Research30

• --sources=all (default) - All sources
• --sources=preprints - bioRxiv + medRxiv + arXiv only
• --sources=pubmed - PubMed only
• --sources=huggingface - HuggingFace only
• --sources=arxiv - arXiv only
• --sources=openalex - OpenAlex only
• --sources=semanticscholar - Semantic Scholar only

Step 2: Synthesize the results

The script outputs a flat ranked list sorted by score (0-100). Each item includes:

• Score, title, source tag, date, URL
• Metadata (journal, DOI, MeSH terms, citations, downloads)
• Abstract snippet (first 200 chars) — use these to understand what each paper is about
• Relevance explanation (why it matched)

Read every abstract snippet. They are the most important signal for understanding what's actually being studied. Use them to:

1. Identify themes — Group papers by what they study, not just that they matched keywords. Papers with score 70+ that share abstract themes represent active research fronts.

2. Synthesize findings — Combine insights across papers. If 3 papers describe similar methods or results, that's a trend. If one paper contradicts others, that's notable.

3. Assess quality signals:

   • PubMed articles are peer-reviewed (highest reliability)
   • "PEER REVIEWED" flag on bioRxiv items means the preprint was later published in a journal
   • Higher citation counts indicate established impact
   • Semantic Scholar results may use different terminology for the same concepts (it does semantic matching, not just keyword matching)

4. Note source diversity — A finding reported across OpenAlex, PubMed, AND Semantic Scholar is higher confidence than one from a single source.

Step 3: Save the full synthesis to a file

IMPORTANT: Always save the full synthesis before showing anything to the user.

1. Create the reports directory:

mkdir -p ~/.local/share/research30/reports

2. Generate a filename from the topic: lowercase, replace spaces/special chars with hyphens, append today's date. Example: crispr-gene-editing-2026-02-07.md

3. Use the Write tool to save the full synthesis (using the format below) to: ~/.local/share/research30/reports/{slug}-{date}.md

Full synthesis format (saved to file):

# Recent Research: {TOPIC}
*{date range} | Generated {today's date}*

## Summary
[2-3 sentence overview of the research landscape — what are scientists actively working on? Any breakthroughs or shifts?]

## Key Findings

### 1. [Major finding]
[What was discovered/demonstrated. Reference specific papers by title.]
**Why it matters:** [significance]

### 2. [Second finding]
...

### 3. [Third finding]
...

## Active Research Fronts
- **[Theme 1]:** [brief description with paper references]
- **[Theme 2]:** [brief description with paper references]

## Notable Methods & Tools
- [New method or tool, if any emerged from the abstracts]

## Gaps & Opportunities
- [What's underrepresented or missing from current research]

## Top Papers
[List the top 10 papers by score with title, source, date, URL, and a one-line description of what it contributes]

---
*Based on {N} papers from {sources}. Scores reflect relevance + recency + academic signals.*

Key principles for synthesis:

• Be specific. Reference actual papers by title.
• Synthesize, don't summarize. Identify patterns, contradictions, and trends across papers.
• Prioritize by score but verify with abstracts. A score of 85 means high relevance + recency + academic signal, but the abstract tells you what is relevant.
• Flag limitations. If results are sparse or heavily weighted to one source, note this.

Step 4: Append to the research log

Append a summary entry to ~/.local/share/research30/research-log.md. This builds a cumulative research journal over time.

Use the Read tool to read the existing log (if it exists), then use the Write tool to write the full content back with the new entry appended at the top (after the header). If the file doesn't exist, create it with a header.

Log entry format:

---
### {date}: {TOPIC}
**Sources:** {source summary} ({N} total)
**Summary:** [1-2 sentence summary]
**Key findings:** [finding 1] | [finding 2] | [finding 3]
**Report:** `~/.local/share/research30/reports/{slug}-{date}.md`

Step 5: Show a brief summary in chat

Do NOT show the full synthesis in chat. Instead, show a concise summary with clear links to saved files:

## {TOPIC} — Last 30 Days

[2-3 sentence summary]

**Key findings:**
1. [One-line finding]
2. [One-line finding]
3. [One-line finding]

**{N} papers** from {sources} | Top score: {max}

**Saved files:**
- Full report: `~/.local/share/research30/reports/{slug}-{date}.md`
- HTML report: `~/.local/share/research30/out/report.html`
- Research log: `~/.local/share/research30/research-log.md`
- Raw data: `~/.local/share/research30/out/report.json`

Always show all four file paths so the user knows exactly where to find everything.

Step 6: Offer follow-up actions

After the summary, ask what the user wants to do next:

What next?

• "deep dive on [finding]" — expand on a specific finding with paper details
• "compare methods" — compare approaches across the top papers
• "top papers" — show the full top 10 list with abstracts
• "search [related topic]" — run a new search on a related area
• "open report" — display the full saved report in chat

Follow-up Mode

When the user requests a follow-up:

• Deep dive: Pull details from the raw script output for the relevant papers. Show titles, full abstracts, URLs, and how they connect.
• Compare methods: Identify methodological approaches across papers and compare.
• Top papers: Show the top 10 from the script output with full abstract snippets.
• Related search: Run a new /research30 search with the new topic.
• Open report: Use the Read tool to display the saved report file.
• Only run new research if the user asks about a DIFFERENT topic.

Optional Setup

Semantic Scholar API key (recommended — enables semantic search):

mkdir -p ~/.config/research30
echo 'S2_API_KEY=your_key_here' >> ~/.config/research30/.env
chmod 600 ~/.config/research30/.env

Get a free key at: https://www.semanticscholar.org/product/api#api-key-form

NCBI API key (for faster PubMed, optional):

echo 'NCBI_API_KEY=your_key_here' >> ~/.config/research30/.env

Get a free key at: https://www.ncbi.nlm.nih.gov/account/settings/