zotero-write

Write, tag, annotate, and edit a local Zotero SQLite database. Use when the user wants to: (1) Add tags or labels to papers in their Zotero library, (2) Add notes or annotations to specific papers, (3) Update paper metadata (title, authors, journal, date, DOI, etc.), (4) Create new Zotero items manually. Activates on: 'tag this paper', 'add a note to', 'update the metadata of', 'add this to my Zotero', 'create a new Zotero entry', 'edit Zotero', 'organize my Zotero with tags', any request to modify, annotate, or write to the Zotero database.

Zotero Write Skill

Write, tag, annotate, and edit a local Zotero SQLite database.

Database & Safety

• Database: E:\Refer.Hub\zotero.sqlite
• ⚠️ SAFETY: Always use --backup before any write operation. Backups saved to E:\Refer.Hub\backups/
• Required: Close Zotero application before writing to the database
• Rule: Never run write operations without --backup — the script will refuse

Scripts

• scripts/write_items.py — All write operations

Scripts Usage

0. Always backup first

bash

py -3 scripts/write_items.py --backup "E:\Refer.Hub\zotero.sqlite"

This saves a timestamped backup before any write. Always do this first.

1. Add tags to a paper

First find the item key from zotero-browse skill, then:

bash

py -3 scripts/write_items.py --backup "E:\Refer.Hub\zotero.sqlite" \
  --add-tag ZL42EGES "NAFLD" "FGF15" "silymarin"

2. Add a note to a paper

bash

py -3 scripts/write_items.py --backup "E:\Refer.Hub\zotero.sqlite" \
  --add-note ZL42EGES "This paper shows FGF15 is the key mediator of silibinin's anti-NAFLD effect."

3. Update a field (metadata)

bash

# Update title
py -3 scripts/write_items.py --backup "E:\Refer.Hub\zotero.sqlite" \
  --set-field ZL42EGES title "New Title Here"

# Update date
py -3 scripts/write_items.py --backup "E:\Refer.Hub\zotero.sqlite" \
  --set-field ZL42EGES date "2024"

# Update journal
py -3 scripts/write_items.py --backup "E:\Refer.Hub\zotero.sqlite" \
  --set-field ZL42EGES publicationTitle "Journal Name"

# Update DOI
py -3 scripts/write_items.py --backup "E:\Refer.Hub\zotero.sqlite" \
  --set-field ZL42EGES DOI "10.1234/example"

4. Create a new Zotero entry

bash

py -3 scripts/write_items.py --backup "E:\Refer.Hub\zotero.sqlite" \
  --new-item journalArticle \
  --title "Example Title" \
  --authors "John Doe" "Jane Smith" \
  --date "2024" \
  --journal "Nature Medicine" \
  --doi "10.1038/s41591-024-0001-z"

5. List available field names

bash

py -3 scripts/write_items.py --list-fields

6. Show full item details (before editing)

bash

py -3 scripts/write_items.py --item-info ZL42EGES

---

Available Fields

Run --list-fields to see all. Common fields:

fieldName	Description
title	Paper title
creators	Authors (use --authors for new items)
date	Publication date (YYYY or YYYY-MM-DD)
publicationTitle	Journal name
DOI	Digital Object Identifier
url	Web URL
abstractNote	Abstract
tags	Tags (use --add-tag instead)
volume	Volume number
issue	Issue number
pages	Page range
publisher	Publisher
ISBN	ISBN
ISSN	ISSN
journalAbbreviation	Journal abbreviation

Item Types

When creating new items, use one of:

• journalArticle (default for papers)
• book
• bookSection
• conferencePaper
• thesis
• report
• webpage
• note

Workflow: Tag a paper

1. Use zotero-browse skill to find the paper's attachment key
2. Run with --backup first
3. Add tags:

   bash

   py -3 scripts/write_items.py --backup "E:\Refer.Hub\zotero.sqlite" \
     --add-tag ZL42EGES "NAFLD" "FGF15" "biomarker"
   

4. Confirm backup was created at E:\Refer.Hub\backups/

Important Notes

• Backup is automatic with --backup — always use it
• Tags use exact string matching; case-sensitive
• Setting a field that already has a value will overwrite it
• Notes are added as child items linked to the parent paper
• New items get a random 8-char Zotero key
• After writing, Zotero will sync changes on next launch