Pubmed daily digest

PubMed Daily Digest

A Claude Code skill that pulls fresh PubMed articles every day across a few thematic queries, refills missing abstracts via CrossRef, summarises each in English, picks 3–5 notable highlights, and writes a Markdown digest to a local output directory. Publishing the digest anywhere is up to you.

Configuration

Edit these values in this file before running in a new setup:

Key	Default	Notes
OUTPUT_DIR	output/ (inside this skill folder)	Where {DATE}.md, {DATE}_raw.json, {DATE}_daily.json go
TIMEZONE	UTC	IANA name passed to ZoneInfo in Step 0
CROSSREF_MAILTO	[email protected]	CrossRef polite-pool identifier
QUERIES	Four thematic queries, see Step 1 table	Customise freely — see README.md for guidance

Scripts in scripts/ resolve sjr_curated.json and the rolling .seen_pmids.json cache relative to their own path, so they work from any cwd as long as the folder layout is intact.

Before the first run, build your own sjr_curated.json. The repo ships sjr_curated.example.json only as a schema reference — its contents reflect the original author's specialty interests. Either copy and edit it for your own journals, or ask Claude to bootstrap one for your specialty using the Maintenance workflow below. If sjr_curated.json is absent, the filter still runs but every article gets if_score = 0 and the per-section IF sort becomes order-of-arrival.

Date handling

Runs use the system clock + a configured timezone to derive today's date. Don't infer the date from filenames, git logs, or chat context — only the Python clock is trustworthy.

from datetime import datetime
from zoneinfo import ZoneInfo

TIMEZONE = "UTC"          # change to e.g. "Asia/Taipei", "America/New_York"
DATE = datetime.now(ZoneInfo(TIMEZONE)).strftime("%Y-%m-%d")

DATE is the canonical label used for output filenames and PubMed edat queries. If PubMed returns 0 articles for DATE across all four queries (common early in the morning), Step 1 falls back to DATE − 1.

---

Step 0 — Confirm today's date

Get DATE via the snippet above, then sanity-check:

1. If {OUTPUT_DIR}/{DATE}.md already exists: today's digest was already built. Stop and tell the user (don't silently overwrite).
2. Confirm DATE is within 2 days of the most recent existing .md in {OUTPUT_DIR}/. A bigger gap usually means a system-clock anomaly — stop and ask the user.

---

Step 1 — PubMed search + Python filter

Call mcp__PubMed__search_articles in parallel with datetype=edat, date_from=date_to=DATE, max_results=200. Four default queries:

Section	Query
transplant_id (part 1)	aspergillosis[tiab] OR mucormycosis[tiab] OR "invasive fungal infection"[tiab] OR "invasive fungal disease"[tiab] OR candidemia[tiab] OR "invasive candidiasis"[tiab] OR cryptococcosis[tiab] OR "pneumocystis jirovecii"[tiab] OR "pneumocystis carinii"[tiab] OR PJP[tiab] OR "BK virus"[tiab] OR BKV[tiab] OR fusariosis[tiab] OR scedosporiosis[tiab] OR Scedosporium[tiab] OR PTLD[tiab] OR "post-transplant lymphoproliferative"[tiab]
transplant_id (part 2)	(cytomegalovirus[tiab] OR CMV[tiab] OR EBV[tiab] OR "Epstein-Barr virus"[tiab] OR toxoplasmosis[tiab] OR Strongyloides[tiab] OR histoplasmosis[tiab] OR nocardiosis[tiab] OR Nocardia[tiab] OR mycobacterium[tiab] OR tuberculosis[tiab] OR NTM[tiab]) AND (transplantation[tiab] OR SOT[tiab] OR HSCT[tiab] OR immunocompromised[tiab] OR immunosuppressed[tiab] OR HIV[tiab] OR AIDS[tiab] OR letermovir[tiab] OR maribavir[tiab])
one_health	zoonosis[tiab] OR zoonoses[tiab] OR zoonotic[tiab] OR "one health"[tiab] OR "zoonotic spillover"[tiab] OR "viral spillover"[tiab] OR "pathogen spillover"[tiab] OR "interspecies transmission"[tiab]

Customising the queries: edit this table to fit your interests, then update SECTION_HEADERS / SECTION_ORDER in scripts/build_daily_md.py to match. See README.md → "Customising the queries" for worked examples.

