Pharmaclaw Literature Agent

# 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

```bash
# 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 pa...