Publications related to variants

Biomedical Named Entity Recognition tagging in VarSome.

We have developed our Biomedical Named Entity Recognition tagger which identifies: genes, variants, diseases, phenotypes, chemical compounds, drugs, coding impact, protein impact, functional studies, clinical significance, inheritance mode, organs, tissues, species in abstracts of publications from PubMed.

In VarSome we show publications from PubMed related to the variant of interest and its related gene in the "Publications" tab:

When selecting the "Show timeline"option:

you can see a timeline of the publications of the variant of interest or its related gene and its co-occurrence with the categories of biological entities mentioned above. You can select to show all categories at once by selecting "All" (as shown above) or select to show only the timeline of publications with diseases co-occurring with the variant of interest or its related gene.

By selecting the "Show tags individually" option at the top right, you can see the timeline of the publications related to each identified disease co-occurring with the variant of interest or its related gene.

Bellow the timeline graph you can use the search box in order to find the papers where the tags of interest have been tagged in. In the following example we have searched for "Kuf disease" and the article that contains it appears at the bottom.

From the "General Information" tab:

you can access the Mastermind Genomic Search Engine, which allows you to find disease-gene-variant associations from the scientific literature. You can also explore publications on neighboring variants in the same gene. VarSome users can sign up for a Mastermind Free Edition account.

You can also link publications to variants. For more information about our Publication Link Program please look here.

In VarSome Clinical we show publications from PubMed related to the selected variant and its related gene in the "Publications" tab under the variant table results: