Describing the evolution of the life sciences industry over the past 15 to 20 years, Nasri Nahas, CEO of Geneva Bioinformatics (www.genebio.com), states that "we are now more in a knowledge-limited rather than information-limited era," marked by the need to create new ways of organizing information and generating knowledge.
"In my opinion, the tools available today do not yet properly address this challenge; the majority of the available tools are more targeted at information stacking rather than informationintegration, which calls for putting together the right information in a contextualized manner in order to allow research scientists to corroborate those separate and disparate pieces of information, and thus to generate pertinent biological knowledge," says Nahas.
In March, GeneBio announced a joint venture with the Current Science Group (www.current-science-group.com), resulting in the formation of Current BioData, a company that will develop and distribute the ProXenter platform, readying it for launch into the marketplace.
ProXenter is GeneBio's web-based Protein Exploration Center, a protein relational database that contains an annotated dataset for each of the specific groups of proteins of interest to the drug discovery industry. The platform also provides bioinformatics tools for browsing, visualizing, and analyzing data.
GeneBio was established to commercialize the products developed by the Swiss Institute of Bioinformatics, including the Swiss-Prot database, which is available via subscription to corporate customers and free of charge to academia.
Available products include Prosite, a protein domains database, Swiss-2DPAGE, Phenyx MS protein-identification software, and Melanie 2-D gel-analysis software. ProXenter will likely be made available on a yearly subscription model.
The philosophy underlying the development of ProXenter, according to Nahas, points to two desired characteristics of a protein database: "A product that any bench scientist can easily use without being an expert in bioinformatics and high-quality editorial content" that is defined, structured, and provided by experts in the field who also develop the tools needed to access and work with the data.
Given that the bottleneck has shifted from the information level to the interpretation or knowledge level, Nahas identifies goals in the evolution of proteomics databases:
Encompass heterogeneous but congruent types of data
Present this data to life scientists in an accessible and searchable manner
Provide the necessary tools for cross-reference information and sources to facilitate data interpretation
Be open to editorial content that increases the breadth of information while keeping it uniform
Nahas envisions an "intensive software publishing platform" in which highly specialized, editorially intensive databases collate publicly available data and organize it in a structure that is useful and understandable, adding analysis and commentary.
"Today we have thousands of journals sold via subscriptions, in 10 to 20 years there will be thousands of editorially intensive databases integrated in a single platform and probably sold on individual subscriptions," says Nahas.
"In the future, protein database entries could replace traditional review articles," with scientists submitting their data or knowledge about a particular protein family or molecular process and becoming an "author" of the database.
"The original raw data and basic annotation can be, or even must be, freely available to all, because science cannot progress without wide access to and sharing of basic research findings." Editorial annotation and proteomics databases built from the raw data "should be payable," in Nahas' view.