Introducing OMNI, a new browser that harmonizes knowledge at the single nucleotide level.

by Ginger Tsueng

One of our pride points for being able to pool, standardize, and share gene and variant annotation data as a service, is that our service is fast! The reason that MyGene.info and MyVariant.info are made with speed in mind is that we want them to be useful to bioinformaticians and tool/resource developers alike! How can we tell if we’ve successfully provided a useful service?

One measure we LOVE, is when a user builds something useful or amazing with our service--and our fellow researchers here at Scripps Research have done just that! Dr. Amalio Telenti, the genomics professor behind OMNI, is the chief data scientist for the Scripps Translation Science Institute and was the recipient of the Swiss Cloetta Award for medical research. Dr. Telenti and Li Yin, the software engineer behind OMNI, were kind enough to answer some of our questions.

Without further ado, we’d like to introduce OMNI, a powerful, integrative browser that harmonizes knowledge, functional significance, population prevalence and available literature at the single nucleotide level.

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In one tweet or less, introduce us to OMNI:
Browse genetic information just like you would use Google
Aim at a one-stop-shop for variant information

What was the original intent behind OMNI (how did OMNI come about)?
OMNI was created to address the need in clinical genetics to easily find information. It can provide information on ALL 3 billion positions.

How has OMNI since improved?
OMNI includes novel scores of variants from constrained genomic regions (for the coding and non-coding genome) that are not readily available elsewhere. We have deployed a Natural Language Processing (NLP) tool that extracts information from PUBMED abstracts that cite the genetic variants in OMNI.

Who is currently the intended audience for OMNI?
OMNI is intended to support clinical geneticists in their work on understanding variants of unknown significance, but can just as easily be used by researchers who wish to rapidly check for information at the single nucleotide level

How does OMNI use MyGene.info or MyVariant.info services?
OMNI uses MyVariant.info to gather the majority of information of variants for their positions, frequency and effects. When querying a specific variant, OMNI will try to capture its related genes and then query MyGene.info to retrieve summaries of these genes.

What are some of OMNI’s successes?
OMNI is very new (a couple of months in existence), but it has been accessed by some 300 users across the globe, with a user return rate of 20%. We hope that it will be receiving increasing attention and that we will receive constructive feedback to build new useful features.

What improvements are planned for OMNI?
We will increase the content (biochemical, topological domain information) for the non-coding genome to support the interpretation of non-coding variants
We are very excited about the coming rollout of an annotator tool for users themselves: the idea is to create a “comments” window where users that have observed a variant of unknown significance (VUS) can discuss their possible phenotypic consequences. Those users descriptions will be processed via NLP and returned in future queries.

Additional information/links:
About us: https://omni.telentilab.com/about
Submit issues and feedback: https://github.com/TelentiLab/Omni
Contact us: omni@telentilab.com