Crate biblib

A comprehensive library for parsing, managing, and deduplicating academic citations.

biblib provides robust functionality for working with academic citations in various formats. It focuses on accurate parsing, format conversion, and intelligent deduplication of citations.

Features

The library has several optional features that can be enabled in your Cargo.toml:

• csv - Enable CSV format support (enabled by default)
• pubmed - Enable PubMed/MEDLINE format support (enabled by default)
• xml - Enable EndNote XML support (enabled by default)
• ris - Enable RIS format support (enabled by default)
• dedupe - Enable citation deduplication (enabled by default)

To use only specific features, disable default features and enable just what you need:

[dependencies]
biblib = { version = "0.2.0", default-features = false, features = ["csv", "ris"] }

Key Characteristics

• Multiple Format Support: Parse citations from:

  • RIS (Research Information Systems)
  • PubMed/MEDLINE
  • EndNote XML
  • CSV with configurable mappings

• Source Tracking: Each parser can track the source of citations

  • with_source() method available on all parsers
  • Source information preserved in Citation objects
  • Useful for tracking citation origins

• Rich Metadata Support:

  • Authors with affiliations
  • Journal details (name, abbreviation, ISSN)
  • DOIs and other identifiers
  • Complete citation metadata

Basic Usage

use biblib::{CitationParser, RisParser};

// Parse RIS format with source tracking
let input = r#"TY  - JOUR
TI  - Example Article
AU  - Smith, John
ER  -"#;

let parser = RisParser::new().with_source("Pubmed");
let citations = parser.parse(input).unwrap();
println!("Title: {}", citations[0].title);
println!("Source: {}", citations[0].source.clone().unwrap());

Citation Formats

Each format has a dedicated parser with format-specific features:

use biblib::{RisParser, PubMedParser, EndNoteXmlParser, csv::CsvParser};

// RIS format
let ris = RisParser::new();

// PubMed format
let pubmed = PubMedParser::new().with_source("Pubmed");

// EndNote XML
let endnote = EndNoteXmlParser::new().with_source("Google Scholar");

// CSV format
let csv = CsvParser::new().with_source("Cochrane");

Citation Deduplication

use biblib::{Citation, CitationParser, RisParser};

let ris_input = r#"TY  - JOUR
TI  - Example Citation 1
AU  - Smith, John
ER  -

TY  - JOUR
TI  - Example Citation 2
AU  - Smith, John
ER  -"#;

let parser = RisParser::new();
let mut citations = parser.parse(ris_input).unwrap();

// Configure deduplication
use biblib::dedupe::{Deduplicator, DeduplicatorConfig};

// Configure deduplication
let config = DeduplicatorConfig {
    group_by_year: true,
    run_in_parallel: true,
    source_preferences: vec!["PubMed".to_string(), "Cochrane".to_string()],
};

let deduplicator = Deduplicator::new().with_config(config);
let duplicate_groups = deduplicator.find_duplicates(&citations).unwrap();

for group in duplicate_groups {
    println!("Original: {}", group.unique.title);
    for duplicate in group.duplicates {
        println!("  Duplicate: {}", duplicate.title);
    }
}

Error Handling

The library uses a custom Result type that wraps CitationError for consistent error handling across all operations:

use biblib::{CitationParser, RisParser, CitationError};

let result = RisParser::new().parse("invalid input");
match result {
    Ok(citations) => println!("Parsed {} citations", citations.len()),
    Err(CitationError::InvalidFormat(msg)) => eprintln!("Parse error: {}", msg),
    Err(e) => eprintln!("Other error: {}", e),
}

Performance Considerations

• Use year-based grouping for large datasets
• Enable parallel processing for better performance
• Consider using CSV format for very large datasets

Thread Safety

All parser implementations are thread-safe and can be shared between threads. The deduplicator supports parallel processing through the run_in_parallel option.

Re-exports

pub use csv::CsvParser;

pub use endnote_xml::EndNoteXmlParser;

pub use pubmed::PubMedParser;

pub use ris::RisParser;

Modules

csv

CSV format parser implementation with source tracking support.

dedupe

Citations deduplicator implementation.

endnote_xml

EndNote XML format parser implementation with source tracking support.

pubmed

PubMed format parser implementation with source tracking support.

ris

RIS format parser implementation with source tracking support.

Structs

Author

Represents an author of a citation.

Citation

Represents a single citation with its metadata.

DuplicateGroup

Represents a group of duplicate citations with one unique citation

Enums

CitationError

Represents errors that can occur during citation parsing.

Traits

CitationParser

Trait for implementing citation parsers.

Functions

detect_and_parse

Format detection and automatic parsing of citation files

Type Aliases

Result

A specialized Result type for citation operations.