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Literature Monitoring Strategies — Reference Guide

Purpose

Comprehensive reference for setting up post-research literature monitoring across major academic databases and platforms. Used by the monitoring_agent to configure monitoring strategies tailored to the user's research field and publication velocity.

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1. Google Scholar Alerts

Setup

1. Go to Google Scholar
2. Enter your search query (use the same keywords from your systematic search)
3. Click the envelope icon (📧) in the left sidebar, or go to scholar.google.com/scholar_alerts
4. Set email address and frequency

Best Practices

• Create separate alerts for each major keyword cluster (not one giant query)
• Use quotes for exact phrases: "quality assurance" "higher education"
• Use OR for synonyms: "quality assurance" OR "quality evaluation"
• Limit to 10-15 active alerts to avoid email overload
• Review alerts monthly and deactivate stale ones

Limitations

• No Boolean NOT support in alerts
• Cannot filter by date, journal, or document type
• May include non-peer-reviewed sources (theses, reports, patents)
• Coverage varies by discipline (strong in STEM, weaker in humanities)

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2. PubMed Email Alerts

Setup

1. Go to PubMed
2. Run your search using MeSH terms and filters
3. Click "Save" below the search box
4. Log in to My NCBI account (free)
5. Set email alert frequency: daily, weekly, or monthly

Best Practices

• Use MeSH terms for precise matching (e.g., "Quality Assurance, Health Care"[MeSH])
• Combine with free-text search for newer terms not yet in MeSH
• Set weekly frequency for active research areas, monthly for stable fields
• Use the "Sort by: Most Recent" option to prioritize new publications
• Save your search strategy for reproducibility

Advanced Features

• MyNCBI Collections: Organize saved articles into folders
• Filters: Limit by date, article type, language, species
• RSS feed: Available for any saved search (click RSS icon)

Limitations

• Biomedical focus — limited coverage of social sciences, education, humanities
• Indexing lag: 1-4 weeks for new articles to appear
• No citation tracking built in

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3. RSS Feeds for Major Databases

What is RSS?

RSS (Really Simple Syndication) allows you to subscribe to content updates from websites without checking each site manually. Use an RSS reader (e.g., Feedly, Inoreader, NewsBlur) to aggregate feeds.

Recommended Feeds

Source	Feed URL Pattern	Content
PubMed	Saved search → RSS icon	New articles matching your search
arXiv	arxiv.org/rss/[category] (e.g., cs.AI, cs.CL)	Preprints by category
bioRxiv	connect.biorxiv.org/biorxiv_xml.php?subject=[subject]	Biology preprints
medRxiv	connect.medrxiv.org/medrxiv_xml.php?subject=[subject]	Medical preprints
SSRN	Subscribe to specific research networks	Social science preprints
Journal TOC	Most journals offer RSS on their homepage	New issues of specific journals
Retraction Watch	retractionwatch.com/feed/	Retraction news and updates

RSS Reader Recommendations

Reader	Platform	Cost	Best For
Feedly	Web, iOS, Android	Free (basic) / $6/mo (Pro)	Organized categorization, AI features
Inoreader	Web, iOS, Android	Free (basic) / $5/mo (Pro)	Power users, rules/filters
NewsBlur	Web, iOS, Android	Free (limited) / $36/yr	Open source option
Zotero RSS	Desktop	Free	Integrates with reference manager

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4. Retraction Watch Integration

Retraction Watch Database

• URL: retractiondatabase.org
• Coverage: 40,000+ retracted or corrected papers
• Searchable by: author, journal, subject, reason, date

Monitoring Workflow

1. Baseline check: Search all cited authors and paper titles in the Retraction Watch Database
2. Ongoing monitoring: Subscribe to Retraction Watch blog RSS feed
3. Periodic re-check: Every 3-6 months, re-run the baseline check for cited sources

Retraction Reasons to Watch For

Reason	Severity	Action Required
Data fabrication/falsification	Critical	Remove citation; add note explaining removal
Plagiarism	High	Replace with original source
Duplicate publication	Moderate	Keep the primary publication; remove duplicate
Honest error	Moderate	Check whether the error affects cited findings
Author dispute	Low	Usually no impact on findings
Publisher error	Low	Update citation to corrected version

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5. Preprint Server Monitoring

arXiv

• Coverage: Physics, mathematics, computer science, statistics, quantitative biology, economics
• Monitoring: Subscribe to RSS feeds by category and cross-list
• Alert service: arxiv-sanity for AI-curated recommendations
• Update frequency: Daily (new submissions posted ~8 PM ET)

