Skip to content

Your First Search

Step-by-step tutorial for your first Lixplore search.

Let's search PubMed for recent COVID-19 research:

lixplore -P -q "COVID-19 vaccine" -m 20

What this does: - -P: Search PubMed - -q "COVID-19 vaccine": Search query - -m 20: Get 20 results

Expected output: 

Searching for query: COVID-19 vaccine
Sources: PubMed
  Searching PubMed...

Found 20 results:
[1] Effectiveness of COVID-19 vaccines...
[2] Safety profile of mRNA vaccines...
...

Step 2: Add Abstracts

Now let's see abstracts:

lixplore -P -q "COVID-19 vaccine" -m 10 -a

New flag: - -a: Show abstracts

Step 3: Export Results

Export to Excel:

lixplore -P -q "COVID-19 vaccine" -m 50 -X xlsx -o covid_research.xlsx

New flags: - -X xlsx: Export to Excel format - -o covid_research.xlsx: Output filename

Check the file: covid_research.xlsx is created in the current directory.

Step 4: Filter by Date

Search only recent publications:

lixplore -P -q "COVID-19 vaccine" -d 2024-01-01 2024-12-31 -m 30

New flag: - -d 2024-01-01 2024-12-31: Date range filter

Step 5: Search Multiple Sources

Search across all databases:

lixplore -A -q "machine learning healthcare" -m 50 -D

New flags: - -A: All sources (PubMed, arXiv, Crossref, DOAJ, EuropePMC) - -D: Deduplicate results

Note: With -A, -m 50 means 50 per source = 250 total results.

Step 6: Interactive Browsing

Browse results interactively:

lixplore -P -q "CRISPR therapy" -m 50 -i

New flag: - -i: Interactive mode

In interactive mode: - Use arrow keys to navigate - Press Enter to view details - Press 'q' to quit

Step 7: Find Open Access PDFs

lixplore -x -q "neural networks" -m 20 --show-pdf-links

What this does: - -x: Search arXiv (preprint server) - --show-pdf-links: Show clickable PDF links

Output: 

[1] Deep Learning with Neural Networks
    Open PDF → https://arxiv.org/pdf/2306.12345.pdf

Click the link to open the PDF!

Step 8: Annotate Important Papers

# Step 1: Search
lixplore -P -q "stem cell research" -m 30

# Step 2: Annotate article #5
lixplore --annotate 5 --rating 5 --tags "important,cite" --comment "Groundbreaking work"

# Step 3: View your annotations
lixplore --list-annotations

Complete Example: Literature Review

Let's do a complete literature review workflow:

# 1. Comprehensive search across all sources
lixplore -A -q "cancer immunotherapy" -m 100 -D --sort newest

# 2. Browse interactively
lixplore -i

# 3. Annotate key papers (replace numbers with actual article numbers)
lixplore --annotate 3 --rating 5 --tags "key-paper,cite"
lixplore --annotate 7 --rating 4 --tags "methodology"
lixplore --annotate 12 --rating 5 --tags "results,important"

# 4. Export top 50 to Excel
lixplore -S first:50 -X xlsx -o cancer_immuno_review.xlsx

# 5. Export to BibTeX for citations
lixplore -S first:50 -X bibtex -o references.bib

# 6. Export your annotations
lixplore --export-annotations markdown -o my_notes.md

What You've Learned

  • [x] Basic search with -P -q -m
  • [x] Show abstracts with -a
  • [x] Export to Excel with -X xlsx
  • [x] Filter by date with -d
  • [x] Search all sources with -A -D
  • [x] Interactive browsing with -i
  • [x] Find PDFs with --show-pdf-links
  • [x] Annotate papers with --annotate
  • [x] Complete workflow: search → annotate → export

Next Steps

Congratulations! You're ready to use Lixplore for your research.