LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC

Nucleic Acids Research
Alexis AllotZhiyong Lu

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literature and high cost of expert curation, curated variant information in existing databases are often incomplete and out-of-date.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.

References

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Jun 9, 2012·PloS One·Chih-Hsuan WeiZhiyong Lu
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Citations

May 23, 2019·Nucleic Acids Research·Chih-Hsuan WeiZhiyong Lu
Feb 19, 2020·Journal of Pediatric Endocrinology & Metabolism : JPEM·Reza Jafarzadeh-EsfehaniAriane Sadr-Nabavi
May 8, 2020·Journal of Cardiovascular Translational Research·Qian-Chen Wang, Zhen-Yu Wang
Dec 24, 2018·Database : the Journal of Biological Databases and Curation·Qingyu ChenKarin Verspoor
Nov 9, 2020·European Journal of Human Genetics : EJHG·David BauxAnne-Françoise Roux
May 11, 2021·Briefings in Bioinformatics·Florian BorchertMatthieu-P Schapranow
May 27, 2021·American Journal of Medical Genetics. Part a·Chawan ManasponVorasuk Shotelersuk
Jun 20, 2021·Scientific Reports·Eric B NonneckeCharles L Bevins
Jun 13, 2021·Bioinformatics·Kunal KunduJohn Moult
Aug 5, 2021·Brain, Behavior, & Immunity Health·Hyunah LeeSandrine Thuret
Sep 21, 2021·Internal Medicine Journal·Varun KaushikFinlay Macrae
Jul 8, 2021·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Mayher J PatelUNKNOWN ClinGen Hearing Loss Clinical Domain Working Group
Nov 23, 2021·The Journal of Gene Medicine·Ivan Yurievich BakutenkoNadezhda Ivanovna Ryabokon

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