nixos/shared/linked-dotfiles/opencode/skills/research-medical/SKILL.md

name	description
research-medical	Use when researching medical/scientific topics and encountering paywalled journals, access failures, or needing primary sources - provides strategies for PubMed Central, DOI resolution, preprint servers, and fallback approaches for medical literature access

Medical Research Access

Strategies for accessing medical and scientific literature when direct web access fails or sources are paywalled.

When to Use This Skill

Use when:

• Webfetch fails on medical journal sites (NIH, Nature, JAMA, NEJM, etc.)
• Research requires primary sources (studies, trials, systematic reviews)
• Need to access paywalled medical literature
• Looking for recent research not yet peer-reviewed
• Extracting citations when full text unavailable

When NOT to use:

• General web research (use standard webfetch)
• Medical journalism is sufficient (STAT News, MedPage Today)
• Topic well-covered in open-access sources

Quick Reference: Access Strategies

Source Type	Primary Method	Fallback	Notes
Peer-reviewed studies	PubMed Central	DOI resolution, preprints	Always check PMC first
Recent research	Preprint servers	Author websites	May not be peer-reviewed yet
Clinical trials	ClinicalTrials.gov	Trial registries	Protocol vs results
Meta-analyses	Cochrane Library	PubMed search	Often open access
Medical journalism	STAT News, Medscape	Press releases	Secondary sources
Guidelines	Professional societies	NIH, CDC	Usually open access

Access Strategies

1. PubMed Central (PMC) - First Stop

Why PMC: Free full-text archive of biomedical literature, subset of PubMed with actual paper content.

Search approaches:

# Direct PMC search
https://www.ncbi.nlm.nih.gov/pmc/?term=ivermectin+COVID-19+randomized+controlled+trial

# Filters to add:
- Free full text
- Article type (Clinical Trial, Meta-Analysis, Systematic Review)
- Publication date range

When webfetch fails on PMC:

• Try PubMed instead (has abstracts even without full text)
• Search by PMID if you have it: https://pubmed.ncbi.nlm.nih.gov/[PMID]/
• Look for "Free PMC article" badge in PubMed results

2. DOI Resolution Services

What is DOI: Digital Object Identifier - permanent link to research papers.

Primary resolver:

https://doi.org/[DOI-HERE]

Example: https://doi.org/10.1056/NEJMoa2115869

When DOI resolution hits paywall:

• Try adding DOI to Google Scholar: https://scholar.google.com/scholar?q=[DOI]
• Check for "All versions" link in Scholar (may include preprint or author PDF)
• Look for institutional repository versions

Extracting DOI from citations:

• Usually in format: 10.XXXX/journal.year.number
• Found at end of citation or in URL
• Can search PubMed by DOI to get PMID

3. Preprint Servers - Recent Research

Primary servers:

Server	Focus	URL Pattern
medRxiv	Medicine	https://www.medrxiv.org/content/[ID]
bioRxiv	Biology	https://www.biorxiv.org/content/[ID]
SSRN	Social science, econ	https://papers.ssrn.com/sol3/papers.cfm?abstract_id=[ID]

Important notes:

• Preprints are NOT peer-reviewed
• Always note preprint status in citations
• Check if preprint later published in journal (search by title)
• Good for very recent research (last 6-12 months)

Search strategy:

# Search medRxiv directly
https://www.medrxiv.org/search/ivermectin%20COVID-19

# Or use Google Scholar with "preprint" filter
site:medrxiv.org OR site:biorxiv.org [search terms]

4. Medical Journalism Without Paywalls

Freely accessible sources:

• STAT News (statnews.com) - High-quality medical journalism, no paywall
• Medscape (medscape.com) - Free with registration, clinical news
• The Conversation (theconversation.com) - Academic experts, open access
• Science Daily (sciencedaily.com) - Press releases and summaries
• NIH News (nih.gov/news-events) - Government research announcements

