Literature library and citations

To find new papers online, describe your topic, date range and selection criteria in a conversation, then review the proposed records in Library → Inbox. See the topic-search journal-club workflow. Search references filters records already in the Library; it does not run an online literature search.

The Library is a shared local bibliography. Projects and collections link to its records; adding the same paper to another collection does not require another copy. This guide uses the three real PRISMA papers from the core-reading workflow. That workflow owns the research goal and acceptance checklist; this page explains the Library's controls and record lifecycle.

To reuse a figure or table from an attached PDF, follow PDF extraction. Metadata import and automatic full-text retrieval do not themselves extract figures or tables.

Choose the correct view

Open Library from Home or the workspace. Back to Home returns to project navigation. The Library's Settings opens citation styles, not global Model settings.

View	Contains	Use it for
Inbox	Agent-discovered candidates awaiting your review	Check identities and sources before acceptance
All references	Accepted active records	Search, edit and organize your bibliography
Duplicates	Suspected identifier/metadata match groups	Compare before merging
Trash	Removed reference records	Restore or deliberately delete permanently
Project	References linked to that project	Keep the bibliography relevant to a research question
Collection	A thematic group, including nested collections	Reuse a reading set across projects

Add or import a record

Select Add and choose the source. Selecting one PDF opens its metadata editor; selecting several opens Import PDFs.

Entry	Input	Check before saving
Add reference	Manually entered bibliography	Required title, reference type and identifiers
Import PDF	One or several local PDFs	Extracted metadata against each paper; multi-file selection uses the batch flow below
Import references	BibTeX, RIS or NBIB	Valid/invalid entries, destination and identifier matches

Import a folder's selected PDFs

Import a folder's selected PDFs

1. Select the PDFs for the reading set. Wait for metadata extraction; a detected DOI can be used to complete bibliographic fields. Check the result against the paper.
2. Check the destination displayed beside Import to; it comes from the Library view where you started the import. Under When identifiers match, choose a policy from the table below.
3. Use each checkbox or Select all to choose this batch. Show more reveals additional listed files.
4. Select Import selected. Read the overall progress and each file's status; a failed file is not a completed import.
5. To stop, select Stop and wait for Stopping… to settle. Already committed references remain; an in-flight operation may finish.
6. After stopping, select the remaining Ready files and use Import selected. If the dialog offers Retry unfinished after a failure, use it for the unfinished selection. Inspect any retained reference before starting a fresh import, particularly if its PDF upload was interrupted.
7. Use Done or Close when the dialog offers it, then open the destination and verify its records and PDFs. Cancel abandons preparation before import.

Identifier-match policy	Result
Reuse existing reference	Reuse the matching record instead of creating another bibliography entry
Keep as separate reference	Keep a distinct record for later comparison and duplicate review
Fill empty fields	Fill missing fields while retaining existing/conflicting values

The batch can show Pending, Reading…, Ready, Importing…, Completed, Failed or Skipped. Selection, metadata readiness and import completion are separate states. If the app reports PDF upload cancelled. The reference was kept., check that retained record's attachments; cancelling the upload did not remove the bibliography entry.

With Reuse existing reference, a PDF whose extracted title or DOI does not match can still create a separate record. After import, open each paper and confirm its title and DOI. Correct mismatches before merging duplicates. Completed confirms import, not accurate identification.

Stop a batch without losing completed work

Stop a batch without losing completed work

A Stop request allows the current item to finish. Inspect every row: Completed items are retained and cannot be selected again; select remaining Ready rows and use Import selected to continue. If failures expose Retry unfinished, correct the reported cause before retrying and check that completed records were not duplicated.

The reference was kept. Retry to finish adding its PDF. means the bibliography entry was saved but its attachment is unfinished. Check that the original PDF is still available at the selected location and opens normally, then select Retry unfinished. After retrying, return to the destination collection and open the PDF to check its content. If the result could not be confirmed, inspect your library before starting another import.

Bring a bibliography from another reference manager

Bring a bibliography from another reference manager

Worked example Import PRISMA records with three matching policies

Open the destination collection first, then choose Import references and a .bib, .ris or .nbib file. The preview reports the detected format, destination, new/existing/skipped counts and matching records. Expand View details to inspect titles and authors before importing. Bibliographic imports do not download PDFs.

Choice	Checked result with the PRISMA statement
Keep as separate reference	BibTeX created one record; Duplicates then contained one matching-DOI group
Reuse existing reference	RIS reused one record, with zero created, skipped or failed
Fill empty fields	The PubMed NBIB record added PMID 19621072 and PMCID PMC2707599; existing title and five creators remained

Click Import references, wait for Import complete, inspect Created/Reused/Skipped/Failed, then select Done. Reopen the record: an import count alone does not establish correct metadata. Filling empty fields can add identifiers and an abbreviated journal name without replacing the full journal title.

