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. 2012 Jan;40(Database issue):D1288-94.
doi: 10.1093/nar/gkr1054. Epub 2011 Nov 23.

Xanthusbase After Five Years Expands to Become Openmods

Free PMC article

Xanthusbase After Five Years Expands to Become Openmods

Philip C Pratt-Szeliga et al. Nucleic Acids Res. .
Free PMC article


Xanthusbase (, a model organism database for the bacterium Myxococcus xanthus, functions as a collaborative information repository based on Wikipedia principles. It was created more than 5 years ago to serve as a cost-effective reference database for M. xanthus researchers, an education tool for undergraduate students to learn about genome annotation, and a means for the community of researchers to collaboratively improve their organism's annotation. We have achieved several goals and are seeking creative solutions to ongoing challenges. Along the way we have made several important improvements to Xanthusbase related to stability, security and usability. Most importantly, we have designed and implemented an installer that enables other microbial model organism communities to use it as a MOD. This version, called Openmods, has already been used to create Xenorhabdusbase (, Caulobacterbase ( and soon Bdellovibriobase.


Figure 1.
Figure 1.
Openmods data sources and sinks. Motifs and Pathways are pulled using the KEGG SOAP API. Blast on Genes and Blast2GO are used to produce GO terms. The Genbank file is automatically downloaded via FTP, and the following information is then parsed from it: Locus, Coordinates, Length, Strand, Gene Name, Gene Products, Note and Sequence. Users are allowed to edit most of the fields, but Gene Name, Gene Products and Note are the only ones saved to the updated Genbank file. All data from the website is saved to the automatic backup.
Figure 2.
Figure 2.
Openmods genepage screenshot. From top to bottom, the genepage contains: Geneome browser, Locus (static), Coordinates (static), Gene Length (static), Strand (static), Gene Name (editable), Gene Products (editable), Note (editable), Motifs (periodically updated but not editable), Pathways (periodically updated but not editable), GO information (periodically updated but not editable), Mutant Strains (editable), Protein Synonyms (editable), Gene Synonyms (editable), Mutant Phenotypes (editable) and Community Description (editable). The genepage also contains the protein and nucleotide sequence but is not shown due to space constraints. The Gene Name, Gene Products and Note are included in Genbank file updates.

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    1. Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L. The distributed annotation system. BMC Bioinformatics. 2001;2:7. - PMC - PubMed
    1. Arshinoff BI, Suen G, Just EM, Merchant SM, Kibbe WA, Chisholm RL, Welch RD. Xanthusbase: adapting wikipedia principles to a model organism database. Nucleic Acids Res. 2007;35:D422–D426. - PMC - PubMed
    1. National Science Foundation (2005). US NSF - NSB-05-40, Long-Lived Digital Data Collections. Enabling Research and Education in the 21st Century.
    1. Goodner BW, Wheeler CA, Hall PJ, Slater SC. Massively parallel undergraduates for bacterial genome finishing. Asm. News. 2003;69:584–585.
    1. Forst S, Goodner B. Comparative bacterial genomics and its use in undergraduate education. Biol. Control. 2006;38:47–53.

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