The Biosystems Informatics Institute (Bii) and Lucidyx have announced a joint agreement to develop new bioinformatics tools to integrate data storage and Lucidyx's genomic search engine technology to better contextualise off-target drug effects.
"These tools are critical as we attempt to further understand the data flowing from proteomics and transcriptomics experiments across the industry," noted Ian Humphrey-Smith, chief executive officer of the Bii .
Under the terms of the agreement, Bii will assist Lucidyx in developing products enabling life science software developers who develop tools to access genomic data through application programming interfaces (APIs), to query and retrieve information from Searcher, a genomic annotation search engine developed by Lucidyx.
The collaboration focuses on the development of Lucidyx Oracle Gateway, a bridge between Oracle and the Lucidyx search engine, allowing Oracle SQL queries to combine data from Oracle with data from Searcher as if all the data was stored in Oracle tables.
The pharmaceutical and biotech industries have spent many billions of pounds in an attempt to learn more about gene expression and the mechanisms of drug action, investing heavily to fill the absence of appropriate mathematics and computer power.
The industries are currently inundated by masses of data from many different sources and are mostly unable to take advantage of the experimental and clinical data at their disposal - again due mostly to a lack of appropriate mathematical tools for data integration and extraction of highly-complex combinations of elements.
Searcher is a web-based application with a powerful search engine that allows users to more rapidly find, view, analyse and save relevant entries in any genomic database. It also includes auto-updating capabilities, as well as automated versioning and archiving, thereby minimising data loss.
Customers using the two compatibility products will be able to use the search-and-retrieve functionality that Searcher provides without having to change their existing infrastructure, thereby providing a bioinformatics audit trail that will become increasingly critical as pharma clients consider the implications of Voluntary Genomic Data Submissions to the FDA.
The second product, Lucidyx Puma will facilitate access to the Lucidyx search engine for programmers using Java or Perl, through http, or through a command-line program. The API follows the SRS getz/wgetz syntax, thus both lessening the learning curve and simplifying the conversion of legacy code.
"In recognition of the needs of life science software developers to access genomic data through either SQL queries or through application programming interfaces (APIs), we are developing two additional software products," said Manuel Glynias, president and chief executive officer of Lucidyx.
"The Lucidyx Oracle Gateway and Lucidyx Puma, will facilitate access to the Lucidyx search engine by life science programmers through either Oracle/SQL or through a well known API."
Humphrey-Smith added: "Such interfaces will be essential to allow integration of diverse databases within pharma with applications such as Lucidyx Searcher."