Upgrade StorageLattice for Zotero: From Grounded PDF Q&A to a Complete Research-Organization Workflow
Hi everyone,
I recently expanded my Zotero plugin, originally called Grounded Q&A, into a broader research tool now called Lattice for Zotero.
Original features
The first version focused mainly on grounded AI question answering:
Ask questions about a single PDF directly from the Zotero reader.
Ask questions across multiple selected papers.
Receive answers with clickable [Page N] or [Paper N, Page M] citations.
Jump directly from a citation to the relevant PDF page.
Choose your own AI provider, including Anthropic, OpenAI, Ollama, DeepSeek, and Grok.
Use Ollama for a fully local workflow without sending PDF content to a cloud-based provider.
Features added in Lattice 4.0
Lattice expanded beyond AI Q&A into cross-paper annotation and idea management:
All Annotations: View highlights, notes, and underlines from across your Zotero library in one window.
Combined filtering: Filter annotations by color, tag, keyword, or annotation type.
Cited exports: Copy filtered annotations as Markdown or HTML, or save them as a Zotero note with citations.
Idea Layer: Promote important highlights into independent Zotero notes that can be searched, tagged, linked to other ideas, and connected back to their original sources.
Save AI answers: Turn useful Q&A responses into page-anchored Zotero annotations so they become part of the same research workflow.
New in Lattice 4.1: Knowledge Organizer
The latest update introduces a Citavi-style Knowledge Organizer designed to connect reading, outlining, and drafting:
Build a hierarchical outline for a paper, book, thesis, or literature review.
Add, rename, reorder, indent, and outdent headings.
File highlights and notes beneath specific headings while reading.
Use normal Zotero tags beginning with § to assign annotations to outline sections.
Search and file annotations directly from the Organizer panel.
Automatically gather every filed quotation and note into the correct outline order.
Generate a first draft with citations in Markdown or HTML.
Copy the generated draft or save it as a standalone Zotero note.
The goal is to create one connected workflow:
Read → highlight → organize ideas → build an outline → generate a cited first draft
The annotation browser, idea layer, and organizer use native Zotero notes, tags, annotations, and relations, so the research material remains accessible inside Zotero rather than being locked into a separate proprietary database.
The plugin is free and open source and requires Zotero 7 or newer:
https://github.com/birugit/zotero-grounded-qa
I would greatly appreciate feedback from Zotero users, especially about the Knowledge Organizer, large-library performance, and features that would make the plugin more useful for real research and writing workflows.
I recently expanded my Zotero plugin, originally called Grounded Q&A, into a broader research tool now called Lattice for Zotero.
Original features
The first version focused mainly on grounded AI question answering:
Ask questions about a single PDF directly from the Zotero reader.
Ask questions across multiple selected papers.
Receive answers with clickable [Page N] or [Paper N, Page M] citations.
Jump directly from a citation to the relevant PDF page.
Choose your own AI provider, including Anthropic, OpenAI, Ollama, DeepSeek, and Grok.
Use Ollama for a fully local workflow without sending PDF content to a cloud-based provider.
Features added in Lattice 4.0
Lattice expanded beyond AI Q&A into cross-paper annotation and idea management:
All Annotations: View highlights, notes, and underlines from across your Zotero library in one window.
Combined filtering: Filter annotations by color, tag, keyword, or annotation type.
Cited exports: Copy filtered annotations as Markdown or HTML, or save them as a Zotero note with citations.
Idea Layer: Promote important highlights into independent Zotero notes that can be searched, tagged, linked to other ideas, and connected back to their original sources.
Save AI answers: Turn useful Q&A responses into page-anchored Zotero annotations so they become part of the same research workflow.
New in Lattice 4.1: Knowledge Organizer
The latest update introduces a Citavi-style Knowledge Organizer designed to connect reading, outlining, and drafting:
Build a hierarchical outline for a paper, book, thesis, or literature review.
Add, rename, reorder, indent, and outdent headings.
File highlights and notes beneath specific headings while reading.
Use normal Zotero tags beginning with § to assign annotations to outline sections.
Search and file annotations directly from the Organizer panel.
Automatically gather every filed quotation and note into the correct outline order.
Generate a first draft with citations in Markdown or HTML.
Copy the generated draft or save it as a standalone Zotero note.
The goal is to create one connected workflow:
Read → highlight → organize ideas → build an outline → generate a cited first draft
The annotation browser, idea layer, and organizer use native Zotero notes, tags, annotations, and relations, so the research material remains accessible inside Zotero rather than being locked into a separate proprietary database.
The plugin is free and open source and requires Zotero 7 or newer:
https://github.com/birugit/zotero-grounded-qa
I would greatly appreciate feedback from Zotero users, especially about the Knowledge Organizer, large-library performance, and features that would make the plugin more useful for real research and writing workflows.