Review Inbox evidence

Worked example Review three PRISMA candidates

Open the candidate title or View details. Inspect its provider, source link and DOI/other identifiers, then compare year, author order and publication with the publisher. Accept promotes it into the Library; Dismiss removes it from the review queue. Check the row selection before batch actions.

In this example, the three candidates were accepted individually, and Inbox became clear. A provider match is a starting record, not complete bibliographic validation. The 2020 statement's publication year is 2021. The two 2009 papers have distinct DOIs and author lists.

Inspect and correct metadata

Open a reference, then More actions → Edit metadata. Review the current values before using Complete metadata, which performs a lookup rather than a purely local edit.

Field/control	Input and effect
Reference type	Select the bibliographic kind: article, review, preprint, book, dataset and other supported kinds
Title	Required; preserve the published title
Year / Publication	Publication year and journal/container; a year embedded in the title may differ
Advanced settings	Volume, Issue, Pages, Publisher, Place and Edition
Add creator / Remove creator	Add or remove a creator row in the draft
Creator role	Choose Author, Editor or Translator to match the source
Name type → Person	Enter Given name and Family name
Name type → Organization	Enter the complete organization name; do not split it into invented person names
Add identifier	Type and value: DOI, PMID, PMCID, ARXIV, ISBN, ISSN or OTHER
Preferred for DOI / ISSN, etc.	Choose the preferred identifier within that type; the choice is not one global flag across all types
Remove identifier	Remove the draft identifier row
URL / Abstract	Source address and bibliographic summary
Save	Persist valid edits
Cancel / Close	Discard the draft

Worked example Preserve The PRISMA Group as an organization author

To add The PRISMA Group, select Add creator → Creator role: Author → Name type: Organization, enter the full name and Save. Reopen the record and check that the organization follows its four personal authors. Compare the generated citation with the publisher's author list.

Organize the accepted records

Create a collection with New collection, fill Name and optional Description, then Create collection. The description is organizational text, not Agent Context. Cancel/Close discards the draft. Select records in All references and use Add to collection or Add to project. Selection clears after the operation; reselect if adding another destination.

In a detail view, project and collection checkboxes show the links. Manage Tags adds organizational tags. The table's one-to-five-star rating is your annotation, not an automatic evidence-quality score. Clear selection leaves the records unchanged.

Table control	Scope
Search references	Bibliographic fields including title, creators, publication, identifiers, abstract and notes
Sort references	Choose the displayed order
Filters	Narrow by the available type, year, tag and full-text conditions
Customize	Choose/reorder displayed columns
References per page	25, 50 or 100 rows
Row checkbox / Select all	Set the targets for the available bulk actions
Export	Export selected bibliographic records; it does not automatically package all PDFs

The total library count is independent of the current search/filter result. Read the displayed view and selection counts before a batch action; a smaller filtered result does not mean records were removed.

Clear search and filters before concluding a record has disappeared. Project/collection links do not create independent metadata versions for each destination.

Add and read full text

Find full-text PDF checks applicable public providers: Europe PMC/PMC, OpenAlex, Unpaywall and arXiv. Available identifiers and configured contact/credentials determine applicability. Inspect the source, version label and URL before Add attachment.

Worked example Attach the publisher PDF to the PRISMA 2020 record

If Add attachment fails after a source is found, download the publicly available PDF from the publisher and use Add PDF on the same record. Open the attached PDF and compare its title and DOI with the publisher record. In this example, Preview prisma-2020-statement.pdf shows the matching PRISMA 2020 paper: 806.1 KB and 15 pages.

A source result is not a saved attachment. An attached PDF is not proof of agent reading. Read with agent supplies context for a subsequent request. A Composer @ reference can select an exact record, a project Library or a Collection: a collection grants retrieval scope, not automatic inclusion of every paper's full text. PDF reading controls are in Previews.

If no public copy is found, retain the checked metadata and use a legitimately available local PDF when appropriate. Background lookup/download tasks can expose pause-after-current, resume, review and cancel controls; cancellation does not imply that completed earlier items are undone.

Retrieve full text in batches and resume later

Retrieve full text in batches and resume later

1. Select the intended records in the Library and open the selection's More actions → Find full-text PDF.
2. After searching starts, choose Pause when needed. The current item finishes before the task pauses.
3. Check Checked and Pending, then select Continue search. After closing the panel, return to the same task through Background tasks → Open.
4. Review each candidate source and warning before selecting items and clicking Add selected.
5. Downloading also supports pause and Continue download. Inspect the final Added / Failed / Skipped states and reopen any successfully added attachment.
6. To discard an unwanted review-ready task, use Remove task in Background tasks. After removal, confirm that the task is gone and that its references and attachments still open. Removing the task does not delete them.

A paused search retains its checked and pending records. After continuing or reopening the task, inspect the final counts and each item’s outcome. Candidate discovery and successful PDF attachment are separate results.

A source exists but the PDF cannot be added

A source exists but the PDF cannot be added

For PDF could not be added, check source sign-in requirements, link validity, the displayed size limit and the current proxy/DNS configuration. Avoid creating duplicate references as a retry mechanism.

