litvar

is a Data Source.

LitVar is a comprehensive NCBI web service for searching and retrieving variant-specific information from the biomedical literature using advanced text mining and machine learning techniques. Developed by the National Library of Medicine's Computational Biology Branch, LitVar automatically extracts variant-related information from over 35 million PubMed articles and 5.7 million full-text articles in PubMed Central including supplementary materials, with monthly updates to capture the latest research. A key innovation of LitVar is its sophisticated variant normalization system that standardizes different forms of the same variant into unique identifiers, enabling comprehensive search results regardless of which variant nomenclature is used in the query, whether protein level names, DNA level annotations, dbSNP RS identifiers, ClinGen identifiers, or SPDI format. LitVar leverages PubTator, a state-of-the-art literature annotation tool, to identify and display key biological entities including genes, diseases, drugs, chemicals, and mutations within retrieved articles, providing rich contextual information around variants of interest.

Domains

genomics, literature

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Homepage

litvar

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Infores ID

infores:litvar

FAIRsharing ID

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Product Summary

Products

From this Resource
ID Name URL Category Format Description
litvar.web_interface LitVar Web Interface litvar2 GraphicalInterface http Web interface for searching and retri...
litvar.api LitVar API api ProgrammingInterface http RESTful API providing programmatic ac...

Details

LitVar

Overview

LitVar is the National Center for Biotechnology Information’s advanced literature search tool specifically designed for tracking genetic variants in the biomedical literature. Using sophisticated text mining and natural language processing, LitVar provides comprehensive access to variant information extracted from millions of scientific publications.

Information Resource ID

This resource has the Information Resource identifier: infores:litvar

Key Features

Variant Normalization

LitVar’s core strength lies in its ability to normalize different representations of the same variant into a standardized form. Users can search using any of the following formats and retrieve the same comprehensive results:

  • Protein-level names (e.g., P871L, p.P871L, Pro871Leu)
  • DNA-level annotations (e.g., c.2612C>T, g.13843A>G)
  • dbSNP RS identifiers (e.g., rs799917)
  • ClinGen identifiers (e.g., CA123643)
  • SPDI format (e.g., NC_000007.14:140753335:A:C)
  • Gene plus variant combinations (e.g., BRCA1 P871L)

Literature Coverage

  • Over 35 million PubMed articles
  • 5.7 million full-text articles from PubMed Central
  • Supplementary materials from applicable PMC articles
  • Monthly updates to capture latest research

Entity Annotation

LitVar integrates PubTator technology to automatically identify and highlight biological entities within articles:

  • Genetic variants and mutations
  • Genes and gene symbols
  • Diseases and phenotypes
  • Drugs and chemicals
  • Providing contextual relationships between variants and related concepts

Search and Discovery

  • Autocomplete: Real-time suggestions as users type queries
  • Gene-level search: Find all variants associated with a specific gene
  • Keyword filtering: Combine variant searches with additional text terms
  • Multi-variant queries: Search for multiple variants simultaneously
  • Publication filters: Filter by section, journal, date, and publication type
  • Ranking options: Sort by relevance (BM25 algorithm) or date

Result Presentation

For each variant, LitVar provides:

  • Standardized variant identifier and nomenclature
  • Associated genes and their relationships
  • Related diseases and phenotypes
  • Drug and chemical interactions
  • Complete publication list with highlighted sections
  • Statistics on publication trends over time

Data Access

Web Interface

User-friendly search interface with autocomplete, filters, and interactive visualization of results. Downloads available in TSV format for PMIDs.

RESTful API

Comprehensive programmatic access including:

  • Variant Summary: Detailed information about specific variants
  • Search Variant: Autocomplete and search functionality
  • Variant Publications: PMIDs and PMCIDs for all publications mentioning a variant
  • Variants for Gene: All variants associated with a specific gene
  • Sensor: Integration endpoint for external tools

RSS Feeds

Subscribe to updates for specific variants to track new publications automatically.

Technology Foundation

LitVar is powered by cutting-edge NLP tools developed by NCBI:

  • tmVar 3.0: Advanced variant recognition and normalization
  • PubTator: Entity recognition and annotation
  • TaggerOne: Multi-entity recognition
  • GNormPlus: Gene normalization
  • SR4GN: Species recognition
  • SimConcept: Concept similarity

Use Cases

  • Clinical genetics: Assess pathogenicity and clinical significance of variants
  • Genetic counseling: Find literature support for variant interpretation
  • Research: Track variant studies and relationships
  • Database curation: Identify literature for variant annotation
  • Drug development: Understand variant-drug relationships
  • Precision medicine: Connect genomic findings to published evidence

Maintenance and Support

LitVar is maintained by NCBI’s Computational Biology Branch with monthly data updates incorporating new publications and improved text mining algorithms. Free access without registration requirements ensures broad availability to the research and clinical communities.

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Created: November 08, 2025 | Last modified: November 08, 2025