PubMed Publications

A lightweight WordPress plugin that pulls PubMed/NCBI publications for each author (e.g., physicians) and renders Divi-friendly publication cards—no hand-curating posts or heavyweight academic stacks.

• Custom Post Type: pubmed_publication (renameable)
• Taxonomy (per-author/doctor): pubmed_doctor (renameable)
• Shortcodes for Latest and Per-Author lists
• Optional modal viewer so PubMed/PMC pages open inside your site
• Sorting that matches PubMed’s “Most Recent” (uses sortpubdate → epubdate → pubdate)
• Delete authors/doctors from the admin with two safe modes (+ success notices)

This repo typically contains a single plugin file, e.g. pubmed-publications/pubmed-publications.php.

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Features

• Pulls from PubMed via NCBI E-utilities (esearch + esummary)
• Accurate dates: stores an ISO date using sortpubdate when available (falls back to epubdate, then pubdate), and syncs WP post_date for consistent sorting
• Chronological lists (newest → oldest), no year separators
• Bibliography links per author/doctor (MyNCBI or PubMed results pages)
  • If a PubMed results URL contains ?term=..., the plugin extracts the term to mirror that exact search when importing
• Modal open (optional) for PubMed/PMC links
• Caching via WordPress transients (default 6h); manual Fetch bypasses cache
• De-duplication by PMID (falls back to title)
• Admin: Delete doctor with two safe modes:
  • Delete doctor (keep publications) → removes the taxonomy term; posts remain
  • Delete doctor + publications (exclusive only) → moves exclusive posts to Trash; co-authored posts are kept (doctor detached)
• Admin notices show success messages after actions
• Divi-friendly HTML/CSS out of the box
• Single top-level admin menu for a clean UX

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Requirements

• WordPress 6.0+
• PHP 7.4+ (8.x supported)
• A monitored email address (set in the plugin constant) to comply with NCBI’s tool policy

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🔧 Install

1. Create the folder:
   wp-content/plugins/pubmed-publications/
2. Copy the plugin file into that folder (e.g., pubmed-publications.php).
3. Activate PubMed Publications in Plugins.

After activation, you’ll see a single admin menu: PubMed Publications

• Authors & Import (setup + fetch + delete)
• Publications (CPT list)
• Add New (optional manual entries)

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Admin: Authors & Import

Add an author/doctor

• Name: e.g., Johnson or Jones (used as the taxonomy term)
• PubMed query: supports boolean OR and parentheses
  Example:

  (Johnson A[au] OR Johnson AM[au]) AND (YourHospital[ad] OR YourCity[ad])

  • [au] = author, [ad] = affiliation
  • Do not put the entire expression in quotes
• Bibliography URL (optional): any public link (MyNCBI or PubMed results)
  • If it’s a PubMed results URL containing ?term=, the plugin automatically extracts and uses that term for fetching so your site mirrors the exact search.
  • If it’s a MyNCBI bibliography page (e.g., https://www.ncbi.nlm.nih.gov/myncbi/.../bibliography/public/), the link is displayed, and imports use the stored query.

Click Save → Fetch/Refresh (per author or ALL).

What happens on fetch

• The plugin queries PubMed for the newest items (default up to 100).
• It creates/updates pubmed_publication posts, attached to the author taxonomy term.
• It stores:
  • pubmed_pmid, pubmed_pmcid, pubmed_doi, pubmed_journal
  • pubmed_pubdate_display (nice string, prefers Epub date)
  • pubmed_pubdate_iso (YYYY-MM-DD, from sortpubdate/epubdate/pubdate)
  • pubmed_url (PubMed article URL)
• It also sets the WordPress post_date to the ISO date so sorting is consistent everywhere.

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Deleting an author/doctor (safe options)

From Authors & Import, each row has a Delete control with two modes:

• Delete doctor (keep publications): removes the taxonomy term. Existing posts remain; the doctor is detached.
• Delete doctor + publications (exclusive only):
  • Posts that are only tagged with this doctor are moved to the Trash (not permanently deleted).
  • Posts with multiple doctors are kept; this doctor is detached.

After deletion, a success notice confirms what happened.

Tip: If you want an extra guardrail, add a “type the name to confirm” field in the delete form. (Optional snippet available in the issues/wiki.)

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Shortcodes

Prefix note: The examples below use the current shortcode names (pubmed_...). If you rename your prefixes in code, adjust accordingly (e.g., pubmed_publications).

Latest across all authors

[pubmed_latest_publications
  limit="10"
  open="modal"
  title="Latest Publications"
  subtitle=""
  anchor=""
  heading="h2"]

Per-author list

[pubmed_publications
  doctor="Johnson"
  limit="10"
  open="modal"
  title="Dr. Johnson — Recent Publications"
  subtitle=""
  anchor="johnson"
  heading="h2"
  show_bibliography="true"
  bib_label="View full bibliography"]

Attributes

• doctor – taxonomy term name (e.g., Johnson, Jones) — represents the author
• limit – number of items (default 10)
• open – modal or newtab (default newtab)
• title, subtitle, anchor, heading – section header options (heading: h2..h5)
• show_bibliography – true|false (default true for per-author)
• bib_label – link text for the bibliography button

year_groups is ignored (kept for backward compatibility).

