Source Selection Flags¶

Complete documentation for all source selection flags in Lixplore

Table of Contents¶

Overview
Individual Source Flags
Combined Source Flags
Custom API Integration
Source Comparison
Best Practices

Overview¶

Lixplore supports searching across 5 major academic databases plus custom API integrations. You can search individual sources or combine multiple sources in a single query.

Total Source Flags: 8

Available Sources¶

PubMed - Biomedical and life sciences literature (MEDLINE)
Crossref - Scholarly works with DOIs (70+ million records)
DOAJ - Directory of Open Access Journals
EuropePMC - Europe PubMed Central (biomedical + life sciences)
arXiv - Preprint repository (physics, math, CS, etc.)
Custom APIs - User-configured sources (Springer, BASE, etc.)

Individual Source Flags¶

`-P, --pubmed`¶

Description: Search PubMed (MEDLINE) database for biomedical and life sciences literature.

Syntax:

lixplore -P -q "QUERY" [OPTIONS]
lixplore --pubmed -q "QUERY" [OPTIONS]

Type: Boolean flag (no value required)

Default: Not enabled

Database Info: - Coverage: 35+ million citations - Focus: Biomedical, life sciences, clinical medicine - Provider: U.S. National Library of Medicine (NLM) - Update Frequency: Daily - Full Text: Links to PMC when available

Examples¶

Example 1: Basic PubMed Search

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

Search PubMed for cancer treatment articles, retrieve 20 results.

Example 2: PubMed with Abstracts

lixplore -P -q "diabetes type 2" -m 15 -a

Search diabetes articles and display abstracts inline.

Example 3: PubMed with Date Filter

lixplore -P -q "COVID-19 vaccine" -d 2020-01-01 2024-12-31 -m 30

Search COVID-19 vaccine articles published between 2020-2024.

Example 4: PubMed Export to EndNote

lixplore -P -q "neuroscience" -m 50 -X enw -o brain_research.enw

Search neuroscience articles and export to EndNote Tagged format.

Example 5: PubMed with Boolean Operators

lixplore -P -q "(cancer OR tumor) AND (treatment OR therapy)" -m 40

Advanced query using AND/OR operators for precise results.

Tips¶

PubMed excels at biomedical and clinical research
Use MeSH terms for better precision (e.g., "diabetes mellitus" instead of "diabetes")
Author search format: lixplore -P -au "Smith J" -m 10
Combine with -a flag to preview abstracts before exporting

Warnings¶

PubMed API rate limit: 3 requests/second (handled automatically)
Results may not include full text (check PMC availability)
Date filters may not work for all queries (PubMed limitation)

-au, --author - Search by author name
-d, --date - Date range filter
--download-pdf - Download PMC PDFs

`-C, --crossref`¶

Description: Search Crossref database for scholarly works across all disciplines with DOI registration.

Syntax:

lixplore -C -q "QUERY" [OPTIONS]
lixplore --crossref -q "QUERY" [OPTIONS]

Type: Boolean flag

Default: Not enabled

Database Info: - Coverage: 140+ million records - Focus: All academic disciplines with DOIs - Provider: Crossref (DOI registration agency) - Update Frequency: Real-time - Full Text: Links to publisher websites

Examples¶

Example 1: Crossref Multi-Disciplinary Search

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

Search across all disciplines for machine learning papers.

Example 2: Crossref with Sorting

lixplore -C -q "climate change" -m 50 --sort newest

Get latest climate change research sorted by publication date.

Example 3: Crossref DOI Lookup

lixplore -C -DOI "10.1038/nature12345"

Retrieve article metadata using DOI.

Example 4: Crossref Export to BibTeX

lixplore -C -q "quantum computing" -m 25 -X bibtex

Export quantum computing papers for LaTeX citations.

Example 5: Crossref with Enrichment

lixplore -C -q "CRISPR" -m 20 --enrich crossref

Search and enrich metadata with additional Crossref data.

Tips¶

Crossref has excellent coverage across ALL disciplines
DOI lookup is extremely reliable and fast
Metadata is generally very complete (journal, volume, pages, etc.)
Best source for citation metadata and journal information

Warnings¶

No full-text access (only metadata and DOI links)
Some preprints may not be included
Publisher paywalls may prevent access to full articles

-DOI, --doi - Direct DOI lookup
--enrich - Metadata enrichment
--sort - Sort by date/journal/author

`-J, --doaj`¶

Description: Search Directory of Open Access Journals (DOAJ) for freely accessible peer-reviewed content.

Syntax:

lixplore -J -q "QUERY" [OPTIONS]
lixplore --doaj -q "QUERY" [OPTIONS]

Type: Boolean flag

Default: Not enabled

Database Info: - Coverage: 19,000+ journals, 8+ million articles - Focus: Open access peer-reviewed journals - Provider: DOAJ (community-driven) - Update Frequency: Weekly - Full Text: Always freely available

Examples¶

Example 1: DOAJ Open Access Search

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

Search open access journals for renewable energy research.

