TY - JOUR
T1 - Pseudomonas aeruginosa Genome Database and PseudoCAP
T2 - Facilitating community-based, continually updated, genome annotation
AU - Winsor, Geoffrey L.
AU - Lo, Raymond
AU - Ho Sui, Shannan J.
AU - Ung, Korine S.E.
AU - Huang, Shaoshan
AU - Cheng, Dean
AU - Ching, Wai Kay Ho
AU - Hancock, Robert E.W.
AU - Brinkman, Fiona S.L.
N1 - Funding Information:
The authors thank Peter Karp and Randy Gobbel for assistance with implementing the necessary changes to PseudoCyc. Primary funding for this project was provided by the Cystic Fibrosis Foundation. Ancillary funding provided by Genome Prairie, Genome BC, Inimex Pharmaceuticals and the CCFF. R.E.W.H. has a Canada Research Chair and F.S.L.B. is a Michael Smith Foundation for Health Research Scholar.
PY - 2005/1/1
Y1 - 2005/1/1
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gki047
DO - 10.1093/nar/gki047
M3 - Review article
C2 - 15608211
AN - SCOPUS:13444302756
SN - 0305-1048
VL - 33
SP - D338-D343
JO - Nucleic acids research
JF - Nucleic acids research
IS - DATABASE ISS.
ER -