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Afforai Comprehensive User Guide with Videos
Afforai Comprehensive User Guide with Videos

Unlock efficient research with Afforai’s AI-driven reference manager—perfect for academics seeking streamlined citation and collaboration.

Alec at Afforai avatar
Written by Alec at Afforai
Updated this week

Welcome to Afforai 👋

We'll be showing what Afforai can do to help you with your research project in this guide.

Resources you should know

  1. Afforai Community: Connect and discuss ideas with other Afforai users

  2. Product Roadmap: Share feedback, report bugs, and request features

  3. AI Prompts Library: Created and shared by Afforai users.

  4. Help Center: Answers to most questions can be found here.

  5. Data Security: We take AI data privacy and security seriously.

What is Afforai?

Afforai is a reference management tool built for researchers of all experience levels. Afforai allows you to manage, cite, collaborate and take notes on all of your research papers, as well as leverage AI to summarize, search and compare papers across multiple libraries.

Who can use Afforai?

If you are a researcher, professor or student who is looking to organize your reference library, or research your papers with an AI tool that you can trust, then Afforai is the tool for you.


Reference Manager

Afforai is a reference management tool built for researchers of all experience levels. Afforai allows you to manage, cite, collaborate and take notes on all of your research papers, as well as leverage AI to summarize, search and compare papers across multiple libraries.

Uploading your references

Afforai offers a number of different ways to upload references into your library. Every reference you upload will have its citation automatically generated.

Uploading a file

To upload a file into Afforai, press the ‘upload file’ button, and select which files you want to upload. You can upload multiple files into Afforai at once. The following file types are supported with Afforai:

  • PDF

  • DOCX

  • TXT

  • MDOWN

  • EPUB

  • PPTX

Uploading a URL

Upload any news articles, journal articles, book snippets etc. into Afforai by uploading the URL into your reference manager.

Uploading a DOI

Upload a research paper by using it’s DOI (Digital Object Identifier). Afforai also allows you to upload other identifiers including:

  • ArXiv

  • PMID

  • ISBN

Note - Afforai only allows you to upload an identifier for a reference if there is a valid file attached. If there isn’t a file attached, you can add one manually before uploading if you have a copy available by clicking on the upload icon that will appear next to the upload.

Ensure files are usable with AI

Afforai will attempt to index your files as they are uploading however, in the unlikely instance your file doesn’t index, press the index button as showcased below, and your file will be re-indexed.


Organizing your library

You can organize your library in Afforai with folders and tags.

Organizing with folders

To create a folder, right click on the library you would like it nested inside of. You can also create up to four layers of sub-folders inside your folders. Once you have created a folder, you can store your references inside them by simply dragging them in.

Organizing with tags

To create a tag, press the ‘create tag’ button in the tag pop-up. You can color code your tags for extra distinction. To assign a tag to a reference, drag and drop it into the reference you would like to assign it to.


Generating citations and bibliographies

Afforai supports over 10,000 citation styles that you can populate on any reference in just a couple of clicks.

How to generate a citation or bibliography

To generate a citation or bibliography, right click on the reference you would like to use, then press ‘generate citation’. In the modal, select the citation type, citation locale, and choose whether you would like a citation or bibliography to be produced.


Creating and joining shared libraries

If you would like to collaborate on your research, you can easily do so with shared libraries.

Creating a shared library and inviting users

To create a shared library, first press the ‘add library’ button, then press ‘create shareable library. This will add a shared library to your folder tree. From here, right click and press ‘invite people’. This allows you to invite people via the email they have an Afforai account with, and edit their permissions.

Joining a shared library

You can see who has invited you to join their shared library by pressing ‘add library’ then ‘shared libraries invites’. From here you can accept or reject invitations to shared libraries.

Transferring ownership

You can transfer the ownership of your library to someone else in the library, just right click and press ‘transfer ownership’ and select the person you would like to transfer your library to.


Import data from Zotero, Mendeley, EndNote

Here’s a concise guide to help you transfer your references from other reference managers like Zotero, Mendeley, and EndNote into Afforai.

Step 1: Export data from your old reference manager

  1. Log into your existing reference manager.

  2. Locate and select the references you wish to transfer.

  3. Export your data as RIS, BibTex, or CFF file.

Step 2: Import your data into Afforai

  1. Log into your Afforai and locate the "Import Items" button.

  2. Select the RIS, BibTex, or CFF file you exported from your previous manager.

  3. Click "Upload" to complete the import of your research data.

Note - Afforai will try to find publicly available PDFs for your references, as a valid file must be attached to upload a reference. If Afforai cannot locate a PDF, you can manually add your own copy by clicking the upload icon that appears next to the reference.


Afforai AI Research Assistant

Afforai AI research assistant allows you to search, summarize, and compare hundreds of references across multiple libraries, by leveraging AI, complete with reliable data sources and inline citations.

Using different AI Research modes

Afforai offers you three unique search modes, enabling you to research your papers in an adaptable way.

