Reference Library
Sciorex includes a full-featured reference manager built directly into the IDE. Collect, organize, cite, and export your academic sources without switching to a separate application.
Item Types
The library supports 43 Zotero-compatible item types, ensuring compatibility with existing workflows and imports.
| Category | Types |
|---|---|
| Publications | Journal article, book, book section, conference paper, thesis, dissertation, preprint, report, working paper |
| Digital | Software, dataset, webpage, blog post, podcast, video recording, audio recording |
| Legal & Government | Patent, statute, bill, case, hearing, regulation, government document |
| Media | Newspaper article, magazine article, encyclopedia article, dictionary entry |
| Presentations | Presentation, poster, lecture, speech |
| Other | Letter, manuscript, map, artwork, film, interview, email, forum post, instant message, standard, document |
INFO
All 43 types map directly to Zotero item types. Importing a Zotero library preserves type information without data loss.
Citation Styles
Generate formatted citations and bibliographies in 11 styles.
| Style | Example Use |
|---|---|
| APA 7th | Psychology, education, social sciences |
| MLA 9th | Humanities, literature, cultural studies |
| Chicago | History, arts, some social sciences |
| Harvard | General academic, UK and Australian universities |
| IEEE | Electrical engineering, computer science |
| Vancouver | Medicine, biomedical sciences |
| AMA | American Medical Association journals |
| ACS | Chemistry |
| ACM | Computing, information technology |
| Turabian | Student papers, adapted from Chicago |
| BibTeX | Raw BibTeX entry for LaTeX workflows |
TIP
You can set a default citation style per project. When inserting citations into a LaTeX document, the BibTeX style is used automatically; for Markdown or plain-text contexts, your chosen style is applied.
Import & Export
Export Formats
| Format | Extension |
|---|---|
| BibTeX | .bib |
| RIS | .ris |
| CSL-JSON | .json |
| Zotero RDF | .rdf |
| EndNote XML | .xml |
Import Sources
The library can pull metadata and PDFs from 14 sources.
| Source | Content |
|---|---|
| Semantic Scholar | Computer science, biomedical, broad academic |
| CrossRef | DOI resolution, broad academic metadata |
| arXiv | Preprints in physics, math, CS, biology, and more |
| PubMed | Biomedical and life sciences |
| DBLP | Computer science bibliography |
| OpenLibrary | Books and book metadata |
| Google Books | Book metadata and previews |
| Unpaywall | Open-access PDF links for DOIs |
| DOI lookup | Direct DOI-to-metadata resolution |
| ISBN lookup | Book metadata from ISBN |
| arXiv ID lookup | Direct arXiv paper import |
| PMID lookup | PubMed article import |
| URL import | Metadata extraction from web pages |
| Manual entry | Full manual form for any item type |
WARNING
Some sources enforce rate limits. Sciorex queues requests automatically, but bulk imports of hundreds of items may take a few minutes to complete.
Organization
Collections
- Create hierarchical collections and subcollections
- Assign custom colors and icons to each collection
- Drag-and-drop items between collections
- An item can belong to multiple collections
Tags
- Free-form tags on any item
- Tag autocomplete from existing tags
- Filter the library by one or more tags
Reading Status
| Status | Description |
|---|---|
| To Read | Queued for reading |
| Reading | Currently in progress |
| Read | Finished |
| Archived | No longer active, kept for reference |
Ratings
Rate items from 1 to 5 stars for personal prioritization and filtering.
Metadata
Each item supports 23 custom field types beyond the standard bibliographic fields.
| Field | Example |
|---|---|
| Funding | "NSF Grant #1234567" |
| ORCID | Author ORCID identifiers |
| Affiliations | Institution names per author |
| License | CC-BY-4.0, MIT, etc. |
| Replication status | Replicated, not replicated, partially replicated |
| Code repository | GitHub/GitLab URL |
| Dataset URL | Link to associated data |
| ... and 16 more |
The library also supports 35 creator types (author, editor, translator, director, interviewer, etc.) with full name and institutional affiliation fields.
Notes
- Attach notes to any library item
- Associate notes with specific page numbers in linked PDFs
- Link notes to annotations made in the PDF viewer
- Markdown formatting supported in note content
TIP
When you highlight a passage in the PDF viewer, you can create a linked note that automatically records the page number and highlighted text as a quote block.
Search
Full-text search across your entire library with advanced filtering.
| Filter | Options |
|---|---|
| Item type | Any of the 43 types |
| Reading status | To read, reading, read, archived |
| Tags | One or more tags (AND/OR logic) |
| Collection | Any collection or subcollection |
| Year | Single year or range |
| Rating | Minimum star rating |
| PDF availability | Has PDF, no PDF |
Citations
- In-text formatting — Generate parenthetical or narrative citations in your chosen style
- Bibliography generation — Produce a formatted reference list from selected items or an entire collection
- Clipboard export — Copy a formatted citation to the clipboard with one click
- LaTeX integration — Insert
\cite{}commands directly into the editor with autocomplete from the library
Duplicate Detection
The library automatically detects potential duplicates using two identifiers:
- DOI matching — Items with the same DOI are flagged
- arXiv ID matching — Items with the same arXiv identifier are flagged
INFO
When a duplicate is detected on import, you are prompted to merge, skip, or keep both entries. Merging combines metadata from both records, preferring the more complete fields.
Paper-to-Ticket Linking
Library items can be linked to project tickets for traceability.
- Auto-suggestion — When creating a ticket that references a paper (by DOI, title, or citation key), the library suggests linking it
- Bidirectional links — View linked tickets from the library item, and view linked papers from the ticket
- Useful for literature review tracking and research task management
AI Integration via MCP
The following MCP tools enable AI agents to manage the reference library programmatically.
| Tool | Description |
|---|---|
library_add_item | Add a new item to the library with metadata |
library_list_items | List items with optional filters (type, collection, tags, search query) |
library_update_item | Update metadata fields on an existing item |
library_manage | Manage collections, tags, and organizational structure |
library_add_note | Add a note to a library item, optionally linked to a page number |
library_get_item | Retrieve full metadata and notes for a specific item |
library_delete_item | Remove an item from the library |
library_list_collections | List all collections with their item counts |
library_list_tags | List all tags with usage counts |
TIP
Ask the AI assistant to "add all papers from this bibliography to the library" or "find and import the top 10 cited papers on transformer architectures." The agent uses these tools to automate bulk operations.
Related
- LaTeX Editor — Write papers with integrated citation insertion
- PDF Viewer — Read and annotate linked PDFs
- Paper Discovery — Find new papers and add them to your library
- MCP Servers — Full list of AI-accessible tools