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Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis. Skip when the dataset is already in hand or when only routing a query (use `orchestrator`).
Codex 또는 Claude로 설치 이 Prompt를 복사해 Codex, Claude 또는 다른 어시스턴트에 붙여 넣으면 Skill 페이지를 검토하고 설치를 진행할 수 있습니다.
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| name | literature |
| description | Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis. Skip when the dataset is already in hand or when only routing a query (use `orchestrator`). |
| version | 0.5.0 |
| author | OmicsClaw |
| license | MIT |
| tags | ["literature","pdf","doi","pubmed","geo","metadata"] |
| requires | ["requests"] |
The user provides a scientific paper reference (PDF path, URL, DOI, PubMed ID, or raw text excerpt) and wants OmicsClaw to extract GEO accessions, dataset metadata, and (optionally) download referenced GEO datasets — so a downstream analysis skill can be invoked on real data.
--input-type defaults to auto (sniffs from input shape).
--no-download skips the GEO download step (metadata only).
For dispatching a NL query to an analysis skill use orchestrator.
For scaffolding a new skill from a paper use omics-skill-builder.
| Input | Format | Required |
|---|---|---|
| Reference | --input <URL|DOI|PubMed|PDF path|text> | yes (unless --demo) |
| Input type | --input-type {auto,url,doi,pubmed,file,text} (default auto) | no |
| Skip download | --no-download (extract metadata only) | no |
| Data dir | --data-dir <path> (default data/) | no |
| Output | Path | Notes |
|---|---|---|
| Extracted metadata | output_dir/extracted_metadata.json | written at literature_parse.py:80 |
| Report | output_dir/report.md | written at literature_parse.py:193 |
| Result envelope | output_dir/result.json | written at literature_parse.py:147 |
| Downloaded GEO data | <data-dir>/<GSE...>/... | only when GEO accessions found AND --no-download not set |
--input (or --demo); raise parser.error('the following arguments are required: --input (unless --demo is used)') at literature_parse.py:38 when missing.--input-type auto or honour the explicit value.parse_input (skills/literature/core/parser.py); fetch / parse content.extract_metadata (skills/literature/core/extractor.py) → identify GEO accessions, dataset metadata, study type.--no-download: call download_geo_dataset (skills/literature/core/downloader.py) → save to --data-dir.extracted_metadata.json (literature_parse.py:80) + report.md (:193) + result.json (:147).--input REQUIRED unless --demo — uses parser.error (exit 2). literature_parse.py:38 calls parser.error('the following arguments are required: --input (unless --demo is used)'). Different from most file-pipeline skills which raise ValueError.--input-type auto heuristics are positional, not URL-aware. core/parser.py:35-55 checks the bare-DOI regex ^10\.\d{4,}/\S+ first; URLs always hit the startswith("http") branch and resolve to url, even when they wrap a DOI (https://doi.org/10.1038/...). For PDF / file paths use --input-type file explicitly — Path.exists() has to succeed for auto-detection to pick file.download_geo_dataset issues HTTP requests to GEO FTP. Air-gapped runs must pass --no-download or the run will hang / time out.pypdf / similar. If the PDF parser dependency is missing, the run errors out — verify skills/literature/requirements.txt is satisfied.extracted_metadata.json is at output_dir/ ROOT, not tables/. This skill does NOT follow the tables/<file>.csv convention used by analysis skills.literature_parse.py:64 calls sys.exit(1) on internal parse failure (distinct from the parser.error exit-2 path for missing args).# Demo (built-in local text)
python omicsclaw.py run literature --demo --output /tmp/lit_demo
# DOI
python omicsclaw.py run literature \
--input "10.1038/s41586-021-03689-7" --output results/
# PDF (use --input-type file)
python omicsclaw.py run literature \
--input my_paper.pdf --input-type file --output results/
# URL, metadata-only (no GEO download)
python omicsclaw.py run literature \
--input "https://www.nature.com/articles/..." \
--output results/ --no-download
references/parameters.md — every CLI flag, input-type heuristicsreferences/methodology.md — GEO accession rules, parser fallbacksreferences/output_contract.md — extracted_metadata.json schemaorchestrator (downstream — routes the resulting dataset to an analysis skill), omics-skill-builder (parallel — scaffold a new skill from a paper)