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Styling

Minimal CSS is inlined by the plugin and designed to play nicely with Divi.
Available classes:

• .pubmed-section-header, .pubmed-section-title, .pubmed-section-subtitle
• .pubmed-bib-link
• .pubmed-grid (responsive grid)
• .pubmed-card, .pubmed-title, .pubmed-meta, .pubmed-authors, .pubmed-links a

Example override (Divi → Theme Options → Custom CSS)

.pubmed-card { border-radius: 14px; }
.pubmed-title { font-size: 1.05rem; }
.pubmed-meta em { font-style: italic; }

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Data model

• Post Type: pubmed_publication (renameable)
  • post_date: synced to the article’s ISO date for consistent sorting
• Taxonomy: pubmed_doctor (renameable)
  • Term Meta:
    • pubmed_query – PubMed query (boolean OR supported)
    • pubmed_bib_url – public bibliography URL (MyNCBI or PubMed results)
• Post Meta:
  • pubmed_pmid, pubmed_pmcid, pubmed_doi
  • pubmed_journal, pubmed_authors
  • pubmed_pubdate_display (string shown on cards)
  • pubmed_pubdate_iso (YYYY-MM-DD, used for sorting)
  • pubmed_url (PubMed URL)

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Caching & rate limits

• Results from PubMed API are cached for 6 hours (change CACHE_HOURS).
• The Fetch/Refresh action bypasses the cache.
• The plugin sends tool and your email to NCBI. Update const EMAIL to a monitored address.

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Date logic (why it sorts correctly)

PubMed has several dates:

• sortpubdate (used by PubMed to sort “Most Recent”)
• epubdate (online first)
• pubdate (print)

We use: sortpubdate → epubdate → pubdate to build an ISO date and set post_date to that value.
Cards show the display date (prefers Epub string if present).

This avoids issues like “Epub 2024 / Print 2025” appearing under the wrong year or out of order.

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Maintenance

• Periodically click Fetch/Refresh ALL to pull new publications.
• If you imported before the date logic existed, use Rebuild Dates to re-sync post_date from stored ISO dates.
• To refine results: expand author variants and/or add an affiliation clause
  e.g., (Johnson A[au] OR Johnson AM[au]) AND (YourHospital[ad] OR YourCity[ad])

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Troubleshooting

Nothing imports for an author

• Remove outer quotes around the entire query.
• Test your query directly at PubMed (confirm results).
• If using a bibliography URL, ensure it’s a PubMed results link with ?term= for import mirroring. MyNCBI bibliography pages are displayed only, not parsed for the term.

Sorting looks wrong

• Ensure you’re on the latest plugin with sortpubdate logic.
• Click Fetch/Refresh for that author (or ALL).
• Run Rebuild Dates (optional) to re-sync post_date.

I see duplicates

• The plugin dedupes on PMID, falling back to title. If an item appears twice in PubMed under different PMIDs, it can appear twice here (expected).

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Security & Privacy

• Fetches public bibliographic data from PubMed (no PHI).
• Follows NCBI’s E-utilities guidelines (tool + email).
• Stores no sensitive data beyond publication metadata.

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Development notes

• Single-file plugin for portability.
• Hooks:
  • admin_post_pubmed_save_doctors
  • admin_post_pubmed_fetch
  • admin_post_pubmed_rebuild_dates (optional)
  • admin_post_pubmed_delete_doctor
• Easy extension ideas:
  • Add EFetch to store abstracts
  • Add WP-Cron weekly refresher
  • Add a second taxonomy for Posters/Presentations
  • Add “type the name to confirm” before deletion

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Versioning

• 1.2.0 — Delete doctor (keep vs. delete exclusive to doctor → Trash), admin success notices; consolidated admin language.
• 1.1.0 — Bibliography links, section headers, modal, PubMed term extraction from results URLs, date logic (sortpubdate) + post_date syncing, single chronological lists (no year separators).

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License

MIT (or update to your preferred license).

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Maintainers

• Your organization / site vendor
• Dev contact: update const EMAIL in the plugin for NCBI contact and support

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Quick Start (TL;DR)

1. Activate the plugin.
2. PubMed Publications → Authors & Import
   • Add an author, e.g., query: (Johnson A[au] OR Johnson AM[au]) AND (YourHospital[ad] OR YourCity[ad])
   • Add bibliography URL (e.g., MyNCBI public page)
   • Save → Fetch/Refresh
3. In your Divi page:

   [pubmed_latest_publications title="Latest Publications" limit="10" open="modal"]
   [pubmed_publications doctor="Johnson" title="Dr. Johnson’s Recent Publications" show_bibliography="true" open="modal"]

4. (Optional) Delete a test author to see the safe delete modes + notices.
5. Done.