When to use journalism vs primary sources:

• Journalism: Background, context, expert opinions, controversy overview
• Primary sources: Specific claims, data, methodology, for fact-checking

Citation approach:

• Use journalism to identify key studies
• Track down primary sources for verification
• Cite primary source when making factual claims
• Cite journalism when discussing expert opinions or controversy

5. Clinical Trial Registries

ClinicalTrials.gov - Official US registry:

https://clinicaltrials.gov/search?term=[drug/intervention]

Filter by:
- Study Status (Completed, Published)
- Study Type (Interventional)
- Study Results (Studies with Results)

What you get:

• Trial protocol and design
• Primary/secondary outcomes
• Results summary (if published)
• Links to published papers

Other registries:

• WHO ICTRP (international): https://trialsearch.who.int/
• EU Clinical Trials Register: https://www.clinicaltrialsregister.eu/

6. Professional Society Guidelines

Often open access:

• CDC guidelines: cdc.gov
• WHO guidelines: who.int
• NIH treatment guidelines: covid19treatmentguidelines.nih.gov
• Professional societies (AMA, ACP, IDSA) - check guidelines sections

Good for:

• Official recommendations
• Evidence summaries
• Standard of care
• Consensus positions

7. Google Scholar Strategies

When direct access fails:

# Search with specific terms
"ivermectin" "COVID-19" "randomized controlled trial"

# Use "All versions" link to find:
- Preprint versions
- Author PDFs
- Institutional repository copies

# Filter by date range for recent research

Citation extraction when full text unavailable:

• Scholar provides formatted citations
• Shows "Cited by" count (impact indicator)
• Links to related articles
• May show abstract even without full text

8. Author Websites and ResearchGate

When other methods fail:

• Search author name + paper title
• Check university faculty pages (often have PDFs)
• ResearchGate (researchgate.net) - researchers share papers
• Academia.edu - similar to ResearchGate

Caution:

• Verify version matches published paper
• Note if it's a preprint or draft
• Check publication date

Webfetch vs Direct Access Decision Tree

Use webfetch when:

• Source is known to be open access
• Medical journalism sites (STAT, Medscape)
• Government sites (NIH, CDC, FDA)
• Preprint servers
• Professional society guidelines

Skip webfetch, use search strategies when:

• Major journal sites (Nature, JAMA, NEJM, Lancet) - usually paywalled
• You have DOI - use DOI resolver or Scholar
• Need recent research - go to preprint servers
• Previous webfetch attempts failed on similar sources

General agent with web search when:

• Exploratory research (don't know specific sources yet)
• Need to identify key studies first
• Looking for expert commentary or summaries
• Building initial source list

Citation Extraction Techniques

When Full Text Unavailable

From abstracts (PubMed):

• Study design and methods
• Primary outcomes
• Sample size
• Key findings (usually in abstract)
• Limitations (sometimes mentioned)

From press releases:

• High-level findings
• Author quotes
• Institution and funding
• Link to actual paper (follow this)

From systematic reviews/meta-analyses:

• Summary of multiple studies
• Effect sizes across studies
• Quality assessments
• Usually cite all included studies (mine these)

Citation Format Best Practices

Minimum required:

Author(s). Title. Journal Year;Volume(Issue):Pages. DOI: [DOI]

Enhanced format:

Author(s). Title. Journal Year;Volume(Issue):Pages. DOI: [DOI]. PMID: [PMID]. [Access status]

Example:
Lopez-Medina E, et al. Effect of Ivermectin on Time to Resolution of Symptoms Among Adults With Mild COVID-19. JAMA 2021;325(14):1426-1435. DOI: 10.1001/jama.2021.3071. PMID: 33662102. [Free full text via PMC]

Always include:

• DOI (for verification and access)
• PMID if available (PubMed tracking)
• Access status (open access, PMC free, paywalled)
• Preprint status if applicable

Common Mistakes

❌ Giving up after first webfetch failure

Problem: Many medical sites block automated access or require authentication.

