Case 00415

Helper Behavior Review

python scripts/_core.py is an optional helper whose behavior should be compared with this skill's documented purpose before use. Show what the script does, explain any mismatch with the user-facing description, and run it only when the user explicitly wants that diagnostic path.

Literature Agent v1.0.0

Overview

Dual-source literature search combining PubMed (biomedical focus) and Semantic Scholar (broader CS/ML/AI coverage). Deduplicates across sources, enriches with citation metrics and TLDR summaries.

Key capabilities:

• PubMed search with MeSH terms, abstracts, publication types
• Semantic Scholar search with citation counts, influential citations, TLDR
• Paper lookup by DOI or PMID
• Citation tracking (who cited this paper?)
• Related paper discovery (what did this paper reference?)
• Automatic query construction from compound/target/disease inputs
• Cross-source deduplication and enrichment

Quick Start

# Search by topic
python scripts/pubmed_search.py --query "KRAS G12C inhibitor" --max-results 5

# Search Semantic Scholar (includes ML/AI papers)
python scripts/semantic_scholar.py --query "graph neural network drug discovery"

# Full chain: compound + disease context
python scripts/chain_entry.py --input-json '{"compound": "sotorasib", "disease": "lung cancer"}'

# Look up a specific paper and find who cited it
python scripts/semantic_scholar.py --paper-id "DOI:10.1038/s41586-021-03819-2" --citations

# Recent papers only (last 3 years)
python scripts/pubmed_search.py --query "organometallic catalyst drug synthesis" --years 3

Scripts

scripts/pubmed_search.py

PubMed via NCBI E-utilities (public, no key required, rate limit: 3 req/sec).

--query <text>          Required. Search query
--max-results <N>       1-50 (default: 10)
--sort <type>           relevance | date (default: relevance)
--years <N>             Limit to last N years

Returns: PMID, title, authors, journal, year, DOI, abstract, MeSH terms, keywords, publication types.

scripts/semantic_scholar.py

Semantic Scholar API (public, no key required, rate limit: 100 req/5 min).

--query <text>          Search query
--paper-id <id>         Paper ID (DOI:xxx, PMID:xxx, ArXiv:xxx)
--related               Get references of a paper (requires --paper-id)
--citations             Get papers citing a paper (requires --paper-id)
--max-results <N>       1-50 (default: 10)
--year-range <range>    e.g., "2020-2026" or "2023-"

Returns: title, authors, year, abstract, TLDR, citation count, influential citations, DOI, ArXiv ID, open-access PDF URL.

scripts/chain_entry.py

Standard PharmaClaw chain interface. Searches both PubMed and Semantic Scholar, deduplicates, and sorts by citation impact.

Input keys: query, compound/name, target, disease, mechanism, reaction, topic, doi, pmid, max_results, years, context

Automatic query building: {"compound": "aspirin", "disease": "colorectal cancer"} → searches "aspirin colorectal cancer"

Chaining

From	Input	To
Chemistry Query	Compound name/SMILES	Literature → find published studies
Catalyst Design	Reaction type	Literature → find catalyst optimization papers
Literature	Key findings	Pharmacology → validate claims
Literature	Synthesis references	Chemistry Query → retrosynthesis
Literature	Patent mentions	IP Expansion → FTO analysis