# Pubmed Weekly Digest > Weekly medical-literature digest agent — searches the past 7 days on PubMed across a configurable list of journals, fills in missing abstracts via CrossRef, writes a TL;DR and a one-line Hot Take for each article (English by default; language is configurable in Step 4), and renders a Markdown digest to a local output directory. Trigger when the user says "跑週報", "weekly journal", "weekly digest", or otherwise asks to run a weekly journal summary. - Skill: `didiowen/pubmed-weekly-digest` (Agent Skill, multi-file: 9 files) - Install (CLI): `npx skillmds@latest add didiowen/pubmed-weekly-digest` - Raw SKILL.md: https://api.skillmd.com/api/skills/didiowen/pubmed-weekly-digest/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: AI & ML - Author: didiowen (https://skillmd.com/u/didiowen) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/didiowen/pubmed-weekly-digest --- # PubMed Weekly Digest > A Claude Code skill: searches the past 7 days on PubMed across a configurable > list of journals, refills missing abstracts via CrossRef, writes a TL;DR and > a one-line Hot Take per article, and renders a Markdown digest to a local > output directory. Committing or publishing the digest is up to you. ## Configuration Edit these values before running the skill in a new vault: | Key | Default | Notes | |--------------------|-------------------------------------------------|----------------------------------------------------| | `OUTPUT_DIR` | `output/` (inside this skill folder) | Where `{week_label}.md` is written | | `JOURNALS` | See Step 1 table | The list of `[Journal]` queries — customise freely | | `CROSSREF_MAILTO` | `pubmed-weekly-digest@noreply.example` | CrossRef polite-pool identifier (any valid email) | `CROSSREF_MAILTO` can also be supplied via an environment variable `UNPAYWALL_EMAIL` if you prefer not to bake it into the file. If neither is set, CrossRef calls still go out (some endpoints just rate-limit harder). See `README.md` (same folder) for setup details and a step-by-step guide to swapping the journal list. ## ⚠️ ISO week calculation (read this first) This skill runs at the start of a week and covers the **just-ended** week. ```python from datetime import date, timedelta today = date.today() # Search window: past 7 days (excluding today) date_to = today - timedelta(days=1) # yesterday date_from = today - timedelta(days=7) # 7 days ago # Week label: use the ISO week of the just-ended week, NOT today's week target_date = today - timedelta(days=7) iso_year, iso_week, _ = target_date.isocalendar() week_label = f"{iso_year}-W{iso_week:02d}" # e.g. 2026-W19 filepath = f"{OUTPUT_DIR}/{week_label}.md" ``` **Example**: today is 2026-05-11 (W20) → `week_label = 2026-W19`, search range 2026-05-04 to 2026-05-10. > **Pitfall**: do NOT use `today.isocalendar()` for the label — that mis-labels > W19 content as W20. --- ## Step 1 — PubMed search Call `mcp__PubMed__search_articles` (datetype=`edat`) **in parallel** for each journal. The default list is six ID/haematology journals; replace freely: | Query string | max_results | |---------------------------------------|-------------| | `Clin Infect Dis[Journal]` | 50 | | `Emerg Infect Dis[Journal]` | 50 | | `MMWR Morb Mortal Wkly Rep[Journal]` | 30 | | `Transpl Infect Dis[Journal]` | 50 | | `Blood[Journal]` | 50 | | `N Engl J Med[Journal]` | 50 | **date_from** = `date_from` (YYYY/MM/DD), **date_to** = `date_to` (YYYY/MM/DD) **PubMed query caveats** — these apply to every entry in the table: - The MCP wrapper rejects **wildcards** (`mycobacteri*` → `INVALID_PARAMETERS`). Expand with `OR` instead: `mycobacterium OR tuberculosis`. - The **boolean-operator cap is 20**. A single query like `(a OR b OR ... OR u)` fails; split into two parallel queries if needed. - Add a topic filter with `AND (term1 OR term2)` to high-volume generals, e.g. `N Engl J Med[Journal] AND (infection OR sepsis OR antimicrobial)`. **If search fails (MCP error or 0 articles for all journals): stop and report.