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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.

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Overview

An effective research workflow combines systematic organization with flexibility. Freiya supports every phase of the research cycle:
1

Discover

Find and collect relevant papers
2

Organize

Structure your library with collections and tags
3

Read & annotate

Deep dive into papers with Focus mode
4

Analyze

Use AI to understand and connect ideas
5

Write

Export citations and use notes for drafting
6

Iterate

Refine and expand your research
Circular workflow diagram showing the 6 research phases with Freiya features labeled at each stage

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Phase 1: Discovery and collection

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Finding papers

Search strategies:

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Rapid paper triage

Quick evaluation to decide what to keep:
1

Add via DOI

Import papers quickly using DOI search
2

Read abstract

Skim the auto-fetched abstract
3

Tag immediately

Add “to-read”, “maybe”, or topic tags
4

Quick notes

Jot down why it’s relevant (one sentence)
5

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.

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Phase 2: Organization

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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

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Tagging system

Develop a consistent tagging strategy: Multi-dimensional tags:
Track reading progress:
  • to-read - Haven’t read yet
  • reading - Currently reading
  • read - Finished reading
  • review-needed - Need to re-read
Use lowercase with hyphens for consistency. Decide on your system early and stick to it.

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Weekly organization routine

Sunday prep (15 minutes):
  1. Review papers added this week
  2. Verify tags are applied
  3. Move to appropriate collections
  4. Update reading priorities
  5. Plan next week’s reading

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Phase 3: Reading and annotation

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Deep reading workflow

1

Start Focus session

Open paper in Focus mode
2

First pass - skim

  • Abstract and conclusions
  • Figures and tables
  • Section headings
  • Highlight key points (yellow)
3

Second pass - detailed

  • Read introduction thoroughly
  • Understand methodology (green highlights)
  • Analyze results
  • Add comments to highlights
4

Third pass - critical

  • Evaluate arguments
  • Note limitations (red highlights)
  • Identify questions (purple highlights)
  • Consider applications
5

Summarize

Write summary in paper notes
PDF in Focus mode showing highlights in different colors according to the reading workflow stages

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Annotation best practices

Color coding strategy:
PhaseColorWhat to Highlight
SkimYellowKey findings, main claims
DetailedGreenMethodology, approach details
AnalysisBlueImportant quotes for citations
CriticalRedLimitations, concerns
SynthesisPurpleQuestions, future work, connections
ExamplesOrangeUseful 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

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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]

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Phase 4: Analysis and synthesis

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Using AI for analysis

Effective AI questions: 
Explain the authors' main argument in simple terms.

What assumptions underlie their methodology?

How does this work relate to [other paper]?

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Literature matrix

Create a comparison table (use external spreadsheet or document):
PaperYearMethodSampleKey FindingLimitationRelevance
Smith 20202020RCT500Effect size 0.8Small sampleDirect comparison
Jones 20212021Survey2000Confirms trendSelf-report biasContext
Lee 20222022Meta50 studiesModerate effectHeterogeneityBackground
Export from Freiya:
  1. Select papers in collection
  2. Export as CSV
  3. Open in spreadsheet
  4. Add analysis columns
  5. Fill in your notes

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Phase 5: Writing and citation

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From annotations to outline

1

Export highlights

Export all highlights from key papers as Markdown
2

Group by theme

Organize highlights by the points you want to make
3

Create outline

Structure highlights into a logical argument flow
4

Draft sections

Write around your organized highlights
5

Add citations

Generate citations for referenced work

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Citation workflow

For LaTeX users:
1

Tag papers to cite

Apply to-cite tag to relevant papers
2

Export BibTeX

Select papers and export as .bib file
3

Include in project

Add .bib file to your LaTeX project
4

Cite in text

Use \cite{key} in your document
5

Update regularly

Re-export when adding papers
For Word/Google Docs users:
1

Generate citations

Create citations in required format (APA, MLA, etc.)
2

Copy to clipboard

One-click copy formatted citations
3

Paste in document

Add to your reference list
4

In-text citations

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

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

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Phase 6: Iteration and maintenance

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Monthly review

End-of-month routine (30 minutes):
1

Review new papers

Check all papers added this month
2

Clean up tags

Remove redundant tags, merge similar ones
3

Update collections

Move papers to appropriate collections
4

Archive completed

Create “Completed Projects” collection for finished work
5

Plan next month

Identify gaps in literature, plan new searches

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Semester/project end

Wrap-up activities:
  1. Export everything - Back up your library
  2. Final organization - Ensure everything is tagged and noted
  3. Create summary - Write project overview with key papers
  4. Archive - Move project to archive collection
  5. Reflect - What worked? What would you improve?

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Advanced workflows

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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

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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

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Literature review projects

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

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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

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Common pitfalls

Avoid these workflow mistakes:
  1. Over-collecting - Adding papers you’ll never read
  2. Under-tagging - Not organizing as you go
  3. Inconsistent highlighting - Random color usage
  4. Skipping summaries - Not writing notes while reading
  5. No backups - Failing to export your work
  6. Perfectionism - Spending too long organizing vs. reading
  7. Ignoring review - Not revisiting and refining annotations

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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

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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