SSRN

• Coverage: Social sciences, humanities, law, economics, management
• Monitoring: Subscribe to eJournal alerts by research network
• Alert service: Email notifications for new papers in subscribed networks
• Note: Now owned by Elsevier; some content behind paywall

bioRxiv / medRxiv

• Coverage: Biology (bioRxiv) and health sciences (medRxiv)
• Monitoring: RSS feeds by subject area
• Alert service: Email alerts for specific keywords
• Note: Preprints are NOT peer-reviewed — flag accordingly in digests

Key Preprint Monitoring Rules

1. Always label preprint sources clearly: [PREPRINT — not peer-reviewed]
2. Check whether a preprint has been published in a peer-reviewed journal (look for "Now published in..." banner)
3. Preprints can change or be withdrawn — re-check before citing
4. Preprint findings may differ from the final published version

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6. Citation Tracking

Web of Science

1. Find your key cited papers in Web of Science
2. Click "Create Citation Alert" (requires institutional access)
3. Receive email when someone cites that paper
4. Use "Cited Reference Search" for older papers not in the database

Scopus

1. Find your key cited papers in Scopus
2. Click "Set Citation Alert" on the document page
3. Configure email frequency
4. Also available: author alerts (track all publications by an author)

Google Scholar

1. Find the paper on Google Scholar
2. Click "Cited by N" to see citing papers
3. Click the "Follow" button (envelope icon) on author profiles
4. Set up alerts for specific papers by quoting the exact title

Semantic Scholar

• URL: semanticscholar.org
• Alerts: Click "Alert" on any paper to track citations
• Advantage: AI-powered relevance ranking of citing papers
• Research feed: Personalized recommendations based on your library

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7. Recommended Monitoring Cadence by Field

Determining Your Field's Publication Velocity

Indicator	High Velocity	Moderate	Low
Papers per month (in your niche)	> 50	10-50	< 10
Median time from submission to publication	< 6 months	6-12 months	> 12 months
Preprint prevalence	> 50% of key papers	10-50%	< 10%
Conference vs. journal dominance	Conference-first	Mixed	Journal-only

Cadence Recommendations

Field	Check Frequency	Digest Period	Sunset
AI/ML, NLP	Daily (arXiv) + Weekly (journals)	Weekly	6 months
Biomedical, Clinical	Weekly (PubMed + preprints)	Biweekly	12 months
Education Technology	Biweekly	Monthly	12 months
Higher Education Policy	Monthly	Quarterly	18 months
Social Sciences (general)	Monthly	Quarterly	18 months
Law, Philosophy	Quarterly	Semi-annually	24 months
History, Classics	Semi-annually	Annually	36 months

Sunset Policy

• Sunset date: The date after which active monitoring stops (topic presumed stable)
• Set based on field velocity and research currency
• After sunset: switch to annual check-ins or opportunistic monitoring
• Exception: extend monitoring if a major development occurs (e.g., retraction of key source, paradigm shift)

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8. Monitoring Maintenance Checklist

Run this checklist every monitoring cycle:

• [ ] Are all alerts still active? (some platforms deactivate after inactivity)
• [ ] Are any alerts returning zero results? (keywords may need updating)
• [ ] Are any alerts returning too many results? (keywords may need narrowing)
• [ ] Has the field's terminology evolved? (add new keywords, retire old ones)
• [ ] Any new major databases or preprint servers for this field?
• [ ] Has any tracked author changed institutions? (update author tracking)
• [ ] Is the sunset date still appropriate?
• [ ] Have you checked the Retraction Watch Database recently?

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Quick Reference: Setting Up in 30 Minutes

1. Google Scholar (5 min): Create 3-5 keyword alerts matching your original search strategy
2. PubMed (5 min): Save your search and set weekly email alerts (if your field is indexed)
3. RSS (5 min): Subscribe to RSS feeds for your top 5 cited journals in Feedly or Inoreader
4. Retraction Watch (5 min): Run baseline check on all cited authors; subscribe to RSS feed
5. Citation tracking (5 min): Set up citation alerts for your 5 most-cited sources in Google Scholar or Scopus
6. Preprints (5 min): Subscribe to relevant arXiv/SSRN/bioRxiv categories if applicable to your field

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SKILL.md Extracted Content: Literature Monitoring (Optional Post-Pipeline)

After any research mode is complete, users can optionally activate the monitoring_agent to set up post-research literature monitoring. This is not part of the main pipeline — it is an auxiliary capability triggered on demand.

See agents/monitoring_agent.md for the detailed agent definition.

Trigger: "monitor this topic", "set up alerts", "track new publications on this"

Capabilities: - Weekly/monthly monitoring digest generation - Retraction alerts for cited sources - Contradictory findings detection - Key author tracking - Keyword evolution tracking

Input: Completed bibliography + search strategy from any research mode Output: Monitoring configuration + digest template (markdown)

Limitation: The monitoring agent produces configurations and templates for the user to act on. It cannot run autonomous background monitoring.