pubmed-watcher/index.html at main · QclawQ/pubmed-watcher · GitHub

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<title>pubmed-watcher — Automated PubMed Paper Alerts</title>
<meta name="description" content="Automated alerting for new PubMed papers. Delta detection — only alerts on unseen papers. Built for cron.">
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<div class="topbar"><div class="topbar-inner">
  <a href="https://qclawq.github.io" class="logo">← Q's Build Lab</a>
  <a href="https://github.com/QclawQ/pubmed-watcher" target="_blank">github ↗</a>
</div></div>

<div class="container">
<div class="hero">
  <div class="badge">pure python · zero dependencies · 617 loc</div>
  <h1>🔬 <span>pubmed-watcher</span></h1>
  <div class="sub">Automated PubMed Paper Alerts</div>
  <p>Watch PubMed queries and get alerted only about <strong>new</strong> papers. Tracks seen PMIDs, supports cron scheduling, outputs to terminal, Markdown, or JSON.</p>
</div>

<div class="section">
  <div class="section-title">// how it works</div>
  <div class="flow-steps">
    <div class="flow-step"><div class="step-num">01</div><div class="step-icon">🔎</div><div class="step-text">Query PubMed E-utilities</div></div>
    <div class="flow-step"><div class="step-num">02</div><div class="step-icon">🔄</div><div class="step-text">Filter against seen.json</div></div>
    <div class="flow-step"><div class="step-num">03</div><div class="step-icon">📥</div><div class="step-text">Fetch new paper details</div></div>
    <div class="flow-step"><div class="step-num">04</div><div class="step-icon">🔔</div><div class="step-text">Alert only NEW papers</div></div>
  </div>
</div>

<div class="section">
  <div class="section-title">// default queries</div>
  <ul class="query-list">
    <li class="query-item"><span class="query-num">[1]</span><span class="query-text">epigenetic reprogramming aging longevity</span></li>
    <li class="query-item"><span class="query-num">[2]</span><span class="query-text">immunosenescence aging immune system</span></li>
    <li class="query-item"><span class="query-num">[3]</span><span class="query-text">senolytics senescent cells therapy</span></li>
    <li class="query-item"><span class="query-num">[4]</span><span class="query-text">AI drug discovery clinical trial</span></li>
    <li class="query-item"><span class="query-num">[5]</span><span class="query-text">biological age clock methylation</span></li>
  </ul>
</div>

<div class="section">
  <div class="section-title">// demo output</div>
  <div class="terminal">
    <div class="terminal-bar"><span class="terminal-dots"><i></i><i></i><i></i></span><span class="terminal-title">$ python3 pubmed_watcher.py watch</span></div>
    <div class="terminal-body">🔔 12 new papers found across 5 queries (last 7 days)

━━━ 🔎 "epigenetic reprogramming aging longevity" — 3 new ━━━

  📄 Epigenetic reprogramming reverses age-associated
     decline in neural stem cell function
     👤 Zhang W … Bhatt DL
     📰 Nature Aging  •  2026 Feb
     🔗 https://pubmed.ncbi.nlm.nih.gov/39847201/

  📄 In vivo partial reprogramming extends lifespan
     in progeroid mice via cellular rejuvenation
     👤 Ocampo A … Izpisua Belmonte JC
     📰 Cell  •  2026 Feb 10
     🔗 https://pubmed.ncbi.nlm.nih.gov/39847202/

━━━ 🔎 "senolytics senescent cells therapy" — 4 new ━━━

  📄 Dasatinib plus quercetin reduces senescent
     cell burden in human adipose tissue
     👤 Kirkland JL … Tchkonia T
     📰 Nature Medicine  •  2026 Feb
     🔗 https://pubmed.ncbi.nlm.nih.gov/39847203/

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
📊 Total: 12 new | 4/5 queries had results</div>
  </div>

  <div class="terminal">
    <div class="terminal-bar"><span class="terminal-dots"><i></i><i></i><i></i></span><span class="terminal-title">$ python3 pubmed_watcher.py history</span></div>
    <div class="terminal-body">📜 Alert History (last 5 runs)

  🔔 2026-02-17 08:00 UTC — 12 new papers (5 queries, 7d window)
      • epigenetic reprogramming aging longevity: 3 new
      • senolytics senescent cells therapy: 4 new
      • AI drug discovery clinical trial: 3 new
      • biological age clock methylation: 2 new
  🔔 2026-02-16 08:00 UTC — 8 new papers (5 queries, 7d window)
  ✅ 2026-02-15 08:00 UTC — 0 new papers (5 queries, 7d window)
  🔔 2026-02-14 08:00 UTC — 5 new papers (5 queries, 7d window)</div>
  </div>
</div>

<div class="section">
  <div class="section-title">// features</div>
  <div class="info-grid">
    <div class="info-card">
      <h4>🔄 Delta Detection</h4>
      <p>Tracks every PMID in <code>seen.json</code>. You only get alerted once per paper, even across multiple queries. Perfect for daily cron jobs.</p>
    </div>
    <div class="info-card">
      <h4>📤 Output Formats</h4>
      <ul>
        <li><code>--terminal</code> — Pretty CLI output</li>
        <li><code>--markdown</code> — Telegram-ready</li>
        <li><code>--json</code> — Machine-readable</li>
      </ul>
    </div>
    <div class="info-card">
      <h4>⏰ Cron Ready</h4>
      <p style="font-family:var(--mono);font-size:.72rem">0 8 * * * python3 pubmed_watcher.py watch --markdown >> /tmp/alerts.md</p>
      <p style="margin-top:.5rem">Run daily, pipe to Telegram, Slack, or email.</p>
    </div>
    <div class="info-card">
      <h4>💻 Commands</h4>
      <ul>
        <li><code>watch</code> — Check all queries</li>
        <li><code>add "query"</code> — Add new query</li>
        <li><code>list</code> — Show queries</li>
        <li><code>remove &lt;id&gt;</code> — Remove query</li>
        <li><code>history</code> — Past runs</li>
        <li><code>reset-seen</code> — Clear DB</li>
      </ul>
    </div>
  </div>
</div>
</div>

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  <p>pubmed-watcher · <a href="https://github.com/QclawQ/pubmed-watcher">source</a> · <a href="https://qclawq.github.io">Q's Build Lab</a> · NCBI E-utilities</p>
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