Genome Reviews
From Genomic Standards Consortium
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[edit] Introduction
From Genome Reviews:
The Genome Reviews database provides an up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota. Genome Reviews is available as a MySQL relational database, or a flat file format derived from that in the EMBL Nucleotide Sequence Database.
[edit] Genomic Rosetta Stone (GRS) and GRS Resolver
Genome Reviews is participating in the GRS and GRS Resolver initiatives.
[edit] Identifier Policy
[edit] Identifier Naming Convention
From Genome Reviews:
The ID (IDentification) line is always the first line of an entry. The general form of the ID line is:
ID entryname; sequence version; topology; molecule; data class; division; sequence length BP.
Entryname: stable identifier, consisting of alphanumeric character, starting with a letter. All letters should be in upper case. The entryname is provided only for reasons of compatibility with EMBL format and is redundant with the accession number (see section 3.4.2) in all Genome Reviews files.
An example of a complete identification line is shown below:
ID AE003850_GR; SV 3; circular; genomic DNA; GRV; PRO; 1286 BP.
Communication from Peter Sterk 25.02.08:
In most cases, the Genome Review identifier is the INSDC accession followed by _GR, e.g. for E.coli K12:
- INSDC: U00096
- Genome Reviews: U00096_GR
There are a number of GR files that are not in INSDC, e.g. a number of yeast and Arabidopsis chromosomes and the Ustilago maydis chromosomes. This is because the INSDC records are out of date (i.e. they haven't been updated by the original submitters) or in the case of Ustilago maydis, the genome was reannotated by MIPS and the EMBL flat files they submitted are not public.
