Research workflow optimization - Freiya Documentation

Optimize your research workflow with Freiya. This guide shows you how to integrate the platform into every stage of your research process, from initial literature discovery to final manuscript preparation.

Overview

An effective research workflow combines systematic organization with flexibility. Freiya supports every phase of the research cycle:

Discover

Find and collect relevant papers

Organize

Structure your library with collections and tags

Read & annotate

Deep dive into papers with Focus mode

Analyze

Use AI to understand and connect ideas

Write

Export citations and use notes for drafting

Iterate

Refine and expand your research

Circular workflow diagram showing the 6 research phases with Freiya features labeled at each stage

Phase 1: Discovery and collection

Finding papers

Search strategies:

Forward search
Backward search
Author tracking
Institution research

Start with a key paper and find newer work that cites it.In Freiya:

Add the seminal paper to your library
Note its DOI
Use Google Scholar to find citing papers
Add relevant papers via DOI

Rapid paper triage

Quick evaluation to decide what to keep:

Add via DOI

Import papers quickly using DOI search

Read abstract

Skim the auto-fetched abstract

Tag immediately

Add “to-read”, “maybe”, or topic tags

Quick notes

Jot down why it’s relevant (one sentence)

Continue or deep-dive

Move on or read more based on relevance

Set aside dedicated time each week for paper discovery. Consistency beats marathon sessions.

Phase 2: Organization

Collection structure

Create a logical hierarchy for your research: Example structure:

Paper Collections:
├── Project: Thesis
│   ├── Ch1 - Introduction
│   ├── Ch2 - Literature Review
│   ├── Ch3 - Methodology
│   └── Ch4 - Results
├── Background Reading
│   ├── Foundational Papers
│   └── Recent Reviews
├── Methodology References
└── Papers to Cite

Chat Collections:
├── Thesis Brainstorming
├── Methodology Questions
└── Paper Analysis

Screenshot of collections sidebar showing a hierarchical organization of paper collections as descri

Tagging system

Develop a consistent tagging strategy: Multi-dimensional tags:

Status tags
Importance tags
Topic tags
Custom tags

Track reading progress:

to-read - Haven’t read yet
reading - Currently reading
read - Finished reading
review-needed - Need to re-read

Prioritize papers:

key-paper - Essential to your work
foundational - Important background
supporting - Supplementary material
to-cite - Plan to reference

Categorize by content:

methodology - Method-focused
theory - Theoretical work
application - Applied research
review - Review papers

Use lowercase with hyphens for consistency. Decide on your system early and stick to it.

Weekly organization routine

Sunday prep (15 minutes):

Review papers added this week
Verify tags are applied
Move to appropriate collections
Update reading priorities
Plan next week’s reading

Phase 3: Reading and annotation

Deep reading workflow

Start Focus session

Open paper in Focus mode

First pass - skim

Abstract and conclusions
Figures and tables
Section headings
Highlight key points (yellow)

Second pass - detailed

Read introduction thoroughly
Understand methodology (green highlights)
Analyze results
Add comments to highlights

Third pass - critical

Evaluate arguments
Note limitations (red highlights)
Identify questions (purple highlights)
Consider applications

Summarize

Write summary in paper notes

PDF in Focus mode showing highlights in different colors according to the reading workflow stages

Annotation best practices

Color coding strategy:

Phase	Color	What to Highlight
Skim	Yellow	Key findings, main claims
Detailed	Green	Methodology, approach details
Analysis	Blue	Important quotes for citations
Critical	Red	Limitations, concerns
Synthesis	Purple	Questions, future work, connections
Examples	Orange	Useful examples, case studies

Comment guidelines:

Summaries - Paraphrase in your own words
Questions - Note what’s unclear
Connections - Link to other papers
Applications - How it applies to your work
Criticisms - Evaluate strengths and weaknesses

Add emojis for quick visual scanning: 💡 insights, ❓ questions, ⭐ very important, 🚨 critical

Note-taking template

Use this structure in paper notes:

# Quick Summary
[One paragraph summary in your own words]

# Key Findings
- Finding 1
- Finding 2
- Finding 3

# Methodology
[Brief description of methods used]

# Strengths
- What this paper does well

# Limitations
- What's missing or problematic

# Relevance to My Work
[How this connects to your research]

# Questions / Follow-up
- Things to investigate further

# Related Papers
- [Link to other papers in your library]

Phase 4: Analysis and synthesis

Using AI for analysis

Effective AI questions:

Understanding
Critique
Synthesis
Application

Explain the authors' main argument in simple terms.

What assumptions underlie their methodology?

How does this work relate to [other paper]?

What are potential weaknesses in their approach?

What alternative explanations weren't considered?

How might these findings be limited by [factor]?

Compare the methodology in this paper to [Paper B].

How do these findings complement [other research]?

What gaps remain in the literature after this work?

How could I adapt this methodology for [my context]?

What would need to change to apply this to [domain]?

What tools or resources would I need to replicate this?

Literature matrix

Create a comparison table (use external spreadsheet or document):

Paper	Year	Method	Sample	Key Finding	Limitation	Relevance
Smith 2020	2020	RCT	500	Effect size 0.8	Small sample	Direct comparison
Jones 2021	2021	Survey	2000	Confirms trend	Self-report bias	Context
Lee 2022	2022	Meta	50 studies	Moderate effect	Heterogeneity	Background

Export from Freiya:

Select papers in collection
Export as CSV
Open in spreadsheet
Add analysis columns
Fill in your notes

Phase 5: Writing and citation

From annotations to outline

Export highlights

Export all highlights from key papers as Markdown

Group by theme

Organize highlights by the points you want to make

Create outline

Structure highlights into a logical argument flow

Draft sections

Write around your organized highlights

Add citations

Generate citations for referenced work

Citation workflow

For LaTeX users:

Tag papers to cite

Apply to-cite tag to relevant papers

Export BibTeX

Select papers and export as .bib file

Include in project

Add .bib file to your LaTeX project

Cite in text

Use \cite{key} in your document

Update regularly

Re-export when adding papers

For Word/Google Docs users:

Generate citations

Create citations in required format (APA, MLA, etc.)

