User Manual

OS-APS is a web-based tool for preparing academic manuscripts for publication. You import a Word document, edit the content and metadata, and produce export-ready files such as PDF, JATS XML, EPUB, and HTML.

This guide walks through the full workflow from import to export.

Quick start

Try the demo with the example manuscript to follow along.

Before you begin

Make sure you have your .docx manuscript ready with the latest changes.

Step 1: Import your document

Open your OS-APS project. The import screen always lets you upload a manuscript. Some instances also show an optional AI-Assisted Import panel on the right.

Upload the file

Click Upload a manuscript (docx) and select the Word file from your computer. Uploading starts the import process automatically.

OS-APS import screen showing Docx and LaTeX format options, manuscript preparation steps, and an Upload a manuscript (docx) button

You can add authors, references, and alt text manually in the editor after import.

Optional: AI-assisted import

If your instance has AI-assisted import enabled, you see an AI-Assisted Import panel on the right side of the import screen before upload.

If you do not see this panel, AI-assisted import is not enabled for your instance. Instance administrators can set it up using the AI-assisted import setup instructions.

OS-APS import screen showing Docx and LaTeX format options, manuscript preparation steps, and an Upload button on the left, with an AI-Assisted Import panel on the right listing toggles for Basic Structural Recognition, Authors and Affiliations, References and Citations, In-Text Citations, and Image Alt Text Generation

The import screen with upload button on the left and optional AI settings on the right.

Enable only the options your document needs:

Setting	What it does	When to use it
Basic Structural Recognition	Detects headings, paragraphs, lists, tables, and captions	Always leave this on
Authors and Affiliations	Reads author names, ORCID, emails, and affiliations into structured metadata	When author information is present at the top of the manuscript
References and Citations	Extracts the reference list into a structured bibliography that supports citation styles	When references are plain text, not managed by a citation tool like Zotero
In-Text Citations	Matches citation markers in the text (like `[1]` or `(Smith, 2024)`) to the extracted references	Turn on together with References and Citations
Image Alt Text Generation	Creates descriptions for figures and tables	When your figures lack alt text and you need accessible output

Review the import preview

After the file processes, review the detected content before opening the editor.

If AI-assisted import is not enabled, the summary shows the structural elements found during rule-based parsing.

Import verification screen showing a document preview on the left with detected headings, authors, and references, and a Verify document panel on the right with a summary of detected elements and a Next button

If AI-assisted import is enabled, the summary can also show detected references and other AI-assisted results.

Import verification screen with a document preview on the left and a Verify document summary on the right showing detected headings, authors, affiliations, references, and figures

Check whether the detected counts look reasonable. For example, if your document has 10 references but only 3 were detected, re-import with different AI options or fix the missing items manually later.

When you are satisfied with the preview, click Next to proceed to editor where you edit the document and its metadata.

Import review screen showing the parsed document preview, a verification summary panel, and a Proceed to Make edits button at the bottom right

Click "Next (Proceed to Make edits)" to continue to the editor.

Tip

After import, always review what was detected. You can correct mistakes in the editor.

Step 2: Edit your document

The editor has a document body on the left and a sidebar on the right. The sidebar has several panels you can switch between using the icons along the right edge.

Document outline

Editor showing the Document Outline panel with heading structure

The Document Outline panel shows the heading structure of your manuscript.

Use the outline to navigate long documents and check that all headings were recognized correctly. If a heading is missing or has the wrong level, click the heading button that appears to the left of the paragraph text to change it.

Managing authors

Authors panel showing a list of four authors

The Authors panel lists everyone associated with the manuscript. Drag to reorder, or click an author to edit their details.

Author metadata editing form with name, ORCID, email, and affiliation fields

For each author you can set their name, ORCID, email, role, and affiliations. Paste a 16-digit ORCID to auto-fetch affiliation data. Click Save when done.

Managing references

References panel showing bibliography entries with Citations in text dropdowns

The References panel shows all bibliography entries. Each reference has a "Citations in text" dropdown that shows where it appears in the document.

Click a reference to edit its metadata.

Reference metadata editing form showing type, title, and author fields

You can change the reference type (Journal Article, Book Chapter, etc.), title, authors, and other fields. This metadata determines how the reference appears in your chosen citation style.

Working with in-text citations

In-text citation editor showing the citation generator and linked reference

Click a citation marker in the document text to open the citation editor. The Citation Generator shows a preview of how the citation will look in your chosen style. You can link the citation to a different reference, or combine multiple references into a single citation.

Saving your work

Click Save changes in the top-right corner of the editor. Always save before exporting — the editor warns you if there are unsaved changes.

Step 3: Export your document

Select a template

Open the Template Configuration panel from the sidebar (the last icon on the right).

Click the Template dropdown and choose the template that matches your publication type.

Available templates include Journal Article, Report, and Monograph. Each template controls the layout, citation style, and structure of your export.

Save and download

After selecting a template, you see its description and a citation style selector.

Template configuration with an orange unsaved changes warning

Save before you export

If you see an orange "Document has unsaved changes" warning, click Save changes in the top-right corner first. Otherwise your export will not include your latest edits.

Once saved, click Download PDF to export a PDF.

Other export formats are also available:

Reader -- an interactive, responsive web version of your document (see a live example)
Reader Snapshot -- a self-contained archive of the Reader for hosting on your own website
JATS XML -- for indexing services and archival (NISO JATS 1.3)
HTML -- a standalone web page
EPUB -- for e-readers and distribution platforms
Data Snapshot -- a ZIP of all structured data
OJS XML -- for Open Journal Systems

Check your export

Open the exported file and spot-check:

Does the title page look right?
Are all authors and affiliations present?
Do citations match the reference list?
Are figures and tables in the right places?

If something is off, fix it in the editor, save, and export again.

Troubleshooting

The Word file does not import

For the Word import workflow, use a single .docx file. Older .doc files, PDFs, and Google Docs links are not supported in this upload step.
If the import stalls, refresh the page and try again.

The exported file does not show my latest edit

This usually means the document had unsaved changes at export time. Save, then export again.

References or citations are missing or wrong

If references were plain text in the Word file, try re-importing with References and Citations enabled.
You can always add or edit references manually in the References panel.
For in-text citation mismatches, click the citation in the text and re-link it to the correct reference in the citation editor.

I don't see AI settings on the import screen

AI-assisted import must be enabled by your instance administrator. If the settings panel is missing, your instance does not have this feature configured.
Point your administrator to the AI-assisted import setup instructions.
You can still import documents without AI. Structural elements like headings and lists are detected using rule-based parsing, and you can add authors, references, and alt text manually in the editor.

Next steps

Journal publishers: See the Journal Workflow for template customization, layout options, and export details.
Book publishers: See the Monograph Workflow for book-specific features like table of contents and double-sided printing.
Preparing manuscripts for import: See Tips for a checklist you can share with authors.