Example 2: DOAJ with PDF Links

lixplore -J -q "public health" -m 15 --show-pdf-links

Display clickable PDF links for open access articles.

Example 3: DOAJ PDF Download

lixplore -J -q "education" -m 10 --download-pdf

Search and automatically download open access PDFs.

Example 4: DOAJ Multi-Format Export

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

Export to multiple formats simultaneously.

Example 5: DOAJ with Statistics

lixplore -J -q "artificial intelligence" -m 100 --stat

Analyze publication trends in open access AI research.

Tips¶

ALL results are open access (no paywalls!)
Great source for freely downloadable PDFs
Excellent for literature reviews requiring full-text access
High-quality peer-reviewed content only

Warnings¶

Smaller coverage compared to PubMed/Crossref
May not have latest articles (indexing delay)
Some disciplines better represented than others

--show-pdf-links - Display PDF links
--download-pdf - Download PDFs
--stat - Statistics dashboard

`-E, --europepmc`¶

Description: Search Europe PubMed Central for biomedical and life sciences literature in Europe.

Syntax:

lixplore -E -q "QUERY" [OPTIONS]
lixplore --europepmc -q "QUERY" [OPTIONS]

Type: Boolean flag

Default: Not enabled

Database Info: - Coverage: 42+ million records - Focus: Biomedical, life sciences (European focus) - Provider: EMBL-EBI - Update Frequency: Daily - Full Text: Open access articles available

Examples¶

Example 1: EuropePMC Search

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

Search European biomedical database for malaria research.

Example 2: EuropePMC with Date Filter

lixplore -E -q "gene therapy" -d 2022-01-01 2024-12-31 -m 25

Recent gene therapy articles from 2022-2024.

Example 3: EuropePMC Author Search

lixplore -E -au "Watson J" -m 15 -a

Find articles by author in EuropePMC.

Example 4: EuropePMC Open Access

lixplore -E -q "immunology" -m 30 --download-pdf

Search and download open access immunology papers.

Example 5: EuropePMC Export

lixplore -E -q "cardiology" -m 40 -X xlsx --export-fields title authors year doi

Export cardiology articles with selected fields.

Tips¶

Good alternative/complement to PubMed
Strong coverage of European research
Excellent open access content availability
Often includes grants and funding information

Warnings¶

Some overlap with PubMed (use deduplication)
European focus may miss some international research
API can be slower during peak hours

-P, --pubmed - Compare with PubMed
-D, --deduplicate - Remove duplicates
--download-pdf - PDF download

`-x, --arxiv`¶

Description: Search arXiv preprint repository for physics, mathematics, computer science, and related fields.

Syntax:

lixplore -x -q "QUERY" [OPTIONS]
lixplore --arxiv -q "QUERY" [OPTIONS]

Type: Boolean flag

Default: Not enabled

Database Info: - Coverage: 2.3+ million preprints - Focus: Physics, math, CS, quantitative fields - Provider: Cornell University - Update Frequency: Daily submissions - Full Text: Always freely available (PDFs)

Examples¶

Example 1: arXiv Computer Science Search

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

Search arXiv for neural network preprints.

Example 2: arXiv with PDF Links

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

Display clickable PDF links for quantum physics papers.

Example 3: arXiv Latest Research

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

Get the latest transformer architecture papers.

Example 4: arXiv PDF Download

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

Search and download deep learning PDFs automatically.

Example 5: arXiv with Statistics

lixplore -x -q "machine learning" -m 200 --stat --stat-top 20

Analyze ML research trends with top 20 authors/topics.

Tips¶

Best source for cutting-edge CS/physics research
ALL articles have freely downloadable PDFs
Often contains latest research before peer review
Great for staying current in fast-moving fields

Warnings¶

Preprints (not peer-reviewed)
Quality varies (no editorial filtering)
Limited to STEM fields (physics, math, CS, etc.)
Author search may be less accurate than PubMed

--show-pdf-links - Display PDF links
--download-pdf - Automatic PDF download
--sort - Sort by date for latest papers

`-A, --all`¶

Description: Search ALL sources simultaneously (PubMed, Crossref, DOAJ, EuropePMC, arXiv).

Syntax:

lixplore -A -q "QUERY" [OPTIONS]
lixplore --all -q "QUERY" [OPTIONS]

Type: Boolean flag

Default: Not enabled

Coverage: All 5 databases combined

Examples¶

Example 1: Comprehensive Search

lixplore -A -q "COVID-19" -m 50 -D

Search all sources and remove duplicates.

Example 2: All Sources with Sorting

lixplore -A -q "climate change" -m 100 -D --sort newest

Get latest research across all databases.