If a PDF source resolves to a reserved address such as 198.18.x.x, the downloader rejects it. Follow Network to restore verifiable public resolution, then retry; do not disable the address check. If you already have a legitimately downloaded PDF, use Add PDF and verify its title, DOI and page count.

Format and copy citations

Open More actions → Citation. Select Citation style, inspect the reference and in-text form, then choose Copy reference, Copy in-text citation, Copy BibTeX or Copy RIS as needed. Check names, year, punctuation and DOI against the source before reuse. The corresponding representation does not repair an incomplete record.

Manage citation styles… opens style management. The bundled set includes APA, MLA, Chicago author-date, Vancouver, IEEE, Nature, AMA and Harvard. Preview shows a style sample, Browse styles opens the external style catalog, and Import CSL imports a local style file. The PLOS CSL import and its application are verified below. Copy and export are separate operations; check both when moving a bibliography.

Check a real citation after importing a journal style

Check a real citation after importing a journal style

Worked example Apply the PLOS citation style to a PRISMA record

In Library → Settings → Import CSL, choose the independent plos.csl file from the CSL styles repository. In this example, Imported styles increased from zero to one and showed Public Library of Science. Return to the real PRISMA record's Citation panel and select that style under Citation style. Check the numbered reference and [1] in-text citation. The style-management preview uses a sample article; inspect your actual record before copying a citation.

Copy a citation or export reusable records

Copy a citation or export reusable records

Worked example Copy and round-trip PRISMA citation records

The four Citation copy buttons write different representations to the clipboard. Paste into your intended editor and inspect the result before leaving the panel.

Button	Result checked for PRISMA 2009
Copy reference	APA reference retained the four personal authors, The PRISMA Group, year and DOI
Copy in-text citation	(Moher et al., 2009)
Copy BibTeX	An @article entry with the organization author enclosed in braces
Copy RIS	A TY - JOUR record with author, title, year and DOI fields

For a file, close Citation, select the required table rows and choose Export → BibTeX or RIS. Choose the location in the system save dialog and wait for Saved. These files contain bibliographic records, not a PDF attachment bundle. Reimport the saved file into a test collection with Reuse existing reference and check its match count. Both exported PRISMA files were reimported and reused the existing DOI without creating another record.

BibTeX stores year and month here, so its round trip returned 2009-7; RIS retained 2009-07-21. Check date precision when merging. Plain RIS author fields may not preserve a separate organization-name type in another manager; inspect the imported creator editor when that distinction matters.

Resolve duplicates and recover references

Worked example Merge and restore a PRISMA record with its attachments

Keep one record and its attachments

Keep one record and its attachments

1. Open Duplicates → Review duplicates. The view scans active Library records, not just the current collection.
2. Under Keep reference, choose the record with the verified identity. Compare DOI, creators, attachment counts and date added. Show all fields reveals fields hidden by the conflict-focused view.
3. For each conflicting field, select its source. In the PRISMA BibTeX comparison, choose the full 2009-07-21 publication date over 2009-7. Empty fields can be filled from the other record.
4. Read After merging and its attachment, collection and project counts. Only then select Merge references; Cancel leaves the records separate.
5. Reopen the survivor and verify metadata, links and PDF contents. The merged-away record appears in Trash as Merged duplicate.

A PDF with an extracted filename in place of its title may not enter a duplicate group. Correct its title and DOI using the publisher record, then review the matching group. After merging, confirm the retained PDF opens and collection/project associations are still present.

Restore an accidentally removed reference

Restore an accidentally removed reference

Use the row's More actions → Move to Trash. It disappears from active Library, project and collection views. In Trash, search by title or identifier, open its row menu and choose Restore. Restore before editing, previewing or exporting: these controls are disabled in Trash. Reopen the original project and collections to verify the restored links. In this example, restoring the PRISMA record retained its PDF and all three links.

Permanently remove an unwanted duplicate

Permanently remove an unwanted duplicate

In Trash, choose More actions → Delete permanently and read the confirmation. Cancel preserves the row. Confirmation removes the selected references and metadata; unshared attached files are cleaned up afterward. Historical outputs are retained and search indexes expire separately, so this is not secure erasure. Export anything required before deleting.

After deletion, check that the selected record has left Trash and that the retained reference still opens with its attachments. Removing a collection link, moving a record to Trash and permanently deleting it have different scopes.

Attachment changes and concurrent edits

Before removing an attachment, read its deletion confirmation and verify the file/version being targeted. Use the available version history to inspect earlier attachment versions. Removing a PDF, moving its reference to Trash and permanently deleting a reference have different scopes; retained conversation evidence can restrict cleanup.

If another client changes a collection while your editor is open, a stale save can be rejected. Reopen the latest collection, compare its saved values with your intended change and retry against that state. A refresh or cleanup error after saving does not automatically mean the save failed: inspect the current record before repeating the action.

Sources: batch import, metadata editor, attachment history/deletion, concurrent edits.