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Frequently Asked Questions (FAQ)

General Questions

What is Lixplore?

Lixplore is a command-line tool for searching, filtering, exporting, and managing academic literature from multiple sources including PubMed, arXiv, Crossref, DOAJ, and EuropePMC.

Is Lixplore free?

Yes, Lixplore is completely free and open source under the MIT License.

Does Lixplore include AI/ML models?

No. Lixplore is purely a search and export tool. It has no machine learning dependencies, making it lightweight and fast. However, it's easy to integrate with AI services like OpenAI or Gemini through JSON export.

What platforms does Lixplore support?

Lixplore works on Linux, macOS, and Windows with Python 3.8 or higher.

Installation & Setup

How do I install Lixplore?

pip install lixplore

See the Installation Guide for details.

I get "command not found" after installing

Add pip's bin directory to your PATH:

export PATH=$PATH:~/.local/bin

Add this to your ~/.bashrc or ~/.zshrc to make it permanent.

How do I upgrade to the latest version?

pip install --upgrade lixplore

Usage Questions

How many results can I fetch?

You can fetch as many as you want using the -m flag. For example:

lixplore -P -q "topic" -m 1000

Note: With -A (all sources), -m applies per source.

Why do I get more results than I requested?

When using -A (all sources), the -m flag applies per source. For example:

lixplore -A -q "topic" -m 50
# Returns: 5 sources × 50 = 250 results

Use -D (deduplicate) to reduce duplicates:

lixplore -A -q "topic" -m 50 -D

How do I search specific date ranges?

Use the -d flag:

lixplore -P -q "topic" -d 2023-01-01 2024-12-31

Can I search by author?

Yes, use the -au flag:

lixplore -P -au "Smith J" -m 50

How do I find open access PDFs?

# Show clickable PDF links
lixplore -x -q "topic" -m 50 --show-pdf-links

# Download PDFs
lixplore -x -q "topic" -m 50 --download-pdf

Export Questions

What export formats are supported?

Lixplore supports 10+ formats:

  • CSV, Excel (XLSX), JSON, XML
  • BibTeX, RIS
  • EndNote (Tagged & XML)
  • Citations (APA, MLA, Chicago, Harvard, Vancouver, IEEE)

How do I export to Excel?

lixplore -P -q "topic" -m 100 -X xlsx -o results.xlsx

How do I export only specific fields?

Use --export-fields:

lixplore -P -q "topic" -m 100 -X csv --export-fields title authors year doi -o results.csv

Can I export in multiple formats at once?

Yes:

lixplore -P -q "topic" -m 100 -X csv,bibtex,xlsx

Add --zip to package them:

lixplore -P -q "topic" -m 100 -X csv,bibtex,xlsx --zip

Annotation Questions

How do I annotate articles?

# First, search to see results with numbers
lixplore -P -q "topic" -m 50

# Then annotate by number
lixplore --annotate 5 --rating 5 --tags "important,cite"
lixplore --annotate 12 --comment "Interesting methodology"

Where are annotations stored?

In ~/.lixplore_annotations.json

You can back up this file to preserve your annotations.

How do I view my annotations?

# List all
lixplore --list-annotations

# Filter by rating
lixplore --filter-annotations --rating 5

# Search annotations
lixplore --search-annotations "CRISPR"

How do I export annotations?

lixplore --export-annotations markdown  # Markdown format
lixplore --export-annotations json      # JSON format
lixplore --export-annotations csv       # CSV format

Interactive Mode Questions

How do I use interactive mode?

# Launch with search results
lixplore -P -q "topic" -m 50 -i

# Or launch standalone
lixplore -i

What's the difference between -i and --tui?

  • -i or --interactive: Simple TUI for browsing results
  • --tui: Enhanced TUI with more features (search, stats, etc.)

Can I annotate in interactive mode?

Yes, the enhanced TUI (--tui) supports annotations. The simple TUI (-i) is for browsing only.

Automation Questions

Can I use Lixplore in cron jobs?

Yes! Lixplore is designed for automation:

# Add to crontab
0 9 * * * lixplore -P -q "topic" -m 50 -X csv -o /path/to/daily_$(date +\%Y\%m\%d).csv

See Automation Guide for more examples.

How do I save search configurations?

Use profiles:

# Save configuration
lixplore -P -q "test" -m 100 -D --sort newest --save-profile my_profile

# Reuse configuration
lixplore -q "new topic" --load-profile my_profile

Where are files saved?

  • PDFs: ~/Lixplore_PDFs/
  • Exports: ./exports/ (or specify with -o)
  • Annotations: ~/.lixplore_annotations.json
  • Cache: ~/.lixplore_cache.json
  • Profiles: ~/.lixplore/profiles.json

Performance Questions

How fast is Lixplore?

Lixplore is very fast:

  • No ML overhead
  • Efficient API calls
  • 7-day result caching
  • Parallel source queries

Does Lixplore cache results?

Yes, results are cached for 7 days. To refresh:

lixplore -P -q "topic" -m 50 --refresh

Why is my first search slow?

The first search to each API may be slower. Subsequent searches use caching and are much faster.

Integration Questions

Can I integrate with OpenAI/Gemini?

Yes! Export to JSON and pipe to your AI script:

lixplore -P -q "topic" -m 100 -X json | python3 ai_analysis.py

See AI Integration Guide.

Does Lixplore work with Zotero?

Yes:

lixplore --configure-zotero YOUR_API_KEY YOUR_USER_ID
lixplore -P -q "topic" -m 50 --add-to-zotero

See Zotero Integration.

Can I use with other tools?

Yes, Lixplore integrates well with:

  • jq for JSON processing
  • csvkit for CSV analysis
  • Citation managers (BibTeX, RIS, EndNote)
  • Spreadsheet software (Excel, LibreOffice)
  • Any tool that accepts JSON, CSV, or XML

Troubleshooting

"No results found"

Try: 1. Broaden your query 2. Check spelling 3. Try different sources (-A for all) 4. Remove date filters 5. Use --refresh to bypass cache

"API error" or "Connection failed"

Check: 1. Internet connection 2. API service status (PubMed, arXiv, etc.) 3. Try again later (may be temporary)

Results look duplicated

Use deduplication:

lixplore -A -q "topic" -m 100 -D

Export file is empty

Check: 1. Search returned results 2. Output path is writable 3. Correct export format specified

"Permission denied" when saving files

Either: 1. Specify a path you have write access to: -o ~/results.xlsx 2. Run from a directory where you have write permissions

Feature Requests

How do I request a new feature?

Open an issue on GitHub: https://github.com/pryndor/Lixplore_cli/issues

Can you add support for [database X]?

Possibly! Either: 1. Open a feature request on GitHub 2. Use the Custom API feature to add it yourself

Will you add a GUI?

Lixplore is designed as a CLI-first tool for automation and scripting. However, the interactive TUI modes provide a visual interface.

Contributing

How can I contribute?

See Contributing Guide.

I found a bug

Report it on GitHub: https://github.com/pryndor/Lixplore_cli/issues

Can I add my own features?

Yes! Lixplore is open source. Fork, modify, and submit a pull request.

Licensing

What license is Lixplore under?

MIT License. See License.

Can I use Lixplore commercially?

Yes, the MIT license allows commercial use.

Do I need to cite Lixplore in my research?

Not required, but appreciated! Citation info coming soon.

Still Have Questions?