Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jul 2;46(W1):W530-W536.
doi: 10.1093/nar/gky355.

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

Alexis Allot  1 , Yifan Peng  1 , Chih-Hsuan Wei  1 , Kyubum Lee  1 , Lon Phan  1 , Zhiyong Lu  1
Affiliations

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

Alexis Allot et al. Nucleic Acids Res. .

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and high cost of expert curation, curated variant information in existing databases are often incomplete and out-of-date.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

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Pre-processing literature data for LitVar. Multiple scripts import publications, detect and normalize biological entities, retrieve relations and continuously update the database.
Figure 2.
Figure 2.
LitVar normalizes user queries in real-time.
Figure 3.
Figure 3.
The distribution of variants in PMC-OA, PubMed and dbSNP. All numbers are RSID-PMID unique pairs. Data accessed on 5 April 2018.
Figure 4.
Figure 4.
LitVar user interface. Multiple clearly delimited zones allow users to perform search and visualize results. This includes the (a) search, (b) disambiguation, (c) filters, (d) entity facets, (e) list of matching publications, (f) knowledge panel, (g) highlight customization panel and (h) automatic notification by RSS feed and download button.
Figure 5.
Figure 5.
LitVar snippets. LitVar displays the queried variation in the context of the sentences in which it appears in the publication. The queried variation has a red background, while other bioconcepts (other variants, genes, diseases, chemicals) are represented by specific colors.
See this image and copyright information in PMC

References

    1. Khare R., Leaman R., Lu Z.. Accessing biomedical literature in the current information landscape. Methods Mol. Biol. 2014; 1159:11–31. - PMC - PubMed
    1. Forbes S.A., Beare D., Boutselakis H., Bamford S., Bindal N., Tate J., Cole C.G., Ward S., Dawson E., Ponting L. et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 2017; 45:D777–D783. - PMC - PubMed
    1. Pundir S., Martin M.J., O’Donovan C.. UniProt protein knowledgebase. Methods Mol. Biol. 2017; 1558:41–55. - PMC - PubMed
    1. Landrum M.J., Lee J.M., Benson M., Brown G.R., Chao C., Chitipiralla S., Gu B., Hart J., Hoffman D., Jang W. et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 2018; 46:D1062–D1067. - PMC - PubMed
    1. Sherry S.T., Ward M., Sirotkin K.. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res. 1999; 9:677–679. - PubMed

Publication types