

how many repositories repackaged it

496

stars on the repo

on the repository, not the skill itself

Install

one command, takes just this skill from the repository

npx skills add https://github.com/WILLOSCAR/research-units-pipeline-skills --skill survey-seed-harvest

What comes with it

2 836 bytes besides the instruction

scripts/run.py

The instruction itself

13 sections, as written by the author

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.

Find likely survey/review papers:
title/abstract contains “survey”, “review”, “systematic”, “meta-analysis”
Extract candidate topic terms and group them into:
~4–10 top-level nodes (“chapters”)
2–6 children per node (mappable leaves)
Write short, *actionable* descriptions:
what belongs here / what does not
(optional) list 2–5 representative titles as seeds
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

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

All Options

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

Examples

More conservative term selection:
uv run python .codex/skills/survey-seed-harvest/scripts/run.py --workspace <workspace> --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.

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How to use it

Copy the folder

Take willoscar/survey-seed-harvest from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.