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Search Parameter Flags

Complete documentation for all search parameter flags in Lixplore

Table of Contents

Overview

Search parameter flags define what to search for and how many results to retrieve. Lixplore supports three types of searches: query search with Boolean operators, author search, and DOI lookup.

Total Search Flags: 4

Search Types

  • Query Search - Text search with Boolean operators (AND, OR, NOT)
  • Author Search - Search by author name
  • DOI Search - Direct DOI lookup
  • Result Limiting - Control number of results per source

-q, --query

Description: Search query string with support for Boolean operators and advanced syntax.

Syntax: 

lixplore [SOURCE] -q "QUERY" [OPTIONS]
lixplore [SOURCE] --query "QUERY" [OPTIONS]

Type: String value (required for search)

Default: None

Boolean Operators: - AND - Both terms must be present - OR - Either term must be present - NOT - Exclude term - () - Group terms for complex queries

Examples

Example 1: Simple Query 

lixplore -P -q "cancer treatment" -m 20
Search for articles containing "cancer treatment" phrase.

Example 2: AND Operator 

lixplore -P -q "diabetes AND obesity" -m 30
Find articles that mention both diabetes AND obesity.

Example 3: OR Operator 

lixplore -P -q "cancer OR tumor" -m 25
Find articles mentioning either cancer OR tumor.

Example 4: NOT Operator 

lixplore -P -q "diabetes NOT type1" -m 20
Find diabetes articles excluding type 1 diabetes.

Example 5: Complex Query with Parentheses 

lixplore -P -q "(cancer OR tumor) AND (treatment OR therapy)" -m 40
Advanced query: (cancer OR tumor) combined with (treatment OR therapy).

Example 6: Multi-Source with Boolean 

lixplore -A -q "COVID-19 AND (vaccine OR treatment)" -m 100 -D --sort newest
Search all sources for COVID-19 vaccines or treatments, deduplicate, sort by newest.

Example 7: Field-Specific Search (PubMed) 

lixplore -P -q "Smith J[Author] AND cancer[Title]" -m 15
PubMed-specific: Author Smith J with cancer in title.

Example 8: Date-Filtered Query 

lixplore -P -q "machine learning" -d 2020-01-01 2024-12-31 -m 50
Search with date range filter for recent ML papers.

Example 9: Query with Export 

lixplore -C -q "quantum computing" -m 30 -X bibtex -o quantum_papers.bib
Search and export quantum computing papers to BibTeX.

Example 10: Multi-Term Complex Query 

lixplore -P -q "((breast OR ovarian) AND cancer) AND (BRCA1 OR BRCA2)" -m 50
Highly specific query for BRCA-related breast/ovarian cancer.

Query Syntax Tips

1. Phrase Matching: 

# Exact phrase (use quotes in your query string)
lixplore -P -q "machine learning" -m 10

# Individual words
lixplore -P -q "machine OR learning" -m 10

2. Boolean Logic: 

# AND (both required)
lixplore -P -q "cancer AND treatment" -m 10

# OR (either acceptable)
lixplore -P -q "cancer OR tumor" -m 10

# NOT (exclude)
lixplore -P -q "diabetes NOT type2" -m 10

3. Grouping with Parentheses: 

# Group related terms
lixplore -P -q "(lung OR breast) AND cancer" -m 10

# Nested groups
lixplore -P -q "((A OR B) AND C) NOT D" -m 10

4. PubMed Field Tags: 

# Author field
lixplore -P -q "Smith J[Author]" -m 10

# Title field
lixplore -P -q "diabetes[Title]" -m 10

# Title/Abstract
lixplore -P -q "CRISPR[Title/Abstract]" -m 10

Tips

  • Use quotes around entire query: -q "your query here"
  • Boolean operators must be UPPERCASE (AND, OR, NOT)
  • Parentheses allow complex logic
  • Field tags work best with PubMed
  • Combine with date filters for recent research

Warnings

  • Complex queries may return fewer results
  • Some sources don't support all Boolean operators
  • Field tags (e.g., [Author]) are source-specific
  • Special characters may need escaping in terminal

-au, --author

Description: Search for articles by specific author name.

