CMBO Perspective

Genes on the Web: A Report from the Internet & Society 2000 Conference

At Harvard University's Internet & Society 2000: Changing Our Lives (IS2K) conference, one of the exciting breakout sessions was "Genes on the Web." A panel of experts discussed the effects of the Internet on the acceleration of discoveries related to the human genome and on the dissemination of information to genome researchers. In the introduction, Josh Lerner, Professor of Business Administration at Harvard Business School, called the current state of genomics research the "marriage of information technology with biotechnology and bioinformatics."

George Church, Professor in Genetics, Biophysics & Health Sciences and Technology and Director of the Lipper Center for Computational Genetics at Harvard Medical School, sees the Human Genome Project as part of the Internet revolution. Church believes that the project to sequence the human genome displays a "community spirit of cooperation unprecedented in human genetics." Previously, a lab would hoard its genetic data. Now, there exists a 24-hour standard for the posting of genomic data on the Web, with input from research labs and biopharmaceutical and genomics companies. In addition, Church is pleased the Internet has allowed free accessibility to tools such as 3-D protein modeling utilities and search engines to mine the genomes of thousands of organisms.

For specific information about the Human Genome Program, visit the U.S. Department of Energy's Human Genome Project Information site. The site posts ongoing progress made toward the ultimate sequencing goal and contains information about the U.S. and worldwide sequencing efforts. General project information describes the goals, history and budget of the program and a research section discusses sequencing, mapping and bioinformatics. An extensive section on Ethical, Legal, and Social Issues (ELSI) discusses ELSI goals and provides publications addressing these issues. The site also maintains an extensive collection of links to online resources, Links to the Genetic World.

The National Center for Biotechnology Information (NCBI) is a worldwide resource for sequence submission and genomic information. The GenBank database contains all publicly available sequences and cross-references with the DNA DataBank of Japan (DDBJ) and the European Molecular Biology Laboratory (EMBL). NCBI's Entrez collection of databases allows searches of nucleotide and protein sequences, 3-D structures and taxonomy, linked directly to PubMed references from the scientific literature. Scientists at NCBI are continually developing new genomics utilities, including visualization tools and enhanced search utilities.

With the explosion in online tools available for research, sites that organize and categorize these resources can be invaluable. The CMS Molecular Biology Resource is an excellent gateway site for bioinformatics information, biomolecular modeling resources, and sequence, structure and genome databases. The WWW Virtual Library: Genetics keeps track of model organism sites, genome resources and genome research sites.

At the IS2K conference, Anthony Kerlavage, Senior Director of Bioinformatics at Celera Genomics, focused on the evolution of biological science. Previously, researchers worked on one gene or one protein; today, technological developments allow the study of entire families of proteins. Kerlavage states that the "explosion of information causes a dilemma - how do we manage that information?" The main mission of Celera is to determine the sequence of the human genome, followed by the elucidation of other model organism genomes, such as mouse and rat. Celera also focuses on developing research tools, such as data mining software and visualization programs. Eventually, Celera would like to improve the personalization of medicine and educate health professionals and the public. The Celera web site presents the Genome News Network with news clips, research news and feature articles about genes and genomes. Access to any genomics data or tools is for paying subscribers only.

Several bioinformatics companies are moving their operations online to allow for easier and less expensive access for the worldwide research community. DoubleTwist (formerly Pangea Systems, Inc.) displays a new focus on information accessibility via the Internet, with the launch the DoubleTwist.com genomics research portal. DoubleTwist uses genomics data from partner databases, licensed databases and their own databases, which are based on public databases. The site provides registered members with automated research agents, research resources, an email alert system and free, but limited, access to DoubleTwist's data mining tools. Subscription fees vary for academic and commercial users. The DailyTwist section presents industry headlines and feature articles.

Incyte Genomics (previously Incyte Pharmaceuticals) also chose a new name to designate a new mission for the company. Incyte is developing online utilities to access their genomic databases for humans, animals, fungi and bacteria and their RNA and protein expression databases. Scientists can also order relevant clones directly from Incyte's warehouse. The Incyte web site provides current news only directly related to Incyte, but does have a nice Bioinformatics Glossary and a good general collection of links.

Brenda Herschbach Jarrell, the final speaker on the IS2K panel, is a biotechnology patent attorney at Choate, Hall & Stewart. Jarrell believes that the explosion of information has changed the types of biotech patent applications in two major ways. The first change is in the definition of "What is an invention?" According to Jarrell, patent attorneys are receiving an increasing number of patent applications for computer programs for the mining and analysis of genomics data, rather than patent applications for gene constructs. The second change relates to the question of "Who owns the invention?" For example, is the person running the DNA sequencer an inventor? To address these questions, the U.S. government is developing more stringent guidelines to define owners and to prevent overlapping patents for research tools. Jarrell believes that one of the challenges in today's information-rich climate is reaching a balance between how scientists can share scientific information and protect intellectual property at the same time. She also recognizes that sharing genomics data with the scientific community is a priority among scientists today.

For online information about patents and intellectual property, visit the U.S. Patent and Trademark Office (USPTO). The site presents new information and press releases about patents. Users can search directly for patents in the USPTO Web Patent Databases (which contains all patents granted since 1976) using keywords in fields such as title, abstract, inventor name or location. The site also provides general information, FAQs about patents and patent forms.

The Trilateral Web Site allows easy access to the European Patent Office (EPO), the Japanese Patent Office (JPO), and the USPTO. These entities have been cooperating on patent functions since 1983. The EPO site is available in English, French and German and provides news, a toolbox and patent information. The new Esp@cenet Network is a free service of the EPO that allows quick searches and searches for patents in their original language or English abstracts. The JPO site is available in English or Japanese. Users can search for patents and view news, FAQs and announcements.

The DNAPatent.com site presents a simple introduction to issues in biotechnology patent law for non-lawyers. The Intellectual Property Law Web Server, provided by the law firm of Oppedahl & Larson, is a low-tech site is full of useful, detailed information about patents and intellectual property. The site provides readable text in a question/answer format addressing such areas as general information about patents, patents in foreign countries, web law and selecting intellectual property counsel. The Law Server also has an extensive list of Intellectual Property Resources on the Internet.

During the "Genes on the Web" IS2K session, all the presenters agreed that in a few years individuals will be able to access and analyze their own genomic sequences. This will raise important educational issues for the public as well as serious implications about the privacy of information. Eventually, genomics research and discovery, expedited by the technology available on the Internet, will have a tremendous impact on human health and disease.

Please note: This article was originally commissioned by HMS Beagle.