CLI Reference¶

Literature Mapper provides a complete command-line interface for managing your research corpus.

Core Workflow¶

Process PDFs¶

Extract text and build the Knowledge Graph:

literature-mapper process ./my_research --recursive

Option	Description
`--recursive`	Process PDFs in subdirectories

Fetch Citations¶

Enrich your corpus with OpenAlex citation data:

literature-mapper citations ./my_research --email you@example.com

Option	Description
`--email`	Your email (optional, for faster rate limits)

View Status¶

Check corpus health and statistics:

literature-mapper status ./my_research

Search & Analysis¶

Synthesize Answers¶

Ask a research question:

literature-mapper synthesize ./my_research "What is the impact of X on Y?"

Validate Hypotheses¶

Test a claim against your corpus:

literature-mapper validate ./my_research "X causes Y."

Find Hub Papers¶

Identify the most referenced papers:

literature-mapper hubs ./my_research --limit 10

Corpus Statistics¶

View comprehensive stats:

literature-mapper stats ./my_research

Temporal Analysis¶

Run temporal first

Temporal commands require computing stats first with literature-mapper temporal.

# Compute temporal stats (run this first!)
literature-mapper temporal ./my_research

# View rising concepts
literature-mapper trends ./my_research --direction rising

# View declining concepts
literature-mapper trends ./my_research --direction declining

# Analyze a specific concept's trajectory
literature-mapper trajectory "homophily" ./my_research

# Detect concept eras (revivals after gaps)
literature-mapper eras ./my_research --gap 5

Gap Detection (Ghost Hunting)¶

Find missing papers and authors:

# Find missing papers (bibliographic ghosts)
literature-mapper ghosts ./my_research --mode bibliographic --threshold 3

# Find missing authors
literature-mapper ghosts ./my_research --mode authors --threshold 5

Option	Description
`--mode`	`bibliographic` (papers) or `authors`
`--threshold`	Minimum citations to be considered a "ghost"

Export & Visualization¶

GEXF Export¶

# Semantic knowledge graph (default)
literature-mapper viz ./my_research -o graph.gexf

# Co-authorship network
literature-mapper viz ./my_research -o authors.gexf --mode authors

# Concept co-occurrence
literature-mapper viz ./my_research -o concepts.gexf --mode concepts

# Paper similarity
literature-mapper viz ./my_research -o similar.gexf --mode similarity --threshold 0.3

Mode	Description
`semantic`	Full knowledge graph
`authors`	Co-authorship network
`concepts`	Topic co-occurrence
`river`	Concepts with temporal data
`similarity`	Paper similarity (Jaccard)

CSV Export¶

literature-mapper export ./my_research output.csv

Environment Variables¶

Variable	Purpose	Default
`GEMINI_API_KEY`	Required. Google AI key	None
`LITERATURE_MAPPER_MODEL`	Default model	`gemini-3-flash-preview`
`LITERATURE_MAPPER_MAX_FILE_SIZE`	Max PDF size (bytes)	`52428800` (50 MB)
`LITERATURE_MAPPER_BATCH_SIZE`	PDFs per batch	`10`
`LITERATURE_MAPPER_LOG_LEVEL`	Log level	`INFO`
`LITERATURE_MAPPER_VERBOSE`	Debug mode	`false`