1. The Main Screen

When you open EssentAI, the main article library screen is your central workspace. Everything in the application is accessible from here.

1.1  Menu Bar

The menu bar runs across the top of the window and contains all of EssentAI's features: File, Projects, Search Articles, Review Article, Notes Manager, View, Synthesis Matrix, Recommend Citations, Paraphrase, Search Databases, Resources and Help.

1.2  Filter Bar and Saved Filters

Directly below the menu bar is the filter bar. Type any keyword or phrase here to narrow the articles displayed in the table. As you type, the table updates to show only matching articles. The Clear Filter button removes the current search and Save Filter saves it for later reuse. In the top right corner, the word Active in green confirms the application is connected and ready.

Once you have applied a filter you want to keep, click Save Filter. A confirmation dialog will appear and the filter will be stored under View → My Searches, where it appears by name for easy retrieval. Clicking a saved search from that submenu immediately applies it to the library.

To remove a saved search you no longer need, go to View → My Searches, hover over the relevant search name, and right-click to reveal the Remove option.

1.3  Article Library Table

The main area shows your article library as a table. Each row is one article, with columns for: row number, Title, Authors, Year, Journal, Status, Flag, and PDF. At a glance, the table gives you a structured overview of your entire literature collection, making it easy to scan, sort, and navigate your work without having to open individual files.

The Status and Flag columns are particularly useful for managing your reading workflow. As your library grows, being able to see at a glance which articles are still to read, which are flagged for priority attention, and which have been excluded helps you stay focused and organised throughout your review. These are covered in detail in sections 1.4 and 1.5.

1.4  Flagging Articles and the Reading List

The Flag column lets you mark articles of interest for focused reading. Click the flag icon next to any article to flag it. The icon turns green to confirm. You can flag as many articles as needed.

To view only your flagged articles, go to View → Reading List → View Flagged. The library will update to show only flagged articles and the status bar will reflect the reduced count.

To unflag an individual article, click its green flag icon again. Once all articles have been unflagged, the full library returns automatically. To clear all flags at once, go to View → Reading List → Clear All Flags.

1.5  Setting Article Status

Each article in your library can be assigned a status label to reflect where it sits in your review process. The available labels are:

• To Read
• Reading
• Read
• Use in Writing
• Seminal Work
• Key Article
• Exclude

Each label appears in a distinct colour in the Status column for quick visual reference. Right-clicking on any article in the library opens a context menu with several options:

• Set Status — choose a label from the list above. The Status column updates immediately.
• References — opens the Reference Preview window for that article, showing the in-text citation and full reference in your chosen citation style such as APA7. From here you can copy the in-text citation, copy the full reference, or export it in RIS format for use in reference management software.
• Add to Project — assigns the article to a project. This is covered in Section 3.
• Delete Article — permanently removes the article record from your library. This cannot be undone, so use this option with care.

To filter the library by status, go to View → Status and select the label you want. The library will show only those articles. To return to the full library, go to View → Status → All Statuses.

1.6  Opening Articles

To open and read a full article, double-click the PDF icon in the PDF column on the right side of the table. The document will open directly for reading.

Reading articles within EssentAI is strongly encouraged as it allows you to engage fully with the application's review and annotation features. Each article also has an Article Details card providing an AI-generated summary covering the research problem, methodology, findings, and more. This is covered in detail in Section 5.

1.7  Status Bar

At the bottom of the screen, a summary line shows your current project name and the total number of articles in your library.

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2. Settings and API Key

EssentAI's AI features require an OpenAI API key. You manage this through the Settings window.

To open it: on Windows, click File in the menu bar and then click Settings. On macOS, go to EssentAI → Preferences.

2.1  Choose GPT Model

EssentAI offers two model options:

• Standard — strong academic outputs with disciplined structure and reliable extraction. Recommended for most journal article reviews, relevance screening, and structured summaries.
• Advanced — deeper synthesis and stronger integration across theory, constructs, methods, and findings. Best suited to theory-heavy papers, doctoral-level work, and complex multi-construct studies.

For most users, the Standard model is the right starting point.

2.2  API Key

Paste your OpenAI API key into the API Key field and click Save API Key. Your key is stored securely on your device and is never shared externally. If you need to verify the key that is saved, click the Show button next to the API Key field to reveal it.

To access the OpenAI platform directly from within EssentAI, click the Open OpenAI Dashboard button. This will open your browser and take you to platform.openai.com where you can manage your API keys and billing.

For step-by-step instructions on creating an OpenAI account, generating a key, and adding billing credit, see the FAQ: How do I add an OpenAI API Key.

