Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation.
Using the Pseudomonas aeruginosa Genome Project as a test case, we have developed a database and submission system to facilitate a community-based approach to continually updated genome annotation (http://www.pseudomonas.com). Researchers submit proposed annotation updates through one of three web-based form options which are then subjected to review, and if accepted, entered into both the database and log file of updates with author acknowledgement. In addition, a coordinator continually reviews literature for suitable updates, as we have found such reviews to be the most efficient. Both the annotations database and updates-log database have Boolean search capability with the ability to sort results and download all data or search results as tab-delimited files. To complement this peer-reviewed genome annotation, we also provide a linked GBrowse view which displays alternate annotations. Additional tools and analyses are also integrated, including PseudoCyc, and knockout mutant information. We propose that this database system, with its focus on facilitating flexible queries of the data and providing access to both peer-reviewed annotations as well as alternate annotation information, may be a suitable model for other genome projects wishing to use a continually updated, community-based annotation approach. The source code is freely available under GNU General Public Licence.
Winsor
Geoffrey L
GL
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C., Canada, V5A 1S6.
Lo
Raymond
R
Ho Sui
Shannan J
SJ
Ung
Korine S E
KS
Huang
Shaoshan
S
Cheng
Dean
D
Ching
Wai-Kay Ho
WK
Hancock
Robert E W
RE
Brinkman
Fiona S L
FS
D004269:DNA, Bacterial / Q000737:chemistry; D030541:Databases, Genetic; D016680:Genome, Bacterial; D023281:Genomics; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000378:metabolism; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface
D004269:DNA, Bacterial