Example 3: All Sources Export

lixplore -A -q "artificial intelligence" -m 200 -D -X xlsx

Comprehensive AI literature review across all sources.

Example 4: All Sources with Statistics

lixplore -A -q "cancer immunotherapy" -m 150 -D --stat

Analyze publication patterns across all databases.

Example 5: All Sources with Selection

lixplore -A -q "genetics" -m 300 -D --sort newest -S first:50 -X enw

Get top 50 latest genetics papers from all sources.

Tips¶

ALWAYS use -D flag to remove duplicates!
Best for comprehensive literature reviews
Provides broader coverage than any single source
Good for discovering research across disciplines

Warnings¶

Much slower than single source (5x API calls)
Will have many duplicates without -D flag
Results can be overwhelming without sorting/selection
API rate limits may apply

-D, --deduplicate - ESSENTIAL with -A
--sort - Organize combined results
-S, --select - Export subset

`-s, --sources`¶

Description: Search specific combination of sources using shorthand codes.

Syntax:

lixplore -s CODES -q "QUERY" [OPTIONS]
lixplore --sources CODES -q "QUERY" [OPTIONS]

Type: String value

Default: None

Source Codes: - P = PubMed - C = Crossref - J = DOAJ - E = EuropePMC - X = arXiv - A = All sources

Examples¶

Example 1: PubMed + arXiv

lixplore -s PX -q "machine learning healthcare" -m 30 -D

Search biomedical and CS sources for ML in healthcare.

Example 2: PubMed + Crossref + EuropePMC

lixplore -s PCE -q "gene therapy" -m 40 -D --sort newest

Comprehensive biomedical search across three databases.

Example 3: DOAJ + arXiv

lixplore -s JX -q "open source software" -m 25 --download-pdf

Search open access sources and download PDFs.

Example 4: All Except arXiv

lixplore -s PCJE -q "clinical trials" -m 50 -D

Search all sources except preprints.

Example 5: Single Source (Alternative Syntax)

lixplore -s P -q "diabetes" -m 20
# Same as: lixplore -P -q "diabetes" -m 20

Tips¶

More concise than multiple individual flags
Easy to remember shorthand codes
Can combine any sources you need
Order doesn't matter (PX = XP)

Warnings¶

Always use -D when combining sources
Invalid codes are silently ignored
A code overrides other codes (searches all)

-D, --deduplicate - Remove duplicates
--sort - Organize results
All individual source flags above

`--custom-api`¶

Description: Use custom-configured API source (Springer, BASE, IEEE, etc.).

Syntax:

lixplore --custom-api NAME -q "QUERY" [OPTIONS]

Type: String value

Default: None

Prerequisites: API must be configured in ~/.lixplore/custom_apis.json

Examples¶

Example 1: Springer API Search

lixplore --custom-api springer -q "nanotechnology" -m 20

Search Springer database (requires API key).

Example 2: BASE (Bielefeld Academic Search Engine)

lixplore --custom-api base -q "open access" -m 30

Search BASE repository for open access content.

Example 3: Custom API with Export

lixplore --custom-api ieee -q "robotics" -m 25 -X bibtex

Search IEEE and export to BibTeX.

Example 4: Combined Custom + Standard Sources

# Note: Cannot combine with -s flag, use separately
lixplore -P -q "query" -m 20 -X csv
lixplore --custom-api springer -q "query" -m 20 -X csv

Example 5: List Available Custom APIs

lixplore --list-custom-apis

Setup Instructions¶

1. Create API Examples:

lixplore --create-api-examples

2. Configure API (edit ~/.lixplore/custom_apis.json):

{
  "springer": {
    "name": "Springer",
    "base_url": "https://api.springernature.com/meta/v2/json",
    "api_key_param": "api_key",
    "query_param": "q",
    "limit_param": "p",
    "requires_auth": true
  }
}

3. Add API Key:

{
  "springer": {
    ...
    "api_key": "YOUR_API_KEY_HERE"
  }
}

Tips¶

Extend Lixplore to ANY REST API
No code modification needed
Great for institutional subscriptions
Can combine with standard sources (separate searches)

Warnings¶

Requires valid API key for most services
Configuration format must match spec
Cannot use with -s or -A flags in same command
API rate limits may apply

--list-custom-apis - Show configured APIs
--create-api-examples - Setup templates

Source Comparison¶

Coverage by Discipline¶

Source	Biomedical	Physical Sciences	Social Sciences	Computer Science	Open Access
PubMed	★★★★★	★☆☆☆☆	★★☆☆☆	★☆☆☆☆	★★★☆☆
Crossref	★★★★☆	★★★★★	★★★★★	★★★★★	★★★☆☆
DOAJ	★★★☆☆	★★★☆☆	★★★☆☆	★★☆☆☆	★★★★★
EuropePMC	★★★★★	★☆☆☆☆	★★☆☆☆	★☆☆☆☆	★★★★☆
arXiv	★☆☆☆☆	★★★★★	★☆☆☆☆	★★★★★	★★★★★