Syntax: 

lixplore [SOURCE] -au "AUTHOR NAME" [OPTIONS]
lixplore [SOURCE] --author "AUTHOR NAME" [OPTIONS]

Type: String value

Default: None

Name Formats: - "Smith J" (Last name + Initial) - "John Smith" (First + Last) - "Smith, John" (Last, First) - "Einstein A" (Famous scientists)

Examples

Example 1: Basic Author Search 

lixplore -P -au "Smith J" -m 15
Find articles by author Smith J in PubMed.

Example 2: Full Name Search 

lixplore -C -au "John Smith" -m 20
Search Crossref for articles by John Smith.

Example 3: Author with Abstracts 

lixplore -P -au "Watson JD" -m 10 -a
Find Watson's articles and display abstracts.

Example 4: Author with Date Filter 

lixplore -P -au "Einstein A" -d 1900-01-01 1955-12-31 -m 25
Find Einstein's papers from his lifetime.

Example 5: Author Export to EndNote 

lixplore -P -au "Darwin C" -m 30 -X enw -o darwin_papers.enw
Export Darwin's work to EndNote format.

Example 6: Multi-Source Author Search 

lixplore -A -au "Hawking S" -m 50 -D
Find Hawking's papers across all sources, deduplicate.

Example 7: Author with Sorting 

lixplore -P -au "Curie M" -m 40 --sort oldest
Get Curie's papers sorted chronologically.

Example 8: Author Statistics 

lixplore -P -au "Feynman R" -m 100 --stat
Analyze Feynman's publication patterns.

Example 9: Recent Author Publications 

lixplore -x -au "LeCun Y" -m 20 --sort newest
Get Yann LeCun's latest arXiv preprints.

Example 10: Author Co-Publication Analysis 

lixplore -P -au "Watson JD" -m 50 --stat --stat-top 20
Analyze Watson's collaborations (top 20 co-authors).

Author Name Format Tips

PubMed Format: 

# Last name + First initial
lixplore -P -au "Smith J" -m 10

# Full last name + Full first name
lixplore -P -au "Smith John" -m 10

# Formal format
lixplore -P -au "Smith, John" -m 10

Crossref/Other Sources: 

# First + Last (more common)
lixplore -C -au "John Smith" -m 10

Handling Common Names: 

# Add date filter to narrow results
lixplore -P -au "Smith J" -d 2015-01-01 2024-12-31 -m 20

# Use query instead for more specificity
lixplore -P -q "Smith J[Author] AND genetics[Title]" -m 10

Tips

  • Try multiple name formats if no results
  • Use initials for PubMed (more reliable)
  • Combine with date filter for recent work
  • Some sources better support author search than others
  • Statistics flag useful for author publication analysis

Warnings

  • Common names may return many irrelevant results
  • Name format varies by source (try both formats)
  • Some databases may not support author search
  • Middle initials often not indexed

-DOI, --doi

Description: Search for a specific article by its Digital Object Identifier (DOI).

Syntax: 

lixplore [SOURCE] -DOI "DOI STRING" [OPTIONS]
lixplore [SOURCE] --doi "DOI STRING" [OPTIONS]

Type: String value

Default: None

DOI Format: 10.XXXX/YYYYY

Examples

Example 1: Basic DOI Lookup 

lixplore -C -DOI "10.1038/nature12345"
Retrieve article metadata using DOI from Crossref.

Example 2: DOI with Details 

lixplore -C -DOI "10.1126/science.1234567" -N 1
Get full article details for DOI.

Example 3: DOI Export to BibTeX 

lixplore -C -DOI "10.1038/nature12345" -X bibtex
Get BibTeX citation for specific DOI.

Example 4: DOI Export to EndNote 

lixplore -C -DOI "10.1126/science.1234567" -X enw
Export DOI article to EndNote format.

Example 5: Multiple DOIs (using multiple commands) 

lixplore -C -DOI "10.1038/nature12345" -X csv -o results.csv
lixplore -C -DOI "10.1126/science.1234567" -X csv -o results.csv
Look up multiple DOIs (append mode).

Example 6: DOI with Enrichment 

lixplore -C -DOI "10.1038/nature12345" --enrich crossref
Get enriched metadata for DOI.

Example 7: DOI PDF Download 

lixplore -C -DOI "10.1371/journal.pone.0123456" --download-pdf
Download PDF for open access DOI (e.g., PLOS).

Example 8: DOI to Zotero 

lixplore -C -DOI "10.1038/nature12345" --add-to-zotero
Add DOI article directly to Zotero library.

