Literature Review: Search & Research for Claude Code | AI Skill Market | AI Skill Market

Literature Review: Search & Research for Claude Code | AI Skill Market | AI Skill Market

Literature Review

Help write academic literature reviews using a multi-engine search integration (S2, OA, CR, PM).

Capabilities

Multi-Source Search: Find relevant academic papers using Semantic Scholar (S2), OpenAlex (OA), Crossref (CR), and PubMed (PM).
Full Abstracts: All sources now return complete abstracts (PubMed uses
```
efetch
```
for full XML records).
DOI Extraction: DOIs are extracted from all sources for cross-referencing and deduplication.
Automatic Deduplication: When searching multiple sources (
```
--source all
```
or
```
--source both
```
), results are automatically deduplicated by DOI.
Polite Access: Automatic email identification for OpenAlex/Crossref "Polite Pool" (via
```
USER_EMAIL
```
env var).
Abstract Reconstruction: Reconstructs abstracts from OpenAlex inverted index format.
Synthesis: Group papers by theme and draft review sections based on metadata.

Environment Variables

Variable	Purpose	Default
`USER_EMAIL`	Email for polite API access	`anonymous@example.org`
`CLAWDBOT_EMAIL`	Fallback if USER_EMAIL not set	—
`SEMANTIC_SCHOLAR_API_KEY`	Optional S2 API key for higher rate limits	—
`OPENALEX_API_KEY`	Optional OpenAlex API key	—

Workflows

1. Broad Search (All Bases)

Get a comprehensive overview from all major academic databases. Results are automatically deduplicated by DOI.

python3 scripts/lit_search.py search "impact of glycyrrhiza on bifidobacterium" --limit 5 --source all

2. Targeted Search

OpenAlex (
```
oa
```
): Fast and comprehensive, good abstracts.
Semantic Scholar (
```
s2
```
): High-quality citation data and TL;DRs.
Crossref (
```
cr
```
): Precise DOI-based metadata (no abstracts).
PubMed (
```
pm
```
): Gold standard for biomedical research, full abstracts and PMIDs.

python3 scripts/lit_search.py search "prebiotic effects of liquorice" --source pm

3. Comparing Sources

Search both S2 and OA simultaneously to ensure nothing is missed. Deduplicated by default.

python3 scripts/lit_search.py search "Bifidobacterium infantis growth" --source both

4. Getting Full Details (S2)

Retrieve detailed metadata including TL;DR summaries.

python3 scripts/lit_search.py details "DOI:10.1016/j.foodchem.2023.136000"

5. Writing the Review

Extract: Pull key findings from the abstracts found.
Organize: Group findings into a logical structure (e.g., chronological or thematic).
Draft: Use the "Think step-by-step" approach to synthesize multiple sources into a coherent narrative.

Output Format

Each result includes:

```
id
```
: Source-specific identifier (PMID for PubMed, OpenAlex ID, S2 paper ID, DOI for Crossref)
```
doi
```
: DOI when available (used for deduplication)
```
title
```
: Paper title
```
year
```
: Publication year
```
authors
```
: List of author names
```
abstract
```
: Full abstract text (when available)
```
venue
```
: Journal or conference name
```
citationCount
```
: Citation count (S2, OA)
```
source
```
: Which database the result came from

Tips for Success

Citations: Always cross-reference the DOI or PMID for accuracy in bibliography.
Filtering: Focus on papers with higher
```
citationCount
```
or recent years for a more modern review.
PubMed for Medicine: Use
```
--source pm
```
for the most reliable biomedical literature.
Deduplication: Multi-source searches automatically remove duplicates; use single sources if you need raw counts.