[Utilities-announce] New NCBI Genome Released on November 9, 2011

[utilities-announce at ncbi.nlm.nih.gov]

New NCBI Genome Released on November 9, 2011

Earlier this month NCBI released a major redesign of the NCBI Genome database. A description of the changes and new features can be found at http://www.ncbi.nlm.nih.gov/About/news/17Nov2011.html.

Briefly, records in the new database, in general, correspond to all available genomic sequence data for a particular organism (usually a species), rather than to a sequence record of a single chromosome.

These changes affect the E-utility API in the following ways:

* Old Genome IDs are no longer valid. A file is available on the NCBI FTP site that maps old Genome IDs to Nucleotide GIs: ftp.ncbi.nih.gov/genomes/old_genomeID2nucGI
* EFetch no longer supports retrievals from Genome (db=genome). The equivalent function now is to use EFetch with db=nuccore to retrieve information about the GI that corresponds to the old Genome ID. Please use the file mentioned above to convert old Genome IDs to Nucleotide GIs.

* The ESummary XML for Genome has been recast to reflect the new data model.
* To view the new search fields and links supported for the new Genome database, please see http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=genome

Please see our release notes for additional information and updates: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.Release_Notes

Historically our policy has been to announce non-backward compatible changes to the E-utility API six months in advance to allow developers sufficient time to make any necessary alterations to existing code. Unfortunately, this did not happen with this release, and we apologize for any inconvenience caused.

Please direct any concerns or questions about this release to info at ncbi.nlm.nih.gov.



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