Searching Literature

Searching Scientific Literature

RC native tools — this skill's pipeline ships as four built-in RC tools. Call them directly; do not shell out to any rp.py script or write curl:

• rp_search({ query, limit?, min_year? }) — Scopus relevance search enriched with OpenAlex abstracts + OA PDF links. The Elsevier key is built in.
• rp_abstracts({ dois }) — batch abstracts + OA links for a DOI list (OpenAlex, no key).
• rp_cite({ doi, direction?, limit? }) — citation traversal (direction: both / backward / forward).
• rp_fulltext({ doi, out? }) — OA full text (Elsevier ScienceDirect OA → OpenAlex OA fallback); pass out to also save the text to a file.

Results return inline as JSON (there is no --json <file> flag). To persist a result set, save the returned JSON with the workspace file tools.

Overview

Discovery runs on one backbone: Scopus (relevance-ranked, all-publisher coverage, real citation counts), with OpenAlex layered on only to supply the data Scopus's personal-key tier withholds (abstracts, OA full-text links). Both are driven by the the rp_* tools tool — you do not hand-write curl.

Core principle: Scopus decides what and in what order; OpenAlex fills in abstracts.

Key entitlement reality (tested): a personal Scopus API key exposes the STANDARD search view only — title, DOI, EID, citation count, year, OA flag. It does not return abstracts, references, or forward citations. That is why abstracts come from OpenAlex and citation traversal lives in traversing-citations (also OpenAlex). Do not try to pull abstracts/refs from Scopus; the calls 403.

How to Search

1. Build the Scopus query

Scopus query syntax (richer than plain keywords — use it):

• TITLE-ABS-KEY( ... ) — search title, abstract, keywords (the default workhorse)
• AND / OR / AND NOT — boolean
• W/n — proximity (e.g. BTK W/3 selectivity)
• PUBYEAR > 2018 — date constraint
• DOCTYPE(ar) — article type (ar=article, re=review)

Examples:

Copy code
TITLE-ABS-KEY(("BTK" OR "Bruton tyrosine kinase") AND inhibitor AND (selectivity OR "off-target"))
TITLE-ABS-KEY("CRISPR" AND cardiomyocyte) AND PUBYEAR > 2019

2. Run the search

bashCopy code
rp_search "TITLE-ABS-KEY(BTK inhibitor selectivity)" \
    --limit 50 --min-year 2015

This single command:

1. Pages Scopus by relevancy (citation counts included).
2. Batch-fetches OpenAlex by DOI (50/call) to attach abstract, oa_status, oa_pdf_url.
3. Writes candidate records ready for scoring.

Each record:

jsonCopy code
{
  "scopus_id": "85...", "eid": "2-s2.0-85...", "doi": "10.1016/...",
  "title": "...", "year": "2023", "cited_by": 42, "oa": true,
  "source": "Journal of Medicinal Chemistry",
  "abstract": "We report ...", "openalex_id": "W...",
  "oa_status": "gold", "oa_pdf_url": "https://..."
}

3. Report

Announce: 🔎 Scopus: N papers · M with abstracts (OpenAlex). Then hand the candidate list to evaluating-paper-relevance for scoring.

Coverage Notes (honest limits)

• Abstract gaps: OpenAlex lacks abstracts for some closed papers (notably parts of Elsevier/ACS). Expect roughly 50–80% abstract coverage. Papers with "abstract": "" must be scored from title + journal + citation count only, or deferred — never silently dropped. Flag them: ⚠️ No abstract (score from title).
• Scopus quota: 20,000 search results/week on the personal key. The pipeline paginates 25/call, so a 50-result search costs 2 calls. Budget accordingly for large sweeps.
• No Scopus abstracts/refs/fulltext-search on this key — by design, see above.

Quick Reference

Common Mistakes

• Hand-writing curl to Scopus → use the rp_* tools; it handles paging, rate limits, caching.
• Expecting abstracts from Scopus → they come from OpenAlex; some will be missing.
• Dropping abstract-less papers → score them from title/citations or defer, don't hide them.
• Ignoring the weekly quota → 20k Scopus results/week; don't burn it on over-broad sweeps.

Next Steps

After search: score with evaluating-paper-relevance; expand high scorers with traversing-citations.