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3. Projects

A project is how EssentAI organises your work. Each project holds its own collection of articles, keeping your library focused on a specific topic, paper, or research question. It is good practice to create a project before you add any articles.

3.1  Creating a Project

1. Click Projects in the menu bar.
2. Click Manage Projects.
3. Click Create Project.
4. Type a name that reflects your research focus.
5. Click OK.
6. Select the project from the list and click Open to begin working in it.

Once a project is open, the status bar at the bottom of the main screen will show the project name and article count.

3.2  Adding Articles to a Project

There are two ways to add articles to a project. The first is through Review Article in the menu bar, which analyses and adds a new PDF directly. The second is through Projects → Add Articles, which lets you select articles that are already in your library and assign them to the current project.

When using Projects → Add Articles, a window will open showing all articles in your library. You can use the search field at the top to filter articles by keyword, then select one or more articles from the list and click Add Selected to add them to the project.

3.3  The All View

As you build up multiple projects, the All option at the top of the Projects dropdown gives you a combined view of every article across all projects. This is useful when you want to find or reuse an article you have already reviewed without re-importing it.

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4. Searching for Articles

EssentAI includes a built-in search tool that queries credible academic sources directly from within the application.

4.1  Running a Search

1. Click Search Articles in the menu bar.
2. Type your search terms in the Query field. Keywords or a short descriptive phrase work well.
3. Set the number of Results (5, 10, 15, or 20) and a Date range if needed.
4. Optionally, tick Broaden search with AI to expand results beyond your exact terms. This uses your API key and is best suited to exploratory searches.
5. Click Search.

4.2  Search Results

The results window shows a table with Title, Authors, Year, Journal or Source, DOI, and Link. Click Open on any row to view the article in your browser.

• If the article is open access, you can download it directly from the publisher's page.
• If it is behind a paywall, copy the title and search for it through your university library or library service.

Use Find more at the bottom of the results window to retrieve the next page of results without starting a new search. Use Save Search to save the query for later. Saved searches do not use any API tokens when reopened.

4.3  Saved Searches

Click the Saved Searches tab in the Search window to view and reopen any previously saved search. Select a search from the list and click Open to reload those results instantly.

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5. Adding and Reviewing an Article

Once you have downloaded an article as a PDF, you can add it to your project and have EssentAI analyse it automatically.

5.1  Adding an Article

1. Click Review Article in the menu bar.
2. Navigate to your saved PDF, select it, and click Open.
3. A progress window will appear while EssentAI reads the PDF and extracts the key academic content. This may take a moment depending on the length of the article.

5.2  The Article Details Window

Once processing is complete, the Article Details window opens and the article is added to your project library. The window displays fields extracted from the article:

• Title
• Reference
• Summary
• Research gap
• Research problem
• Theories and Frameworks
• Key Constructs and Concepts
• Methodology
• Key findings

Read through these fields carefully for each article you add. The Article Details card is designed to help you quickly assess whether an article is relevant to your research before committing time to reading it in full.

5.3  Actions Available

• Read Article — opens the full PDF.
• Notes — opens the Notes window for this article.
• Export RIS — exports the article's reference data in RIS format for use in reference management software such as Zotero, Mendeley, or EndNote. It is good practice to open the imported reference in your reference manager and verify the details are correct before using it in your writing.
• Close — returns you to the main library.

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6. Taking Notes

EssentAI includes a notebook system that lets you capture and organise passages from your articles, with automatic citation insertion.

6.1  Opening the Notes Window

From the Article Details window, you can select any text you want to capture by clicking and dragging with your mouse, then right-clicking and choosing Copy. When you open the Notes window, you can paste the copied text directly into your notebook.

To open the Notes window, click the Notes button at the bottom of the Article Details window. A prompt will ask you to select an existing notebook or create a new one. To create a new notebook, type a name that reflects the theme you are capturing and click OK.

6.2  Inside the Notebook

The notebook editor provides a writing space for capturing and organising your notes. The toolbar includes:

• Basic formatting: Bold, Italic, Underline
• Font and size controls
• A citation style dropdown with the following options: APA7, Harvard, Chicago and Vancouver
• Insert Citation — adds a formatted citation for the current article at the cursor position in your chosen style
• Paraphrase — uses the AI to rephrase selected text

When you have finished, click Save. If there are unsaved changes, a reminder will appear in red at the bottom right of the notebook window. The editor also displays a live word and character count at the bottom of the writing area.

6.3  Notes Manager

The Notes Manager gives you a central view of all your notebooks. To open it, click Notes Manager in the menu bar.

