LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC. Academic Article uri icon

Overview

abstract

  • The identification and interpretation of genomic variants play a key role in the diagnosis of genetic diseases and related research. These tasks increasingly rely on accessing relevant manually curated information from domain databases (e.g. SwissProt or ClinVar). However, due to the sheer volume of medical literature and high cost of expert curation, curated variant information in existing databases are often incomplete and out-of-date. In addition, the same genetic variant can be mentioned in publications with various names (e.g. 'A146T' versus 'c.436G>A' versus 'rs121913527'). A search in PubMed using only one name usually cannot retrieve all relevant articles for the variant of interest. Hence, to help scientists, healthcare professionals, and database curators find the most up-to-date published variant research, we have developed LitVar for the search and retrieval of standardized variant information. In addition, LitVar uses advanced text mining techniques to compute and extract relationships between variants and other associated entities such as diseases and chemicals/drugs. LitVar is publicly available at https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar.

publication date

  • July 2, 2018

Research

keywords

  • Data Curation
  • Data Mining
  • Polymorphism, Single Nucleotide
  • Search Engine
  • User-Computer Interface

Identity

PubMed Central ID

  • PMC6030971

Scopus Document Identifier

  • 85050875921

Digital Object Identifier (DOI)

  • 10.1093/nar/gky355

PubMed ID

  • 29762787

Additional Document Info

volume

  • 46

issue

  • W1