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PAG Plenary Includes Call for Open-Access Publishing in Genomics

SAN DIEGO (GenomeWeb News) – Open-access datasets, software, and bioinformatics strategies have become more or less de rigueur in genomics research.

But the field may also be poised to change the way other sorts of information from scientific studies is conveyed to other researchers and to the broader public, according to open-access proponent Michael Eisen, a computational and evolutionary biology researcher at the University of California, Berkeley.

Eisen, a Public Library of Science co-founder, spoke during the morning plenary session here at the International Plant and Animal Genome Conference.

In his presentation, he argued that the inability to freely and unreservedly access the full text of all genome studies performed to date may have led to missed opportunities for the field.

Using the bacteriophage phiX174 genome sequence as an example, he proposed that the general thinking in the genomics field has developed in ways that promote open-access to sequence data and related software. But, he said, the same type of access is not necessarily available for those interested in delving into the details and rationale behind genomics studies, since the corresponding papers may not be accessible in an open-access format.

The UK Medical Research Council Laboratory of Molecular Biology's Frederick Sanger and colleagues described the phiX174 sequence in 1977, in a publication that's generally considered to be the first genome paper. The sequence data presented in that study is now freely available, Eisen explained, in part owing to the advent of sequence databases such as the European Molecular Biology Laboratory Nucleotide Sequence database or the National Center for Biotechnology Information's sequence database, GenBank.

During the past decade or more, funding agency requirements and pressure from within the genomics community have contributed to the widespread adoption of these and other public genomics resources and repositories.

As these databases have grown and become accepted within the genomics community, Eisen argued that they have spurred the development of computational methods for analyzing genome sequences and datasets that may not have existed otherwise. "Imagine where we would be had we not made the fortunate decision to liberate genome sequences," he said.

But analogous strategies for combing through text from genomics studies in their entirety have not developed in the same manner, according to Eisen, who noted that the text of the phiX174 genome paper remains behind a pay wall.

"We've allowed [journal access] and [data access] to follow very different fates," said Eisen, who says there are ways to use the information housed within the scientific literature more easily and productively.

He urged attendees to consider publishing their own work in open-access publications. Beyond that, though, Eisen also noted that the community is well positioned to influence the ways in which research information is disseminated, since genomics data increasingly serves as a resource for other spheres of research.