PubMed MCP caveats (apply to every query):

• No wildcards — mycobacteri* fails with INVALID_PARAMETERS. Expand with OR: mycobacterium OR tuberculosis.
• 20-operator cap — a single query with more than 20 AND/ORs fails. Split into two parallel sub-queries when needed (as transplant_id does above).
• max_results ceiling is 200.

Union the two transplant_id sub-queries' PMIDs, then for each of the three sections call mcp__PubMed__get_article_metadata in batches of ≤ 20 PMIDs (larger batches are silently truncated).

Write the raw metadata to {OUTPUT_DIR}/{DATE}_raw.json in this shape (reldate: 0 = same-day query; 1 = fallback to DATE − 1):

{
  "meta": {"date": "YYYY-MM-DD", "reldate": 0},
  "raw_sections": {
    "transplant_id": [<get_article_metadata records>],
    "one_health":    [...]
  }
}

Then run the Python filter:

python scripts/daily_feed_filter.py {DATE}

It reads {OUTPUT_DIR}/{DATE}_raw.json, drops noise/basic-science/non-English articles, sorts by the SJR score from sjr_curated.json, applies per-section caps, and writes {OUTPUT_DIR}/{DATE}_daily.json. It also updates a rolling .seen_pmids.json (7-day TTL) so the next run doesn't re-cover the same article.

Fallback to DATE − 1: if all four PubMed queries return 0 articles, rerun with date_from=date_to=DATE−1 and set meta.reldate = 1 in _raw.json — the filter then excludes any PMIDs already present in the previous day's digest (via the <!-- pmids: ... --> marker the digest emits).

---

Step 2 — TL;DR annotation (English by default)

Read {OUTPUT_DIR}/{DATE}_daily.json. Each article record has fields pmid, title, journal_full, journal_abbr, authors, abstract, pubdate, doi, article_types, language, if_score, section, tldr, comment.

Refill missing abstracts via CrossRef (first)

For any article whose abstract is empty or starts with [ (PubMed sometimes returns "[Abstract not available]" as a string), if a doi is present, query CrossRef:

• Endpoint: https://api.crossref.org/works/{urlencoded_doi}?mailto={CROSSREF_MAILTO}
• User-Agent: pubmed-daily-digest/1.0
• Timeout: 15 seconds; cache by DOI within one run.
• If message.abstract is present in the response: strip JATS/HTML tags and collapse whitespace, then write back to the article's abstract field.
• If CrossRef returns no abstract, non-200, timeout, or parse failure: do NOT abort. Keep the article in a "still missing abstract" list (its TL;DR and Hot Take stay blank; report the PMID at the end so the user can backfill).

TL;DR rules

For each article that has an abstract:

• English, 1–2 sentences, focused on study design + key finding + clinical implication.
• Keep drug names and pathogen names (bacterial / viral / fungal) in their canonical form; do not translate the article title.
• No filler openings like "This study investigates…" — state the finding.

Write tldr back into the JSON in place (json.dump(..., ensure_ascii=False, indent=2)).

Change the output language: this step is pure prompting. Replace "English, 1–2 sentences" with "Traditional Chinese, max 50 字" / "Spanish, two sentences" / etc. Claude translates the source abstract on the fly; nothing else in the skill needs editing.

---

Step 3 — Hot Take annotation

For every article that has a tldr, write a one-line Hot Take in English. Pick the register that fits the content:

• Positive — for hopeful findings, breakthroughs, good outcomes (excited / cheerful tone).
• Snarky — for bad news, hard pathogens, depressing epidemiology, or old problems with no new answers (deadpan / self-aware, not cruel).

Length: one short sentence (target ≤ 20 words). If tldr is blank (no abstract), leave comment blank too.

Write back in place.

Same language-swap rule as Step 2 applies. Edit "in English" above to your preferred language.

---

Step 3.5 — Notable Highlights

From articles that have a tldr, select 3–5 worth flagging. Criteria, in priority order:

1. High clinical-practice impact (guideline updates, new therapies, management-changing findings).
2. High-IF journals (≥ 5) with novel or immediately actionable findings.
3. Public-health urgency (new pathogens, confirmed transmission chains, food / zoonotic alerts).
4. Locally relevant epidemiology (adjust this criterion to your region).

