Monday, December 11, 2000

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Sean Eddy and Ewan Birney An Open Letter to Bioinformatics Researchers
"Dear fellow bioinformatics developers:

By now you have probably heard that Celera Genomics has submitted their human genome paper to the journal Science. Science and Celera have agreed to special terms for the release of the human genome sequence data. It will be made available through the Celera website, and will not be submitted to the international DNA database consortium (GenBank, EMBL and DDBJ). Science's statement regarding the agreement is at: http://www.sciencemag.org/feature/data/announcement/genomesequenceplan.shl

All major journals, including Science, have a policy of deposition of sequence data with the "appropriate data bank". The accepted community standard is submission to GenBank/EMBL/DDBJ. The reason for this deposition is to make the results of the work openly available for future research. This principle was specifically mentioned in the Clinton/Blair statement on human genome sequencing - http://www.usinfo.state.gov/topical/global/biotech/00031401.htm - who strongly upheld the view that "unencumbered access" to genome data was critical.

The terms of the Celera/Science agreement will give us access to the genome sequence, but not unencumbered access. Celera is suggesting publishing their data under a MTA (Material Transfer Agreement) which would prevent large scale downloads and incorporation of this data into GenBank/EMBL/DDBJ. In order to download the data, you and your institution will have to sign a contract guaranteeing that you will not "redistribute" the Celera data.

Science believes that the deal is an adequate compromise because it provides us the right to download the data and publish our results. We believe Science is thinking in terms of single gene biology, not large scale bioinformatics. It is probably not hard for you to imagine scenarios in bioinformatics in which "publication" and "redistribution" are virtually the same thing; we cannot imagine Celera allowing us to incorporate data into Pfam, for example, nor into Ensembl.

We are asking for your support in writing to Science to politely insist that genome sequence papers should be accompanied by unencumbered deposition to GenBank/EMBL/DDBJ. Please note that we have no issue with Celera either keeping this data unpublished for commercial reasons, nor with them combining their data with freely available data from the public genome projects. We would defend their right to do either. Our view is simply that the genome community has established a clear principle that published genome data must be deposited in the international databases, that bioinformatics is fueled by this principle, and that Science therefore threatens to set a precedent that undermines our research.

We encourage you to express your views on this matter to Donald Kennedy (kennedyd@kennedyd.pobox.stanford.edu), the Editor-in-Chief of Science, and/or to Barbara Jasny (bjasny@aaas.org), the managing editor in charge of genomics papers at Science."

[via bioinformatics.org]

GenomeWeb Bioinformaticists Debate Science-Celera Agreement
"Two leading bioinformaticists have issued a call to arms to their colleagues in response to Science’s decision to allow Celera to submit its genome data under special circumstances.

“Agitate. Let Science know you care,” write the letter’s authors, Ewan Birney of the European Bioinformatics Institute and Sean Eddy of the Howard Hughes Medical Institute and Washington University. “Even if we can’t change the deal with Celera, we can try to make sure it’s a one-time only deal that’s viewed as a Big Mistake.”"

"The bioinformaticists argue the Celera-Science agreement could set a precedent that would allow researchers to publish their databases under different material transfer agreements, making it impossible for researchers to access a single DNA database to do research, and forcing researchers to enter into a complex web of contracts to get access to data."