Example 9: DOI Citation Format 

lixplore -C -DOI "10.1038/nature12345" -c apa
Get APA-formatted citation for DOI.

Example 10: DOI with Annotation 

lixplore -C -DOI "10.1038/nature12345"
lixplore --annotate 1 --rating 5 --tags "important,methodology"
Look up and annotate a specific DOI article.

DOI Format Examples

Valid DOI Formats: 

# Standard format
10.1038/nature12345

# With URL prefix (works too)
https://doi.org/10.1038/nature12345

# arXiv DOI
10.48550/arXiv.2103.14030

# PubMed Central DOI
10.1371/journal.pone.0123456

Tips

  • Crossref is best source for DOI lookup
  • DOI lookup is extremely fast (single record)
  • Most reliable way to get specific article
  • Automatically validates DOI format
  • Great for citation management

Warnings

  • DOI must exist in database
  • Some very old articles may not have DOIs
  • Invalid DOI format will return no results
  • Not all sources support DOI search equally well

Result Limiting

-m, --max_results

Description: Maximum number of results to retrieve per source.

Syntax: 

lixplore [SOURCE] -q "QUERY" -m NUMBER [OPTIONS]
lixplore [SOURCE] -q "QUERY" --max_results NUMBER [OPTIONS]

Type: Integer value

Default: 10

Range: 1-1000 (recommended: 10-200)

Examples

Example 1: Small Sample 

lixplore -P -q "cancer" -m 5
Quick preview with just 5 results.

Example 2: Medium Search 

lixplore -P -q "diabetes" -m 50
Comprehensive search with 50 results.

Example 3: Large Literature Review 

lixplore -A -q "machine learning" -m 200 -D
Extensive search across all sources (200 per source).

Example 4: Pagination Example 

lixplore -P -q "COVID-19" -m 100 -p 1 --page-size 20
Retrieve 100 results, display 20 per page.

Example 5: Export Top Results 

lixplore -P -q "genetics" -m 100 --sort newest -S first:20 -X xlsx
Get 100 results, sort, export top 20.

Example 6: Statistics on Large Set 

lixplore -A -q "climate change" -m 500 -D --stat
Analyze 500 articles per source for comprehensive statistics.

Example 7: Author Publication Count 

lixplore -P -au "Smith J" -m 200 --stat
Get all author publications for analysis.

Example 8: Multi-Source Balanced 

lixplore -s PCE -q "neuroscience" -m 30 -D
30 results per source (90 total before dedup).

Example 9: Selective Export 

lixplore -P -q "immunology" -m 100 -S odd -X csv
Retrieve 100, export every other one (50 articles).

Example 10: Performance Optimization 

lixplore -P -q "quick check" -m 3
Ultra-fast search for quick verification.

Result Limiting Tips

Performance vs Coverage: 

# Fast (single source, few results)
lixplore -P -q "query" -m 10

# Balanced
lixplore -s PC -q "query" -m 50 -D

# Comprehensive (slow)
lixplore -A -q "query" -m 200 -D

Per-Source Behavior: 

# With -A flag: 50 results PER source
lixplore -A -q "query" -m 50
# Total: up to 250 results (5 sources × 50)

# After deduplication:
lixplore -A -q "query" -m 50 -D
# Total: ~150-200 (depends on overlap)

Pagination Strategy: 

# Instead of loading all at once
lixplore -P -q "query" -m 500

# Use pagination
lixplore -P -q "query" -m 500 -p 1 --page-size 50
lixplore -P -q "query" -m 500 -p 2 --page-size 50

Tips

  • Start small (10-20) for exploratory searches
  • Use 50-100 for literature reviews
  • Use 200+ for comprehensive analysis
  • Results are cached (can review later)
  • Combine with selection for subset export

Warnings

  • Higher limits = slower search
  • API rate limits may apply
  • Very large results may cause memory issues
  • Some sources have maximum limits

Boolean Operators Guide

Operator Reference

Operator Symbol Purpose Example
AND AND Both terms required cancer AND treatment
OR OR Either term accepted cancer OR tumor
NOT NOT Exclude term diabetes NOT type1
Grouping () Group operations (A OR B) AND C

Logic Examples

1. Simple AND: 

lixplore -P -q "diabetes AND obesity" -m 20
Articles must mention BOTH diabetes and obesity.

