Answering Research Questions

Answering Research Questions

Overview

Orchestrate the complete research workflow from query to findings.

Core principle: Systematic, trackable, comprehensive. Search → Evaluate → Traverse → Synthesize.

Announce at start: "I'm using the Answering Research Questions skill to find [specific data] about [topic]."

The Process

Phase 1: Parse Query

Extract from user's request:

Keywords:

• Main concepts (e.g., "BTK inhibitor", "selectivity")
• Synonyms and alternatives (e.g., "Bruton tyrosine kinase")
• Related terms (e.g., "off-target", "kinase panel")

Data types needed:

• Specific measurements (IC50, KD, EC50, etc.)
• Methods or protocols
• Structures or sequences
• Results or conclusions

Constraints:

• Date ranges
• Specific compounds/targets
• Organisms or systems
• Publication types

Ask clarifying questions if needed:

• "Are you looking for in vitro or in vivo data?"
• "Any specific time frame?"
• "Which kinases are you most interested in?"
• "What email address should I use for Unpaywall API requests?" (Required for finding open access papers)

Phase 2: Initialize Research Session

Propose folder name:

research-sessions/YYYY-MM-DD-brief-description/

Example: research-sessions/2025-10-11-btk-inhibitor-selectivity/

Show proposal to user:

📁 Creating research folder: research-sessions/2025-10-11-btk-inhibitor-selectivity/
   Proceed? (y/n)

Create folder structure:

mkdir -p "research-sessions/YYYY-MM-DD-description"/{papers,citations}

Initialize files:

Core files (always create these):

papers-reviewed.json:

{}

citations/citation-graph.json:

{}

SUMMARY.md:

# Research Query: [User's question]

**Started:** YYYY-MM-DD HH:MM
**Keywords:** keyword1, keyword2, keyword3
**Data types sought:** IC50 values, selectivity data, synthesis methods

---

## Highly Relevant Papers (Score ≥ 8)

Papers scored using `evaluating-paper-relevance` skill:
- Score 0-10 based on: Keywords (0-3) + Data type (0-4) + Specificity (0-3)
- Score ≥ 8: Highly relevant with significant data
- Score 7: Relevant with useful data
- Score 5-6: Possibly relevant
- Score < 5: Not relevant

(Papers will be added here as found)

Example format:
### [Paper Title](https://doi.org/10.1234/example)
**DOI:** [10.1234/example](https://doi.org/10.1234/example) | **PMID:** [12345678](https://pubmed.ncbi.nlm.nih.gov/12345678/)

---

## Relevant Papers (Score 7)

(Papers will be added here as found)

---

## Possibly Relevant Papers (Score 5-6)

(Noted for potential follow-up)

---

## Search Progress

- Initial PubMed search: X results
- Papers reviewed: Y
- Papers with relevant data: Z
- Citations followed: N

---

## Key Findings

(Synthesized findings will be added as research progresses)