Evaluating Paper Relevance

What it does

Two-stage screening process: quick abstract scoring followed by deep dive into promising papers.

How it works

The skill defines a staged workflow:

• Stage 1: Abstract Screening (Fast)
  • Score papers on a 0-10 scale using keywords match (0-3), data type match (0-4), and specificity (0-3).
  • Apply decision rules: Score < 5 skip, Score 5-6 note as possibly relevant, Score ≥ 7 proceed to Stage 2.
  • Require reporting to the user for every paper with explicit messages showing the abstract score and the next action (fetching full text or skipping).
• Stage 2: Deep Dive (Thorough)
  • If medicinal chemistry is involved, use skills/research/checking-chembl to check for ChEMBL data and annotate ChEMBL IDs and data presence.
  • Fetch full text in order: PubMed Central (free), DOI resolution, Unpaywall (MANDATORY if paywalled), Preprints (bioRxiv/arXiv).
  • If full text is unavailable, note the paywall status and continue with abstract-only evaluation.
  • Scan for content in Methods, Results, Tables/Figures, and Supplementary Information to extract domain-specific data (e.g., IC50, expression levels, algorithms, datasets).
  • Create structured extractions and update tracking files (papers-reviewed.json and SUMMARY.md) with relevant findings for score ≥ 7; include notes for not-relevant papers (score < 7).
  • Ensure DOIs and PMIDs are presented as clickable links in SUMMARY.md.

When to use it

After literature search returns results. When need to determine if paper contains specific data. When screening papers for relevance. When extracting methods, results, data from papers.

What it can touch

Tools include claude-code for code-related steps and checks, and scripts for ChEMBL checks, full-text fetching, and data extraction as described.

Caveats

License: NOASSERTION. The skill relies on paywall handling via Unpaywall; if no OA version is found, abstract-only evaluation proceeds. It requires reporting for every paper and mandates adding all papers to papers-reviewed.json and updating SUMMARY.md accordingly.