Search Sources Guide¶

Comprehensive guide to searching each academic database

Table of Contents¶

PubMed
Crossref
DOAJ
EuropePMC
arXiv
Multi-Source Strategies

PubMed¶

Overview¶

Coverage: 35+ million citations
Focus: Biomedical and life sciences
Provider: U.S. National Library of Medicine
Best For: Clinical medicine, biology, health sciences

Basic Search¶

lixplore -P -q "diabetes treatment" -m 20

Advanced Search Techniques¶

1. MeSH Terms (Medical Subject Headings)

lixplore -P -q "diabetes mellitus[MeSH]" -m 30

2. Field-Specific Search

# Title field
lixplore -P -q "CRISPR[Title]" -m 20

# Title/Abstract
lixplore -P -q "gene therapy[Title/Abstract]" -m 30

# Author field
lixplore -P -q "Smith J[Author] AND cancer[Title]" -m 15

3. Publication Type Filters

lixplore -P -q "diabetes AND systematic review[pt]" -m 20
lixplore -P -q "COVID-19 AND randomized controlled trial[pt]" -m 30

Best Practices¶

DO: - Use MeSH terms for precision - Combine with date filters for recent research - Search author publications - Use field tags [Title], [Author], [Journal]

DON'T: - Expect full-text availability for all articles - Use for non-biomedical topics - Ignore publication type filters

Common Workflows¶

Clinical Research:

lixplore -P -q "hypertension AND treatment[Title/Abstract]" \
  -d 2020-01-01 2024-12-31 \
  -m 50 \
  --sort newest \
  -X enw

Author Publications:

lixplore -P -au "Smith J" -m 100 --sort newest --stat

Systematic Review Preparation:

lixplore -P -q "cancer immunotherapy" \
  -m 200 \
  --enrich \
  -X xlsx \
  -o systematic_review.xlsx

Crossref¶

Overview¶

Coverage: 140+ million records
Focus: All academic disciplines with DOIs
Provider: Crossref (DOI registration agency)
Best For: Multi-disciplinary research, citation metadata

Basic Search¶

lixplore -C -q "machine learning" -m 30

Advanced Techniques¶

1. DOI Lookup

lixplore -C -DOI "10.1038/nature12345"

2. Journal-Focused Search

lixplore -C -q "artificial intelligence" -m 100 --sort journal

3. Citation Metadata

lixplore -C -q "quantum computing" -m 50 --enrich crossref -X bibtex

Best Practices¶

DO: - Use for DOI lookup - Combine with enrichment for complete metadata - Search across all disciplines - Export to BibTeX for LaTeX

DON'T: - Expect full-text access - Use for preprint-only searches - Rely on abstract availability

Common Workflows¶

Bibliography Building:

lixplore -C -q "topic" -m 100 --enrich crossref -X bibtex -o refs.bib

Multi-Disciplinary Review:

lixplore -C -q "artificial intelligence healthcare" \
  -m 200 \
  --sort newest \
  -S first:50 \
  -X xlsx

DOAJ¶

Overview¶

Coverage: 19,000+ journals, 8+ million articles
Focus: Open access peer-reviewed content
Provider: DOAJ (community-driven)
Best For: Free full-text access, open science

Basic Search¶

lixplore -J -q "renewable energy" -m 20

Advanced Techniques¶

1. Open Access PDFs

lixplore -J -q "public health" -m 15 --download-pdf

2. PDF Link Display

lixplore -J -q "education" -m 20 --show-pdf-links

3. Multi-Format Export

lixplore -J -q "psychology" -m 30 -X csv,ris,bibtex

Best Practices¶

DO: - Use for freely accessible articles - Download PDFs directly - Combine with other sources (deduplicate) - Check for open access versions

DON'T: - Expect comprehensive coverage - Use as only source for lit reviews - Assume latest articles indexed immediately

Common Workflows¶

Open Access Literature Review:

lixplore -J -q "machine learning" \
  -m 50 \
  --download-pdf \
  -X xlsx \
  -o open_access_ml.xlsx

PDF Collection:

lixplore -J -q "climate change" -m 30 --show-pdf-links
# Click links or:
lixplore -J -q "climate change" -m 30 --download-pdf