The Notes Manager displays a list of all your notebooks with their creation and last modified dates. Selecting a notebook from the list shows a preview of its contents on the right, along with a word and character count. From here you can:

• Open — opens the selected notebook in the full editor
• Create Notebook — creates a new blank notebook
• Rename — renames the selected notebook
• Delete — permanently removes the selected notebook
• Close — closes the Notes Manager

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7. Matrix Views

EssentAI includes four matrix views for analysing and synthesising patterns across your article library. Each view approaches your literature from a different angle, helping you identify connections, gaps, and structures that would be difficult to see by reading articles individually.

7.1  Opening a Matrix View

To open any matrix view, click Synthesis Matrix in the menu bar. A dialog will appear asking you to select a matrix view. The four options are:

• Synthesis Matrix — cross-article field intersection analysis
• Overlap Grid — visual mapping of shared concepts across articles
• Components Matrix — structured breakdown of article components
• Themes Matrix — thematic grouping across your library

Select the view you want and click Open.

7.2  Synthesis Matrix

The Synthesis Matrix is a cross-article analysis tool that shows how often two extracted field values appear together across your visible article set. It is one of EssentAI's most powerful features for identifying patterns, gaps, and connections in your literature.

Building the Matrix

The matrix window has three controls at the top:

• Rows — choose the field to display as row labels
• Columns — choose a different field to display as column headers
• Occurrences — filter cells by minimum frequency: All, 2+, 3+, or 5+

Both the Rows and Columns dropdowns offer the same set of fields to choose from: Theory, Constructs, Method, Sample, Source, Key findings and Research gap. You must select two different fields. Once selected, click Build matrix.

Reading the Matrix

Once built, the matrix displays a grid where each cell shows how many articles share that particular row and column combination. Cells with higher counts are shaded more intensely, making high-frequency intersections easy to spot at a glance.

A summary bar above the grid shows key statistics for the current matrix:

• Rows — total number of unique row values found
• Columns — total number of unique column values found
• Populated cells — number of cells with at least one article
• Articles represented — number of articles contributing to the matrix
• Peak cell — the highest intersection count in the matrix

Blank cells mean no article in your current set uses both values together.

Drilling Into a Cell

Double-clicking any populated cell opens the Articles in this matrix intersection window, which lists every article contributing to that cell, showing their title, author, and year. Clicking on any article in that list opens its full Article Details card, where you can read the AI-generated summary, access the PDF, take notes, or export the reference.

7.3  Overlap Grid

The Overlap Grid compares every pair of articles in your visible library and shows how much they have in common. Where the Synthesis Matrix looks at how field values intersect across articles, the Overlap Grid focuses on article-to-article similarity, making it useful for identifying clusters of closely related sources and spotting outliers.

Building the Grid

The Overlap Grid has four controls at the top:

• Included fields — a multi-select dropdown where you choose which extracted fields to include in the comparison. Available fields are: Theory, Constructs, Method, Sample, and Source. You can select any combination. The default is four fields selected.
• Occurrences — filters cells by minimum overlap count: All, 2+, 3+, or 5+. Use this to hide low-overlap pairs and focus on the most meaningful connections.
• Build overlap — builds the grid based on your selected fields and filters.
• Sort by overlap — reorders the articles so the most connected sources appear first, making high-overlap clusters easier to identify.

Once your fields are selected, click Build overlap to generate the grid.

Reading the Grid

The grid displays all articles as both rows and columns. Each cell shows the number of extracted values two articles share across your selected fields. Cells with higher overlap counts are shaded more intensely. Diagonal cells show Same to indicate an article compared with itself.

A summary bar above the grid shows:

• Sources compared — total number of articles in the grid
• Compared pairs — total number of article pairs evaluated
• Overlapping pairs — number of pairs sharing at least one value
• Highest overlap — the maximum overlap count found between any two articles
• Average overlap — the mean overlap count across all pairs

Drilling Into a Cell

Double-clicking any populated cell opens the Shared Evidence Between Sources window. This shows the full details of both articles and breaks down the comparison into three sections:

• Shared values — the extracted values both articles have in common, grouped by field
• Only in Source A — values unique to the first article
• Only in Source B — values unique to the second article

From this window you can open the Article Details card or the full PDF for either source directly, using the buttons at the bottom of the window.

7.4  Components Matrix

The Components Matrix displays one extracted field from every article side by side, letting you read and compare a single component — such as the research problem, methodology, or summary — across your entire visible article set in one view. It is particularly useful for identifying patterns, recurring concepts, and gaps when you want to read across articles rather than count intersections.

