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EBI to Shut Down International Protein Index, Transition Data to UniProt

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By Uduak Grace Thomas

The European Bioinformatics Institute has decided to shut down the International Protein Index at the end of the month, according to a statement on the EBI website.

Following a final release in September, the IPI website will "cease to be maintained," EBI said.

EBI will move the data to the UniProt proteomics database. Replacement proteome datasets are already available through UniProt for human and mouse, to be followed by rat, zebrafish, Arabidopsis, chicken, and cow.

Previous releases of IPI datasets will still be available from the IPI ftp site.

Paul Kersey, the dataflow team leader for the Protein and Nucleotide Database group at EBI, said that although funding is a persistent concern for the EBI, it was not an issue in the decision to close IPI. Rather, he said the closure was an effort to eliminate redundancy among publicly available proteomics resources.

"IPI was conceived with a specific problem in mind — the high degree of diversity in gene predictions made in the early years following the initial publication of vertebrate genome sequences," he told BioInform in an e-mail.

"The development by UniProt of replacement data sets for IPI now enables the final closure of IPI, which we believe will, in the longer term, facilitate the navigability of our data by our users."

Vertebrate genome annotation "has become much more standardized and ... accurate" since IPI was launched in 2001, he said, adding that although IPI has "attracted a specific user base," particularly in the mass spectrometry community, "we believe that the interests of this user base are best met in the future through the development of services in the context of the larger Ensembl and UniProt projects."

IPI provides a top-level guide to several databases, including UnitProtKB/Swiss-Prot, Ensembl, and RefSeq, that describes the proteomes of higher eukaryotic organisms. It includes cross-references between these resources and also offers nonredundant data sets for a number of model species proteomes.

IPI joins a growing list of life science databases that have faced or are currently battling extinction.

In February, the National Center for Biotechnology Information announced that it was phasing out the Sequence Read Archive (BI 2/18/2011) but then reversed the decision in June saying that National Institutes of Health had provided interim funding to maintain the resource through Oct. 1 (BI 6/17/2011).

NCBI officials said that they were "working with staff from other NIH Institutes and NIH grantees to develop an approach to continue archiving a widely used subset of next-generation sequencing data" beyond the cutoff data. At present, it hasn’t provided further details about what those plans are.

Also this year, the developers of the Kyoto Encyclopedia of Genes and Genomics moved the resource to a subscription model as a result of dwindling funds (BI 5/27/2011).

In 2009, the National Science Foundation decided to phase out funding to The Arabidopsis Information Resource (BI 12/4/2009) forcing its developers to launch a corporate sponsorship program to stay afloat (BI 3/19/2010).


Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com

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