Fix: Use systematic fallback strategy:

1. Try PubMed Central search
2. Use DOI resolver if you have DOI
3. Check preprint servers
4. Search Google Scholar for alternative versions
5. Use medical journalism to identify sources, then track down primary

❌ Citing journalism when primary source is accessible

Problem: Secondary source citation when primary is available weakens credibility.

Fix:

• Use journalism to find studies
• Always attempt to access primary source
• Cite primary source for factual claims
• Cite journalism only for expert opinions or controversy framing

❌ Not noting preprint vs peer-reviewed status

Problem: Preprints lack peer review and may contain errors or later be contradicted.

Fix:

• Always check publication status
• Note in citation: "[Preprint, not peer-reviewed]"
• Search by title to see if later published in journal
• Weight peer-reviewed sources more heavily

❌ Ignoring "Cited by" counts and publication dates

Problem: May miss that study was retracted, contradicted, or superseded.

Fix:

• Check "Cited by" in Google Scholar
• Look for retractions or corrections
• Check for more recent systematic reviews
• Note if study is outlier vs consensus

❌ Using only abstracts for detailed claims

Problem: Abstracts omit important limitations, methods details, and context.

Fix:

• Use abstract for high-level findings only
• For specific claims, need full text
• If full text unavailable, note limitation: "[Based on abstract only]"
• Look for systematic reviews that analyzed full text

❌ Not tracking access failures for optimization

Problem: Repeated failures on same source types waste time.

Fix:

• Note which sources consistently fail webfetch
• Build project-specific access strategy
• Document successful access patterns
• Update AGENTS.md with project-specific guidance

Real-World Impact

Session context: Pierre Kory/ivermectin research encountered 4 failed web access attempts (NIH, FDA, Nature, JAMA, MedPage Today), limiting source diversity to 2 primary sources.

With this skill:

• PubMed Central search would provide free full-text access to key trials
• DOI resolution would access Nature and JAMA papers via alternative routes
• Preprint servers would surface early ivermectin research
• Medical journalism (STAT News) would provide controversy context without paywall
• Clinical trial registries would provide TOGETHER trial and other RCT data

Expected improvement: 5-8 accessible sources instead of 2, with mix of primary sources and expert commentary.

Workflow Integration

Research Session Startup

1. Identify topic and key terms
2. Start with PubMed Central search (free full text)
3. Check for systematic reviews (summarize evidence)
4. Search preprint servers (recent research)
5. Use medical journalism (context and expert opinions)
6. Track citations (DOI, PMID, access status)

When Webfetch Fails

1. Don't retry same URL - move to fallback strategy
2. Extract DOI from citation - use DOI resolver
3. Search PubMed by title - may find PMC version
4. Check Google Scholar - look for "All versions"
5. Note failure - document for future optimization

Citation Verification

1. Have DOI or PMID - verify via PubMed lookup
2. Check publication status - preprint vs peer-reviewed
3. Look for retractions - search "[title] retraction"
4. Note access method - for reproducibility
5. Capture full citation - author, title, journal, DOI, PMID

Additional Resources

PubMed search tips:

• Use MeSH terms (Medical Subject Headings) for precise searches
• Combine with Boolean operators (AND, OR, NOT)
• Use filters: Free full text, Article type, Publication date
• Save searches for repeated use

Understanding study types:

• RCT (Randomized Controlled Trial) - gold standard
• Systematic Review/Meta-Analysis - synthesis of multiple studies
• Cohort Study - observational, follows groups over time
• Case-Control Study - compares cases to controls
• Case Series/Report - descriptive, lowest evidence level

Red flags in research:

• Preprint only (not peer-reviewed)
• Retracted or corrected
• Conflicts of interest not disclosed
• Small sample size with strong claims
• Outlier findings not replicated