For each highlight, write a one-sentence reason (≤ 30 words) explaining why this is worth a second look — don't just restate the TL;DR.

Store them on meta.highlights:

{
  "meta": {
    "date": "YYYY-MM-DD",
    "reldate": 0,
    "highlights": [
      {"pmid": "12345678", "title": "...", "reason": "..."}
    ]
  },
  "sections": { ... }
}

Write back in place.

---

Step 4 — Build the Markdown digest

python scripts/build_daily_md.py {OUTPUT_DIR}/{DATE}_daily.json

The script writes {OUTPUT_DIR}/{DATE}.md next to the input JSON. The template (frontmatter, section headers, per-article block, empty-section placeholder, PMID footer) is controlled by the script — edit SECTION_HEADERS / SECTION_ORDER / fmt_* in scripts/build_daily_md.py if you want a different layout.

---

Step 5 — Save (optional commit)

The digest is now at {OUTPUT_DIR}/{DATE}.md. Stop here unless the user explicitly asks to commit or publish.

If they want a vault commit:

git add {OUTPUT_DIR}/{DATE}.md
git commit -m "daily digest {DATE}"

Publishing somewhere else (a notes site, a blog, an SSG) is the user's call.

Clean up intermediate JSON after the digest is safely committed/published:

rm {OUTPUT_DIR}/{DATE}_raw.json {OUTPUT_DIR}/{DATE}_daily.json

Final report to the user: total articles, per-section counts, the highlights list, and any PMIDs still missing abstracts (for manual backfill next run).

---

Maintenance — build / refresh sjr_curated.json

sjr_curated.json is a small lookup table from journal abbreviation / title to SJR (Scimago Journal Rank) score. The filter script uses it to rank and cap articles within each section. Two scenarios use the same workflow:

• First-time bootstrap — the user just installed the skill and there's no sjr_curated.json yet.
• Yearly refresh — SCImago publishes new rankings around June each year; existing scores drift over time.

Trigger phrases: "build sjr_curated", "update SJR scores", "refresh journal rankings".

Schema (preserve this exactly):

{
  "journals": [
    {
      "title": "The New England Journal of Medicine",
      "abbr": "N Engl J Med",
      "sjr": 34.6,
      "if": 96.2,
      "cluster": "general"
    }
  ]
}

abbr (NLM Title Abbreviation) and title are both used for lookup; if is the field the filter script reads as the score. sjr and cluster are metadata for human reference. Look up NLM abbreviations at https://www.ncbi.nlm.nih.gov/nlmcatalog/journals.

Workflow (prompt-driven — no extra script):

1. First-time bootstrap: ask the user which medical specialties / topics they care about (Infectious Diseases, Hematology, Cardiology, Oncology, etc.). For each specialty, pick the top ~10–30 journals by reputation / SJR rank. Aggregate into a single list; aim for 50–200 entries total. If sjr_curated.example.json is present and the user wants to start from it, copy and trim instead of starting empty.
2. Yearly refresh: read the existing sjr_curated.json — that's the curated journal list. Do not expand it during a refresh; only update scores.
3. Visit https://www.scimagojr.com/ and locate the current per-category ranking download (SCImago has changed their URL scheme historically, so check the live site rather than hardcoding a URL).
4. For each journal in the working list, match by NLM abbreviation / full title and pull the latest sjr and if (or the closest available proxy — SCImago publishes SJR; impact factors come from a separate source like Web of Science or Clarivate).
5. Report: how many journals updated, which couldn't be matched (so the user can fix manually), and median SJR shift (sanity check that the right year loaded).
6. Save to sjr_curated.json (preserving the schema).

Skipping a refresh isn't fatal — digests still rank/filter, just with stale or zero scores.

---

Error handling

Situation	Action
All four PubMed queries return 0 articles	Retry with DATE − 1 and set reldate = 1 in _raw.json
daily_feed_filter.py exits non-zero	Report and stop — don't continue to Step 2
One query returns 0 articles	Continue; that section's Markdown shows a placeholder
CrossRef fails for an article (any reason)	Continue; leave tldr and comment blank; report PMID in the final summary
{OUTPUT_DIR}/{DATE}.md already exists	Stop and report — don't silently overwrite a digest
sjr_curated.json missing	Filter still runs (if_score = 0 for all); see the Maintenance section to build / refresh it