Setting Up the View

The Components Matrix has two controls at the top:

• Compare field — select which extracted field to display across all articles. Options are: Summary, Research gap, Research problem, Theories / Frameworks, Key Constructs / Concepts, Methodology, and Key findings.
• Sort — control the order articles appear in the list. Options are: Title A to Z, Author A to Z, Year ascending, Year descending, Selected field present first, and Selected field longest first.

The main panel shows a table with each article as a row. The left columns show the Title and Author / Year, and the wide right column displays the full text of the selected field for each article. Recurring terms are highlighted in bold across all rows so shared concepts are easy to spot at a glance.

The Article Panel

Clicking any article row in the list opens a detail panel on the right side of the window. This panel shows:

• Article details — title, authors, year, selected field, and coverage (how many articles in the current set are populated for that field)
• Common across articles — a list of terms or concepts that appear in multiple articles within the current set, each showing a count. Clicking any term filters the main list to show only the articles containing that term.
• What distinguishes this article — an analysis section showing recurring concepts in the selected article and what is not covered compared to the rest of the set

AI-Assisted Analysis

The What distinguishes this article section includes an AI assisted toggle and an Analyse button. With AI assisted enabled, clicking Analyse generates a written analysis identifying how the selected article differs from the rest of the comparison set, organised under named themes such as focus, framing, and scope. This requires your OpenAI API key to be active.

With AI assisted disabled, the section shows a basic summary of recurring concepts and what terms are not covered in the selected article, based on extracted field metadata only.

Opening the Full Field Text

Double-clicking any cell in the main content column opens a popup window showing the full text of that field for the selected article. The popup includes a Copy button so you can copy the text directly for use in your notes or writing.

From the article panel you can also open the full Article Details card, the PDF, or copy an excerpt using the buttons at the bottom of the panel.

7.5  Themes Matrix

The Themes Matrix extracts every unique concept from your visible articles and shows which articles contain each one. Where the Synthesis Matrix counts intersections between two fields, the Themes Matrix gives you a full inventory of every concept across your library and tells you exactly where each one appears. It is particularly useful for mapping the conceptual landscape of your literature and identifying which themes are widely shared, which are unique to one article, and which are rare but repeated.

How It Works

EssentAI identifies concept labels from structured fields including Theories, Constructs, and Research gaps. Each unique concept becomes a row in the matrix. The columns are your visible articles. A cell is populated when that article contains evidence for that theme.

The window opens with the full matrix already built. Click Rebuild at any time to refresh the matrix after changing your visible article set.

Controls

The toolbar at the top contains five controls:

• Concept search — type any keyword and click Find to filter the theme list. Supports AND (both words must appear in the same field) and OR (either word returns a match). Case insensitive.
• Occurrences — filter themes by how widely they appear across your article set. Options are: All, Unique only, Shared themes, Rare but repeated, Widely shared, and Most shared theme.
• Sort — control the order themes appear. Options are: Alphabetical, Most frequent first, Least frequent first, Coverage high to low, and Origin then theme.
• Articles — shows the total number of articles contributing to the current matrix.
• Rebuild — rebuilds the matrix from the current visible article set.

Reading the Matrix

The stats bar above the table shows:

• Themes — total number of unique concepts found across all articles
• Shared — number of themes that appear in more than one article
• Unique — number of themes that appear in only one article
• Most shared theme — the concept appearing in the most articles, with its count
• Richest source — the article contributing the most themes, with its count

Each row in the table shows the theme name, how many articles contain it, its coverage as a percentage of the total article set, and its origin field (Theory or Construct). The remaining columns show one per article, with the concept text displayed in any cell where that article contains it.

Selecting a Theme

Clicking any theme row selects it and opens the detail panel on the right side of the window. The panel shows the theme name, article count, coverage percentage, origin field, and a Supporting articles list showing every article that contains that theme. Clicking an article in the supporting list highlights it.

From the panel you can also:

• Open evidence — opens the full evidence for the selected theme in the selected article
• Article details — opens the Article Details card for the selected article
• Open PDF — opens the full PDF for the selected article
• Clear search — clears the current concept search filter

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8. Recommend Citations

The Recommend Citations feature searches your entire article library and returns the articles most semantically relevant to a sentence or paragraph you provide. It is useful when you are writing and want to quickly identify which articles in your library best support a specific point or argument.

8.1  Running a Recommendation Search

1. Click Recommend Citations in the menu bar.
2. The Article Recommendation window will open. Type a sentence or short paragraph in the text field that reflects the point you are trying to support.
3. Click Find Relevant Articles.
4. A progress window will appear while EssentAI searches your library. This may take a moment depending on your library size.