EuropePMC¶

Overview¶

Coverage: 42+ million records
Focus: Biomedical, life sciences (European)
Provider: EMBL-EBI
Best For: European research, open access content

Basic Search¶

lixplore -E -q "malaria treatment" -m 20

Advanced Techniques¶

1. Grant-Funded Research

lixplore -E -q "gene therapy" -m 30 --enrich

2. Open Access Filter

lixplore -E -q "immunology" -m 25 --download-pdf

Best Practices¶

DO: - Use alongside PubMed for biomedical - Check for open access content - Use deduplication with PubMed

DON'T: - Use for non-biomedical topics - Expect different results from PubMed always - Skip deduplication

Common Workflows¶

Biomedical Research (EU Focus):

lixplore -s PE -q "cancer therapy" \
  -m 100 \
  -D \
  --sort newest \
  -X enw

arXiv¶

Overview¶

Coverage: 2.3+ million preprints
Focus: Physics, math, CS, quantitative fields
Provider: Cornell University
Best For: Latest research, preprints, open access PDFs

Basic Search¶

lixplore -x -q "neural networks" -m 20

Advanced Techniques¶

1. Latest Research

lixplore -x -q "transformers" -m 30 --sort newest

2. PDF Downloads

lixplore -x -q "deep learning" -m 10 --download-pdf

3. Clickable PDF Links

lixplore -x -q "quantum physics" -m 15 --show-pdf-links

4. Author Tracking

lixplore -x -au "LeCun Y" -m 20 --sort newest

Best Practices¶

DO: - Use for cutting-edge CS/physics research - Download PDFs (always available) - Track specific authors - Sort by newest for latest papers

DON'T: - Expect peer review - Use for medical/clinical research - Trust all methodologies blindly

Common Workflows¶

Stay Current in CS:

lixplore -x -q "machine learning" \
  -d 2024-01-01 2024-12-31 \
  -m 100 \
  --sort newest \
  --stat

Author Monitoring:

lixplore -x -au "Hinton G" -m 50 --sort newest -X xlsx

PDF Collection:

lixplore -x -q "deep learning" -m 20 --download-pdf

Multi-Source Strategies¶

All Sources Search¶

lixplore -A -q "query" -m 50 -D --sort newest

Advantages: - Comprehensive coverage - Cross-disciplinary results - Maximum recall

Disadvantages: - Slower (5x API calls) - Many duplicates (use -D!) - Can be overwhelming

Custom Combinations¶

Biomedical (PubMed + EuropePMC):

lixplore -s PE -q "cancer treatment" -m 50 -D

Computer Science (arXiv + Crossref):

lixplore -s XC -q "machine learning" -m 50 -D

Open Access Only (DOAJ + arXiv):

lixplore -s JX -q "research" -m 50 -D --download-pdf

Peer-Reviewed Recent (PubMed + Crossref):

lixplore -s PC -q "AI" -m 100 -D --sort newest -S first:30

Deduplication Strategy¶

Essential for Multi-Source:

# ALWAYS use -D flag
lixplore -A -q "query" -m 50 -D

Choose Strategy:

# Strict (bibliography)
lixplore -A -q "query" -m 100 -D strict

# Loose (discovery)
lixplore -A -q "query" -m 200 -D loose

# Auto (balanced)
lixplore -A -q "query" -m 150 -D

Source Selection Decision Tree¶

Need biomedical/clinical research?
  ├─ Yes → PubMed or EuropePMC
  └─ No → Continue

Need latest CS/physics preprints?
  ├─ Yes → arXiv
  └─ No → Continue

Need open access PDFs?
  ├─ Yes → DOAJ or arXiv
  └─ No → Continue

Need multi-disciplinary?
  ├─ Yes → Crossref or All sources
  └─ No → Continue

Need comprehensive coverage?
  └─ Use All sources (-A) with deduplication (-D)

Performance Comparison¶

Aspect	PubMed	Crossref	DOAJ	EuropePMC	arXiv
Speed	Fast	Fast	Medium	Medium	Fast
Coverage	★★★★☆	★★★★★	★★★☆☆	★★★★☆	★★★☆☆
Full Text	Some	No	Yes	Some	Yes
Metadata	★★★★★	★★★★★	★★★☆☆	★★★★☆	★★★☆☆

Last Updated: 2024-12-28