literature-morning-report

name	literature-morning-report
description	Generate a personalized research literature morning report from a user-provided research_profile.yml, with PubMed, Europe PMC, Semantic Scholar, OpenAlex, Crossref, arXiv, Web of Science, Scopus, Embase, and IEEE Xplore retrieval where credentials permit, plus deduplication, bilingual summaries, email delivery, and RIS/BibTeX/ENW/CSL-JSON export.

Literature Morning Report

Use this skill when a researcher wants a daily, personalized literature report, literature alert, paper digest, reference export, or research inspiration workflow based on their own discipline and research direction.

Quick Start

1. Copy assets/research_profile.template.yml to research_profile.yml.
2. Fill in the user's research direction, keywords, exclusion rules, journal threshold, email, schedule, and export formats.
3. Run:

python literature-morning-report/scripts/literature_morning_report.py \
  --profile research_profile.yml \
  --history sent_history.tsv \
  --output-dir reports \
  --max-papers 5

4. For a dry run, add --dry-run. For email delivery, configure either SMTP environment variables or Resend environment variables.

Required Profile Fields

The profile must include:

• discipline
• research_direction
• core_keywords
• must_include_logic
• exclude_keywords
• preferred_databases
• journal_threshold
• report_language
• delivery_email
• delivery_time
• export_formats

See references/profile_schema.md for field meanings and examples.

Workflow

1. Validate the profile.
2. Build database-specific queries from core_keywords, must_include_logic, and exclude_keywords.
3. Search the configured databases. Open sources run directly; Web of Science, Scopus, Embase, and IEEE Xplore run only when valid API credentials/entitlements are present.
4. Fetch paper metadata and abstracts, then deduplicate by PMID, DOI, and normalized title against the history file.
5. Rank papers by research fit, recency, DOI/PMID reliability, journal evidence, and mechanism/actionability.
6. Generate a UTF-8 text report and HTML report. Summarize abstracts; do not reproduce long copyrighted abstracts.
7. Export selected papers as RIS, BibTeX, ENW, and/or CSL-JSON for EndNote, Zotero, and NoteExpress.
8. Send the report if email credentials are configured and the run is not dry-run.
9. Append successfully sent papers to the history file.

Quality Rules

Follow references/quality_policy.md.

Key constraints:

• Do not invent DOI, PMID, journal impact factor, JCR quartile, CAS zone, or conclusions.
• If journal metrics cannot be verified locally, label the metric as unverified instead of presenting it as fact.
• Abstracts must be summarized, not copied at length.
• If no new eligible papers are found, still generate a short no-new-literature report.

Email Configuration

SMTP:

SMTP_HOST=smtp.example.com
SMTP_PORT=465
SMTP_USER=[e-mail]
SMTP_PASS=app-password
SMTP_FROM="Literature Report <[e-mail]>"

Resend:

RESEND_API_KEY=re_xxx
RESEND_FROM="Literature Report <[e-mail]>"

Export Targets

• EndNote: prefer RIS or ENW.
• Zotero: prefer BibTeX, RIS, CSL-JSON, or Zotero API integration.
• NoteExpress: prefer RIS or BibTeX.

Use references/export_formats.md when adding new citation formats or reference-manager integrations.

Database Sources

Read references/database_sources.md before changing database coverage. Supported names in preferred_databases:

• Open/low-barrier: pubmed, europepmc, semantic_scholar, openalex, crossref, arxiv.
• Credential-gated: web_of_science, scopus, embase, ieee_xplore.

Credential-gated databases must be reported as skipped when credentials are missing. Do not scrape restricted web interfaces.