8.2  Reading the Results

The Recommended Articles window displays a ranked list of articles from your library, showing Author, Year, Title, and a relevance Score. The score represents semantic similarity between your query and each article. Higher scores indicate stronger relevance to your input.

Double-clicking any row in the results list opens the full PDF for that article directly in your PDF viewer, so you can read and verify the content before citing it.

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9. Paraphrase

The Paraphrase tool lets you rewrite a sentence or passage using the AI. It is available both as a standalone tool from the menu bar and as a button inside the notebook editor.

9.1  Using the Paraphrase Tool

1. Click Paraphrase in the menu bar to open the Paraphrase Tool window.
2. Paste or type the text you want to rewrite into the upper field.
3. Click Paraphrase.
4. The rewritten result will appear in the Paraphrased Result field below.
5. Click Copy Result to copy the output to your clipboard, or Try Again to generate a different version.
6. Click Close when finished.

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10. Search Databases

The Search Databases menu provides direct links to major academic databases, opening them in your browser so you can search for articles outside of EssentAI's built-in search. It also supports custom links you can save and manage yourself.

10.1  Built-in Database Links

Click Search Databases in the menu bar to access the following databases directly in your browser:

• Google Scholar
• ResearchGate
• JSTOR
• CORE
• SpringerLink
• ScienceDirect
• DOAJ (Directory of Open Access Journals)
• CrossRef
• Scopus
• Web of Science

Clicking any database opens it directly in your default browser. From there you can search for articles and download PDFs to add to your EssentAI library.

10.2  Custom Links

The Custom Links submenu lets you save your own frequently used websites — for example your university library or a specialist database — so they are always accessible from within EssentAI.

To manage your custom links, go to Search Databases → Custom Links → Manage Custom Links. The Manage Custom Links window shows all your saved links with Edit and Delete buttons for each. Click Add New Link to add a new entry — give it a name and enter the URL. Once saved, it will appear in the Custom Links submenu for quick access.

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11. Resources

The Resources menu provides quick access to external research tools and a built-in AI declaration statement for use in your writing submissions.

11.1  External Research Tools

Click Resources in the menu bar to access the following tools, each opening in your browser:

• ABDC Journal Quality List (Official) — the Australian Business Deans Council journal ranking list, useful for checking journal quality ratings
• SCIMAGO — journal and country rankings based on Scopus data
• ZoteroBib — a free online reference formatting tool for generating citations in various styles

11.2  Artificial Intelligence Declaration

Many journals and academic institutions now require authors to declare the use of AI tools in their writing process. EssentAI includes a pre-written declaration for this purpose.

To access it, click Resources → Artificial Intelligence Declaration. A window will open with a formal declaration statement. You can toggle between Single author (I) and Multiple authors (We) to match your submission. Click Copy to clipboard to copy the declaration ready to paste into your document.

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12. Replacing a PDF

If an article in your library has been updated, revised, or you have obtained a better copy of the PDF, you can replace the attached file without removing the article record or its AI-generated analysis.

12.1  How to Replace a PDF

1. Click on the article row in your library to highlight it.
2. Go to File → Replace PDF.
3. A confirmation dialog will appear asking whether you want to replace the existing PDF. Click Yes.
4. A file browser will open. Navigate to the new PDF, select it, and click Open.

The article record and all associated data — including the AI analysis, notes, and status — are preserved. Only the attached PDF file is replaced.

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13. Help

The Help menu provides access to information about EssentAI and ways to get support or share feedback.

• About — displays the current version of EssentAI and application information
• Disclaimer — opens the application disclaimer
• Contact support — opens a support contact channel where you can report issues or ask questions
• Have an Idea? — opens a feedback channel where you can submit feature requests or suggestions

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14. Subscription and Trial

EssentAI includes a free trial so you can explore the application before committing. Your trial gives you three complimentary article analyses, enough to get a feel for the workflow before deciding whether to subscribe.

Once your trial analyses are used, a subscription reminder will appear when you next try to add an article. At that point:

1. Click File → Settings (Windows) or EssentAI → Preferences (macOS).
2. Click Subscribe and follow the prompts through the secure checkout.
3. After subscribing, you will receive an email containing a link to your EssentAI Account Page where your subscription code will be displayed.
4. Copy the code, return to EssentAI, paste it into the Subscription / Licence field in Settings, and click Validate.
5. Once validated, the status will turn green confirming your subscription is active.

You can manage or review your subscription at any time from the Settings window. For full subscription steps, see the FAQ: How do I subscribe to EssentAI.

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