2. Simple OR: 

lixplore -P -q "cancer OR tumor" -m 20
Articles can mention cancer, tumor, or both.

3. Simple NOT: 

lixplore -P -q "diabetes NOT type1" -m 20
Articles about diabetes but NOT type 1.

4. AND + OR: 

lixplore -P -q "cancer AND (treatment OR therapy)" -m 20
Cancer articles that mention treatment OR therapy.

5. Complex Nested: 

lixplore -P -q "((lung OR breast) AND cancer) NOT metastatic" -m 30
Lung or breast cancer articles, excluding metastatic.

6. Multiple AND: 

lixplore -P -q "COVID-19 AND vaccine AND efficacy" -m 20
All three terms must be present.

7. Multiple OR: 

lixplore -P -q "cancer OR tumor OR neoplasm OR malignancy" -m 30
Any of these synonyms acceptable.

Truth Tables

AND Operator: | Term A | Term B | Result | |--------|--------|--------| | Present | Present | ✓ Match | | Present | Absent | ✗ No match | | Absent | Present | ✗ No match | | Absent | Absent | ✗ No match |

OR Operator: | Term A | Term B | Result | |--------|--------|--------| | Present | Present | ✓ Match | | Present | Absent | ✓ Match | | Absent | Present | ✓ Match | | Absent | Absent | ✗ No match |

NOT Operator: | Term A | NOT Term B | Result | |--------|------------|--------| | Present | Present | ✗ No match | | Present | Absent | ✓ Match | | Absent | Present | ✗ No match | | Absent | Absent | ✗ No match |

Best Practices

1. Start Broad, Then Refine

# Step 1: Broad search
lixplore -P -q "cancer" -m 10

# Step 2: Add specificity
lixplore -P -q "breast cancer" -m 20

# Step 3: Add more terms
lixplore -P -q "breast cancer AND treatment" -m 30

2. Use Boolean Operators for Precision

# Less precise (phrase search)
lixplore -P -q "cancer treatment" -m 20

# More precise (both terms required)
lixplore -P -q "cancer AND treatment" -m 20

# Most precise (specific combination)
lixplore -P -q "(breast OR ovarian) AND cancer AND BRCA1" -m 30

3. Combine Search Types

# Query search for broad results
lixplore -P -q "genetics" -m 50

# Author search for specific researcher
lixplore -P -au "Watson JD" -m 30

# DOI for specific article
lixplore -C -DOI "10.1038/nature12345"

4. Use Appropriate Result Limits

# Quick check (5-10)
lixplore -P -q "test query" -m 5

# Standard search (20-50)
lixplore -P -q "research topic" -m 30

# Literature review (100-200)
lixplore -A -q "comprehensive topic" -m 150 -D

# Statistical analysis (200+)
lixplore -A -q "analysis topic" -m 300 -D --stat

5. Leverage Date Filters

# Recent research only
lixplore -P -q "COVID-19" -d 2020-01-01 2024-12-31 -m 50

# Historical perspective
lixplore -P -q "genetics" -d 1950-01-01 1970-12-31 -m 30 --sort oldest

Troubleshooting

Problem: No results found

Solution 1: Simplify query 

# Instead of complex query
lixplore -P -q "((A AND B) OR C) NOT D" -m 20

# Try simpler
lixplore -P -q "A OR B" -m 20

Solution 2: Remove Boolean operators 

# Instead of
lixplore -P -q "cancer AND treatment" -m 20

# Try
lixplore -P -q "cancer treatment" -m 20

Solution 3: Try different source 

# If PubMed returns nothing
lixplore -P -q "query" -m 20

# Try Crossref or all sources
lixplore -A -q "query" -m 20

Problem: Too many irrelevant results

Solution: Add more specific terms 

# Too broad
lixplore -P -q "cancer" -m 100

# More specific
lixplore -P -q "breast cancer AND BRCA1 AND treatment" -m 50

Problem: Author search returns wrong person

Solution: Add date filter or query combination 

# Generic author search
lixplore -P -au "Smith J" -m 50

# With date filter
lixplore -P -au "Smith J" -d 2015-01-01 2024-12-31 -m 30

# With topic filter (use query instead)
lixplore -P -q "Smith J[Author] AND genetics[Title]" -m 20

Last Updated: 2024-12-28 Lixplore Version: 2.0+