Skip to main content

LabBook Teams with OSU and OSC to Deliver AnnotatedHumanGenomeDatabase

Premium

Fast on the heels of the public release of the specification for its XML-based BSML format, LabBook announced that it is partnering with Ohio State University and the Ohio Supercomputer Center to deliver OSU’s annotated human genome database through its XML browser.

The database will be available via LabBook’s website (www.labbook.com), and will be free to academic users via standard HTML browsers and LabBook’s free XML viewer. The company’s enhanced XML browser is available to all users for a fee.

Commercial users can either subscribe individually through the LabBook portal or they can purchase a corporate-wide license for use of the entire database. LabBook declined to disclose the pricing schema for commercial licenses.

Under the terms of the partnership, OSU will receive royalties on revenue derived from commercial use of the database. Adel Mikhail, LabBook’s vice president of corporate development, told BioInform that the royalties will fund a LabBook bioinformatics fellowship program at the university.

In addition to the XML browser, which renders the annotated data graphically, LabBook developed a natural-language-based query engine for the database that will make it easier for biologists to use, according to Mikhail. The hypothesis-driven front end will allow users to query “by normal, descriptive biological terms that allow the database to be applicable to non-bioinformaticists,” he said.

OSU created the annotated database by reassembling genomic information contained in both public and proprietary databases. Directed by Bo Yuan, head of bioinformatics at OSU, the project used proprietary algorithms to combine non-fragmented and non-redundant whole genome mapping of expressed genes with comprehensive annotation. It contains information on protein annotation, EST annotation, gene expression, splicing variants for known genes, and cytogenetic marker integration.

The Ohio Supercomputer Center’s Silicon Graphics 1400 cluster provided the compute power necessary to complete the job. OSC will continue to update the database regularly as part of the partnership.

OSU chose to partner with LabBook on the project because of the company’s “biology smart” approach to delivering data, Mikhail said. “Currently all access to genomic information is done through standard HTML browsers, which are rate limiting in the discovery process,” he said.

Mikhail said LabBook is distinguishing itself “significantly” from other portals that offer HTML-based access to databases or other genomic resources. “As long as people are using Explorer or Netscape, their access to information is limited,” he said.

The company is in the process of writing a converter for Celera’s database, Mikhail said, and will continue to write appropriate converters as it identifies new clients.

The database, which is to be launched by the end of the year, is currently in beta testing and the team is putting it on beefed-up servers that will be able to handle the expected volume of traffic.

Mikhail said that LabBook, OSU, and OSC have submitted a joint manuscript describing the development of the database to a “leading journal” for accelerated review, though he declined to name the publication.

Filed under

The Scan

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.