** --- ## Step 2 — Fetch full metadata Call `mcp__PubMed__get_article_metadata` in parallel batches (one batch per journal). Each batch is **≤ 20 PMIDs** — the MCP silently truncates beyond that. --- ## Step 2.5 — CrossRef abstract refill Scan all articles. If `abstract` is empty (or `"[Abstract not available]"`, which PubMed sometimes returns as a string) and a `doi` is present, query CrossRef: - Endpoint: `https://api.crossref.org/works/{urlencoded_doi}?mailto={CROSSREF_MAILTO}` - User-Agent: `pubmed-weekly-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. **Articles still missing abstracts** after CrossRef: - **Interactive mode**: list the affected articles (PMID, title, DOI) and ask the user to paste in abstracts manually, then continue. If the user says skip, leave `TL;DR` blank and note `(no abstract)` in the final output. - **Autonomous mode**: leave `TL;DR` blank for those articles and list the PMIDs in the final report so the user can backfill on a future run. --- ## Step 3 — Filter articles Drop articles where `article_types` contains: - `"Erratum"` or `"Published Erratum"` - `"Editorial"` or `"Comment"` (no abstract → no meaningful annotation) A section with zero surviving articles is fine — show a placeholder in Step 5. ### Optional: per-journal type filtering The default config includes an example for N Engl J Med where only Original Articles and Reviews are kept: - `article_types` contains `"Journal Article"` but NOT `"Case Reports"`, `"Editorial"`, `"Comment"`, `"Letter"`, `"News"`, `"Biography"`, `"Historical Article"`, `"Portrait"`, `"Interview"`, `"Personal Narrative"` → treat as Original Article - `article_types` contains `"Review"` or `"Systematic Review"` → treat as Review Article - Anything else from N Engl J Med → drop from this section Adjust or remove this block for your own journal mix. --- ## Step 4 — TL;DR and Hot Take annotation For each surviving article: - **TL;DR**: a 1–2 sentence English summary covering study design, key findings, and clinical implications. Keep drug names and pathogen names (bacterial / viral / fungal) in their canonical form; do not translate the article title. - **Hot Take**: one short humorous English sentence per article. Pick a 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 tone, not cruel) If `abstract` was never filled in, leave both fields blank. > **Change the output language**: this step is pure prompting. Replace > "English" above with "Traditional Chinese", "Spanish", "Japanese", or > whatever you prefer — Claude will translate the source abstracts on the fly. > The rest of the skill is language-agnostic; only Step 4 needs to be edited. --- ## Step 5 — Render Markdown Write the digest to `{OUTPUT_DIR}/{week_label}.md`. Read `{SKILL_DIR}/template.md` for the output scaffold. **Expand journal sections**: for each journal in your Step 1 list, replace a `## {Journal N}` stub with the real `## {Abbreviation}` section using the article-block format in the template. Add extra sections if you have more journals than stubs; remove extras if fewer. Fill `{journal_list}` in the intro line with a comma-separated list of your journals. **Formatting rules**: - Authors: one author → full name; multiple → `{first_author} et al.` - No DOI → `PMID: {pmid}` instead of the DOI line - Section with no surviving articles → `> No matching articles this week.` - Articles separated by `---` --- ## Step 6 — Save (optional commit) The Markdown file lives at `{OUTPUT_DIR}/{week_label}.md`. Stop here unless the user explicitly asks to commit/push — this fork intentionally does not assume a publish target. If the user wants the file committed to their vault: ```sh git add {OUTPUT_DIR}/{week_label}.md git commit -m "weekly journal digest {week_label}" ``` If they want to push to a public site repo, that's their choice — add the relevant `git remote` / `gh pr` / API call as a follow-up step. --- ## Error Handling | Situation | Action | |--------------------------------|----------------------------------------------| | Step 1 search fails entirely | Report and stop | | One journal returns 0 articles | Continue; that section shows a placeholder | | CrossRef refill fails | Continue; affected articles have blank TL;DR | | Output file already exists | Overwrite (the week label disambiguates) |