Copy to clipboard

One-click copy formatted citations

Paste in document

Add to your reference list

In-text citations

Add (Author, Year) references manually or use Zotero/Mendeley

Writing with AI assistance

Ethical AI use for writing:

✅ Use AI to:

Explain concepts you’re reading
Brainstorm connections between ideas
Understand difficult passages
Explore alternative phrasings
Check logical flow

❌ Don’t use AI to:

Write your paper for you
Generate text to submit as yours
Replace actual reading and thinking
Avoid understanding source material
Bypass proper citation

Best practices:

Always write in your own words
Cite original sources, not AI
Use AI as a tutor, not a ghostwriter
Check institutional policies on AI use
Be transparent about AI usage if required

Phase 6: Iteration and maintenance

Monthly review

End-of-month routine (30 minutes):

Review new papers

Check all papers added this month

Clean up tags

Remove redundant tags, merge similar ones

Update collections

Move papers to appropriate collections

Archive completed

Create “Completed Projects” collection for finished work

Plan next month

Identify gaps in literature, plan new searches

Semester/project end

Wrap-up activities:

Export everything - Back up your library
Final organization - Ensure everything is tagged and noted
Create summary - Write project overview with key papers
Archive - Move project to archive collection
Reflect - What worked? What would you improve?

Advanced workflows

Collaborative research

Team coordination:

Use shared chat collections for team discussions
Create standardized tag systems
Export and share paper lists
Coordinate annotation styles
Regular sync meetings

Multi-project management

Juggling multiple projects:

Separate collections per project
Use project-specific tags
Color-code collections
Dedicated chat collections per project
Weekly project reviews

Literature review projects

Systematic review workflow:

Define scope - Create inclusion/exclusion criteria collection
Search systematically - Document search terms and sources
Screen abstracts - Tag: include, exclude, maybe
Full-text review - Deep read included papers
Extract data - Use annotation system consistently
Synthesize - Use AI to help identify themes
Write - Export citations and highlights

Time-saving tips

Batch processing

Do similar tasks together: add papers in batches, tag in batches

Keyboard shortcuts

Learn and use shortcuts for common actions

Templates

Use consistent note templates for faster writing

Weekly routine

Set aside dedicated time for organization

Common pitfalls

Avoid these workflow mistakes:

Over-collecting - Adding papers you’ll never read
Under-tagging - Not organizing as you go
Inconsistent highlighting - Random color usage
Skipping summaries - Not writing notes while reading
No backups - Failing to export your work
Perfectionism - Spending too long organizing vs. reading
Ignoring review - Not revisiting and refining annotations

Customization ideas

Adapt these workflows to your style: For theory-heavy research:

Add “framework” tag for conceptual papers
Create “theory” vs “empirical” collections
Use more detailed note templates
AI chats for concept clarification

For empirical research:

Tag by methodology type
Create data/methods collections
Highlight statistical details
Note replication considerations

For interdisciplinary work:

Multiple field-specific tag sets
Cross-disciplinary comparison collections
“Bridge papers” that connect fields
AI to explain unfamiliar terminology

Tools integration

Freiya plays well with:

Reference managers - Export to Zotero, Mendeley
Note apps - Export markdown to Obsidian, Notion
LaTeX - BibTeX export
Spreadsheets - CSV export for analysis
Cloud storage - Back up your exports

Tips & best practices

More productivity tips and strategies

Keyboard shortcuts

Speed up your workflow with shortcuts

Collections guide

Deep dive into organizing with collections

PDF viewer

Master annotation and highlighting

​Overview

​Phase 1: Discovery and collection

​Finding papers

​Rapid paper triage

​Phase 2: Organization

​Collection structure

​Tagging system

​Weekly organization routine

​Phase 3: Reading and annotation

​Deep reading workflow

​Annotation best practices

​Note-taking template

​Phase 4: Analysis and synthesis

​Using AI for analysis

​Literature matrix

​Phase 5: Writing and citation

​From annotations to outline

​Citation workflow

​Writing with AI assistance

​Phase 6: Iteration and maintenance

​Monthly review

​Semester/project end

​Advanced workflows

​Collaborative research

​Multi-project management

​Literature review projects

​Time-saving tips

Batch processing

Keyboard shortcuts

Templates

Weekly routine

​Common pitfalls

​Customization ideas

​Tools integration

​Related resources

Tips & best practices

Keyboard shortcuts

Collections guide

PDF viewer

Overview

Phase 1: Discovery and collection

Finding papers

Rapid paper triage

Phase 2: Organization

Collection structure

Tagging system

Weekly organization routine

Phase 3: Reading and annotation

Deep reading workflow

Annotation best practices

Note-taking template

Phase 4: Analysis and synthesis

Using AI for analysis

Literature matrix

Phase 5: Writing and citation

From annotations to outline

Citation workflow

Writing with AI assistance

Phase 6: Iteration and maintenance

Monthly review

Semester/project end

Advanced workflows

Collaborative research

Multi-project management

Literature review projects

Time-saving tips

Common pitfalls

Customization ideas

Tools integration

Related resources