Feature Comparison¶

Feature	PubMed	Crossref	DOAJ	EuropePMC	arXiv
Size	35M+	140M+	8M+	42M+	2.3M+
Full Text	Some	No	Yes	Some	Yes
Peer Review	Yes	Yes	Yes	Yes	No
Latest Research	Medium	High	Medium	Medium	Highest
Metadata Quality	High	Highest	Medium	High	Medium
API Speed	Fast	Fast	Medium	Medium	Fast

Recommended Combinations¶

Biomedical Research:

lixplore -s PE -q "query" -m 50 -D
# PubMed + EuropePMC

Computer Science:

lixplore -s XC -q "query" -m 50 -D
# arXiv + Crossref

Open Access Only:

lixplore -s JX -q "query" -m 50 -D
# DOAJ + arXiv

Comprehensive Review:

lixplore -A -q "query" -m 100 -D
# All sources

Latest Peer-Reviewed:

lixplore -s PC -q "query" -m 50 -D --sort newest
# PubMed + Crossref

Best Practices¶

1. Choose Sources Based on Discipline¶

Biomedical/Health:

lixplore -P -q "clinical trial diabetes" -m 30

Physics/Math:

lixplore -x -q "quantum entanglement" -m 30

Computer Science:

lixplore -x -q "neural networks" -m 30

Multi-Disciplinary:

lixplore -C -q "artificial intelligence" -m 30

2. Always Deduplicate Multi-Source Searches¶

# CORRECT
lixplore -A -q "query" -m 50 -D

# WRONG (will have many duplicates)
lixplore -A -q "query" -m 50

3. Use Specific Combinations¶

# Instead of -A (all sources)
lixplore -A -q "query" -m 50 -D

# Use targeted combination
lixplore -s PE -q "query" -m 50 -D  # Just biomedical

4. Combine with Sorting¶

lixplore -A -q "COVID-19" -m 100 -D --sort newest

5. Export Source Information¶

lixplore -A -q "query" -m 50 -D -X csv --export-fields title authors year source

Troubleshooting¶

Problem: No results from specific source¶

Solution 1: Try different query format

# Instead of exact phrase
lixplore -P -q "machine learning"

# Try individual terms
lixplore -P -q "machine OR learning"

Solution 2: Check source availability

# Test with known query
lixplore -P -q "cancer" -m 5

Problem: Too many duplicates¶

Solution: Use deduplication

lixplore -A -q "query" -m 50 -D strict

Problem: Custom API not working¶

Solution: Verify configuration

# List configured APIs
lixplore --list-custom-apis

# Check configuration file
cat ~/.lixplore/custom_apis.json

Problem: Slow search across all sources¶

Solution: Use targeted combination

# Instead of all sources
lixplore -A -q "query" -m 100

# Use specific sources
lixplore -s PC -q "query" -m 50

Search Flags - Query syntax and search parameters
Filter Flags - Deduplication and sorting
Export Flags - Export and download options
Utility Flags - API configuration and management

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

Source Selection Flags¶

Table of Contents¶

Overview¶

Available Sources¶

Individual Source Flags¶

-P, --pubmed¶

Examples¶

Tips¶

Warnings¶

Related Flags¶

-C, --crossref¶

Examples¶

Tips¶

Warnings¶

Related Flags¶

-J, --doaj¶

Examples¶

Tips¶

Warnings¶

Related Flags¶

-E, --europepmc¶

Examples¶

Tips¶

Warnings¶

Related Flags¶

-x, --arxiv¶

Examples¶

Tips¶

Warnings¶

Related Flags¶

-A, --all¶

Examples¶

Tips¶

Warnings¶

Related Flags¶

-s, --sources¶

Examples¶

Tips¶

Warnings¶

Related Flags¶

--custom-api¶

Examples¶

Setup Instructions¶

Tips¶

Warnings¶

Related Flags¶

Source Comparison¶

Coverage by Discipline¶

Feature Comparison¶

Recommended Combinations¶

Best Practices¶

1. Choose Sources Based on Discipline¶

2. Always Deduplicate Multi-Source Searches¶

3. Use Specific Combinations¶

4. Combine with Sorting¶

5. Export Source Information¶

Troubleshooting¶

Problem: No results from specific source¶

Problem: Too many duplicates¶

Problem: Custom API not working¶

Problem: Slow search across all sources¶

Related Documentation¶

`-P, --pubmed`¶

`-C, --crossref`¶

`-J, --doaj`¶

`-E, --europepmc`¶

`-x, --arxiv`¶

`-A, --all`¶

`-s, --sources`¶

`--custom-api`¶