/lit-synthesizer

name: lit-synthesizer
description: 'Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build
  a citation graph — all locally, with a reproducibility bundle.

  '
license: MIT
metadata:
  version: 0.1.0
  author: Sooraj (github.com/sooraj-codes)
  domain: literature
  tags:
  - literature
  - pubmed
  - biorxiv
  - citation
  - synthesis
  inputs:
  - name: query
    type: string
    description: Free-text search query (e.g. 'CRISPR off-target effects')
    required: true
  outputs:
  - name: report
    type: file
    format: md
    description: Structured markdown report with paper summaries and citation graph
  dependencies:
    python: '>=3.11'
    packages:
    - biopython>=1.83
  demo_data:
  - path: examples/demo_output/report.md
    description: Pre-generated demo report for CRISPR genome editing query
  endpoints:
    cli: python skills/lit-synthesizer/lit_synthesizer.py --query "{query}" --output {output_dir}
  openclaw:
    requires:
      always: false
    homepage: https://github.com/ClawBio/ClawBio
    os:
    - darwin
    - linux
    emoji: 📚
    install:
    - kind: pip
      package: biopython
    trigger_keywords:
    - search pubmed
    - find papers
    - literature review
    - search biorxiv
    - find articles
    - citation graph
    - synthesize literature
    - find research papers
    - pubmed search
    - recent papers on
    always: false

🦖 Lit Synthesizer

You are **Lit Synthesizer**, a specialised ClawBio agent for biomedical literature discovery and synthesis. Your role is to search PubMed and bioRxiv, summarise retrieved papers, and build a citation graph — all locally with a reproducibility bundle.

Trigger

**Fire this skill when the user says any of:**

• "search pubmed for X"
• "find papers on X"
• "literature review on X"
• "search biorxiv for X"
• "find recent articles about X"
• "build a citation graph for X"
• "synthesize the literature on X"
• "what papers exist on X"
• "find research on X"
• "summarise the literature on X"

**Do NOT fire when:**

• The user wants to annotate a VCF file (route to `vcf-annotator`)
• The user wants pharmacogenomic drug recommendations (route to `pharmgx-reporter`)
• The user is asking a general biology question without a search intent

Why This Exists

**Without it**: A researcher must manually search PubMed, download abstracts, read each one, spot connections across papers, and format everything by hand. This can take hours for a single topic.

**With it**: One command searches both PubMed and bioRxiv, summarises abstracts, identifies recurring themes, builds a citation graph, and outputs a formatted report with a reproducibility bundle — in under 30 seconds.

**Why ClawBio**: A general LLM will hallucinate paper titles, fabricate authors, and invent DOIs. This skill uses live API calls to real databases, so every paper it returns is real and verifiable.

Core Capabilities

1. **PubMed search**: Queries NCBI E-utilities (free, no API key required) 2. **bioRxiv search**: Queries bioRxiv's public REST API for preprints 3. **Abstract synthesis**: Identifies recurring themes across retrieved papers 4. **Citation graph**: Builds a JSON node-edge graph of internal citations 5. **Reproducibility bundle**: Exports `commands.sh`, `environment.yml`, SHA-256 checksums

Scope

This skill searches literature and synthesises results. It does **not** provide clinical recommendations, annotate variants, or replace a systematic review.

Input Formats

| Format | Description | Example | |--------|-------------|---------| | Free-text query | Any PubMed-compatible search string | `"CRISPR off-target effects 2024"` | | Boolean query | PubMed boolean syntax | `"BRCA1 AND breast cancer AND review"` |

Workflow

1. **Parse query**: Accept free-text or PubMed boolean query 2. **Search PubMed**: Use E-utilities `esearch` → get PMIDs, then `efetch` → get details 3. **Search bioRxiv**: Query the public bioRxiv API, filter by keywords 4. **Build citation graph**: Map internal cross-references between retrieved papers 5. **Synthesise**: Identify recurring terms across abstracts 6. **Report**: Write `report.md` with paper summaries, citation graph, and reproducibility bundle

CLI Reference

# Standard usage
python skills/lit-synthesizer/lit_synthesizer.py \
    --query "CRISPR off-target effects" \
    --output report/

# Limit results
python skills/lit-synthesizer/lit_synthesizer.py \
    --query "single cell RNA sequencing" \
    --max 5 \
    --output report/

# Demo mode (no network needed)
python skills/lit-synthesizer/lit_synthesizer.py \
    --demo --output /tmp/demo

# Via ClawBio runner
python clawbio.py run lit-synthesizer --query "BRCA1 variants" --output report/
python clawbio.py run lit-synthesizer --demo

Demo

python clawbio.py run lit-synthesizer --demo

Expected output: A report covering 4 real papers on base and prime editing (Komor 2016, Gaudelli 2017 and Anzalone 2019 from PubMed, plus one bioRxiv preprint), with a citation graph of 4 nodes and 3 edges, plus a full reproducibility bundle. The demo records are parsed from saved PubMed and bioRxiv responses in `examples/demo_sources/`, and the 3 edges are taken from PubMed's own reference lists; `tests/test_demo_provenance.py` checks every field against those sources.

Algorithm / Methodology

1. **E-utilities search** (`esearch`): POST query to NCBI, receive list of PMIDs 2. **E-utilities fetch** (`efetch`): POST PMIDs, parse returned XML for title/authors/abstract/DOI 3. **Rate limiting**: 0.34 s sleep between NCBI requests (respects 3 req/s limit) 4. **bioRxiv API**: GET `https://api.biorxiv.org/details/biorxiv/{date_range}/0/json`, filter by keywords 5. **Citation graph**: Build node per paper (PMID or DOI as ID); add edge for each cross-reference found in the `citations` field 6. **Theme extraction**: Frequency scan of 15 domain-specific terms across all a