Document Retrieval Mode

Conduct your research using your uploaded files, complete with citations. You can edit which of your connected files you would like the AI to refer to when it answers your question in settings.

Inline citations and data sources

Answers come complete with inline citations and data sources. Inline citations show where each chunk of information has come from, and data sources allow you to reference the documents that were used by the AI.

Semantic Scholar Mode

Augment your research with data from a 200 million peer-reviewed research papers database. You can customize the areas of Semantic Scholar the AI uses to augment your research in settings. This includes editing fields of study, publication types, and publishing dates.

Inline citations and data sources

Answers will come complete with inline citations and data sources. Inline citations pull citations from Semantic Scholar to support chunks in your answer, whilst data sources allow you to discover new papers that are relevant to your research.

Google Search Mode

Enrich your research with information from Google, complete with citations. You can edit the region, language, and country the AI will use to supplement your research, as well exclude or limit research to certain domains in settings.

Inline citations and data sources

When using Semantic Scholar Mode, your answer will come complete with inline citations and data sources. Inline citations pull citations from Semantic Scholar to support chunks in your answer, whilst data sources allow you to discover new papers that are relevant to your research.


Using different AI models and BYOK

Afforai also allows you to use the most advanced AI models in the market so you can focus on doing your best work.

Available search models

You can use the following search models natively with Afforai:

Standard AI Models

  • Azure GPT-3.5

  • Claude 3 Haiku

Advanced AI Models

  • Azure GPT-4

  • Azure GPT-4 Omni

  • Claude 3.5 Sonnet

Azure GPT models are enterprise AI models provided and hosted by Microsoft Azure. Ensuring top data protection and privacy for your account. For more information on our data security practices, click here.

BYOK (Bring Your Own Key)

BYOK allows you to use AI models in Afforai that are not natively supported via OpenRouter. To use Bring Your Own Key in Afforai, go into settings on the ‘custom’ AI model, and press ‘connect to OpenRouter’. For a detailed guide, click here.


AI Custom Instructions

Custom instructions allow you to tailor the AI's responses to fit specific research needs or project requirements. By defining these instructions, you can ensure that the AI delivers more relevant and precise information, enhancing the efficiency and effectiveness of their research.


Quick Prompts

Prompts allow you to create and use preset questions with the AI research assistant, meaning you can save time when asking repeated questions. To create a prompt, press ‘create new prompt’ in the prompt pop-up. After you give your prompt a name and message, you can use it to ask questions.


Sharing your research

You can share your research by setting your chat to public. To do this, press on the private / public toggle, and change the selected status from private to public. You will then be able to copy the share link below, and share your findings with anyone, regardless of if they have an Afforai account or not.


Afforai Notebook

Right click on any file in your library and press ‘view file’ to access the Afforai notebook. This allows you to make different kinds of annotations on your files.

Making annotations

You can make different types of color-coordinated annotations in the file annotator.

Text highlight

To highlight text, drag your mouse over the body of text you would like to highlight. You can add a comment to your text highlight when the ‘view notes’ panel is open.

Area highlight

To highlight an area, drag your mouse over the area of the page you would like to highlight. You can add a comment to your area highlight when the ‘view notes’ panel is open.

Sticky note

To create a sticky note, just click on the area you would like the sticky note to attach to. You can add a note in the text area that will pop-up after the action is finished. You can also add comments in the notes panel.

Quick note

You can create quick notes when you have the notes panel open. Quick notes will populate in your notes on the side, but won’t be attached to a specific area of the file, unlike other annotation methods.


Tagging yourself and peers in comments

You can tag yourself in your comments, and tag your peers in comments made on files in shared libraries. Just press the ‘@’ key, and select the user you would like to add.


Using AI assistant in Afforai Notebook

To use the AI, press the ‘@’ key and type select the AI model you would like to use. This allows you to use the Afforai AI research assistant to help you summarize, answer questions, or explain concepts about the notes you have made.


Afforai Cite Extension

Insert citations and bibliographies from your library straight into your writing in Microsoft Word with over 10,000 citation styles, use Afforai AI Research Assistant to improve your writing flow, and so much more with Afforai Cite Extension.

Reference Manager

  • Insert citations and bibliographies straight into your writing.

  • Select from over 10,000 supported citation styles.

  • Search and filter your library for easy access to your references.

AI Research Assistant

  • Summarize, extract findings, and compare results between papers with AI.

  • Use AI modes like Document Retrieval, Semantic Scholar, and Google Modes.

  • Use specialized prompts to improve your writing, and overcome your writer’s block.


Afforai Enterprise Organization

Afforai Organization is an enterprise feature that allows you to create an organization, invite your employees, team members, and researchers in your department, and manage their billing, all in one place. We'll explore it further in this guide.


Afforai Keyboard Shortcuts

Afforai prioritizes accessibility and inclusivity by providing industry-standard accommodations for users with disabilities. These keyboard shortcuts are designed to enhance the user experience and facilitate seamless navigation within the Afforai platform. We'll explore it further in this guide.


For more information about all things to do with Afforai, join our Community, or visit our help center.

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